The Human Transcription Factors

HGNC symbol	DBD Family	Is TF?	TF Assessment	Binding Mode	Motif Status	Notes	Comments
NR0B1	Unknown	Yes	Known motif	2 Obligate heteromer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain
AATF	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Likely does not bind to bind to DNA (PMID: 17634135).
ABL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ABRA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		The Costars domain in this protein is an atypical winged helix protein that does not bind DNA but to other proteins (PMID: 21082705)
AC020915.1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ACOD1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ACTR3B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ACTR3C	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Pfam match to an APSES domain - this is likely a false positive, as these domains are mostly present in bacteria and fungi
ADAM8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ADAMTS17	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ADAMTS19	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
ADAR	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		PMID: 21728134 shows the ADAR protein bind to ds RNA and Z DNA. At best it would be a non-sequence specific DNA binding protein. But, it has a well established role as a dsRNA binding protein, so it is unlikely to be a TF.
ADGRA1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ADGRG3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
AEBP1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		This is a protease, but its ability to bind DNA is supported by both gel-shift (PMID: 15654748) and ChIP (PMID: 22723309).
AES	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Likely a transcriptional co-factor
AFAP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		There is no evidence suggesting DNA-binding activity
AFF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	MLL fusion partner
AFF3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		(PMID: 8555498) only says that In vitro-translated LAF-4 was able to bind strongly to double-stranded DNA cellulose - thats more consistent with nonspecific DNA binding. The key issue is whether the Transcription factor AF4/FMR2 (IPR007797) domain really is sequence specific. Most of the work has been done on the one Drosophila ortholog, lilliuputian. I see no evidence of DNA binding. Recent work on this family in human indicate that it functions in coactivation (PMID: 27899651; PMID: 261712
AFF4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		(PMID: 8555498) only says that In vitro-translated LAF-4 was able to bind strongly to double-stranded DNA cellulose - thats more consistent with nonspecific DNA binding. The key issue is whether the Transcription factor AF4/FMR2 (IPR007797) domain really is sequence specific. Most of the work has been done on the one Drosophila ortholog, lilliuputian. I see no evidence of DNA binding. Recent work on this family in human indicate that it functions in coactivation (PMID: 27899651; PMID: 261712
AGER	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Contacts DNA in the structure (PDB: 4OI7)
AGT	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
AIM2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Based on (PDB: 3RN2), the protein binds DNA but contacts only the backbone; AIM2 binds cytrosolic dsDNA in the innate immune response
AKT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ALK	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Operates far upstream in the signaling cascade
ALKBH2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Binds DNA in the crystal structure (PDB: 3BTX)
AMH	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ANAPC2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Scaffolding protein that associates with ubiquitin ligase complexes
ANKRD30A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	GO citation (PMID: 11280766) has no evidence of DNA-binding activity and was based on homology
ANXA3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein operates far upstream on the signaling cascade.
ANXA4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
AP5Z1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		May have helicase activity and play a role in DNA repair (PMID: 20613862)
APBB3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
APEX1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		The structure (PDB:1DEW) is with abasic DNA - the protein is a base excision repair enzyme that cleaves off abasic bases
APOBEC3A	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds ssDNA (PDB: 5KEG)
APOBEC3B	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds ssDNA (PDB: 5TD5)
APOBEC3G	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Restriction factor of HIV-1 that binds ssDNA (PDB: 5K83)
APTX	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds and fixes DNA-RNA hybrids/ APTX efficiently repairs adenylated RNA-DNA and acts in the RNA-DNA damage response (PMID: 24362567)
ARHGAP35	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Binds DNA specifically based on EMSA and nuclease protection assay data (PMID: 1894621), despite lacking any clear DBDs.
ARHGEF2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ARHGEF5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		GO annotation provides no evidence of DNA-binding activity (PMID: 15601624)
ARRB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		ChIP data available, but unclear if it can bind to DNA directly (PMID: 16325578)
ARRB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ASCC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a coactivator that is reported to bind to SRF, NFKB1, and JUN (PMID: 12077347)
ATF7IP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Murine homolog involved in H4K9 trimethylation by SETDB1 (PMID: 14536086)
ATM	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Kinase protein that binds to and activates certain TFs
ATR	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif
ATRX	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		ATRX does not contain any canonical sequence-specific DBDs but it does contain a non-specific DNA binding helicase that allows it to bind repeat sequences (PMID:21029860) and telomeres (PMID:20651253). ATRX is involved in multiple processes (transcription, replication), and is associated with multiple complexes (Swi/Snf, histone chaperones, and repressive complexes including TRIM 28 (PMID:27029610)), and as such does affect transcription. Given the lack of sequence-specific binding it is unlikel
ATXN7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		ATXN7 SCA7 domain facilitates interactions with histone dimers (PMID: 20634802)
BAG1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Antiapoptotic BCL-protein
BANF1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure, contacting only the backbone from the side of the minor groove (PDB: 2BZF)
BANP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	BANP has no DBD and is known to bind other TFs; likely that the Transfac motif is from one of its binding partners
BCL10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Apoptosis associated protein that operates upstream on a cascade that includes NFKB
BCL3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	No DBD - instead, this is a known cofactor of NF-kappaB. The Transfac motif is the NFKB1 motif. GO cites only electronic annotation and needs to be fixed.
BCLAF1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	No DBD. Only weak evidence is available for indirect binding (PMID: 10330179). Suspect motif - it is a clear ETS-site. (PMID: 10330179) shows that the protein binds DNA in filter binding assay, but not that it is sequence specific.
BCOR	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional co-repressor that associates with BCL6 (PMID: 10898795)
BDP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BEX1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Likely a cofactor- (PMID: 16314316) shows results for related BEX2
BIN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BLM	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Helicase involved in DNA replication and repair (PDB: 4CGZ)
BLZF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This is a golgi protein with no evidence for DNA binding.
BMI1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		BMI1 binds to nucleosomes as part of the PRC1 complex but does not contact the DNA directly (PDB: 4R8P)
BMP2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BMP4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Likely a cofactor.
BMP7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BMPR1A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BOD1L1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
BOLA1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BOLA2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BOLA2B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BOLA3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		E. Coli homologue of the BOLA binds DNA; however there is no evidence in the mammalian proteins
BPNT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BPTF	Unknown	Yes	Known motif	1 Monomer or homomultimer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain; Has a putative AT-hook	(PMID: 10575013) obtained a motif by SELEX and showed that mutating the sequence diminished binding in vitro. Unusual for a PHD/Ring finger, but its there in the literature.
BRCA1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	In vivo/Misc source		BRCA1 likely binds to DNA without DNA sequence specificity (PMID: 11353843)
BRD4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Binds acetylated histones
BRD7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BRD8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	TF-coactivator
BRD9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Evidence ony for interaction with histones (PMID: 22464331)
BRF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	GTF - Pol III - TRANSFAC has a motif but its likely not for this protein, but for the complex as a whole
BRF2	Unknown	Yes	Likely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Makes backbone and sequence-specific interactions with DNA (PDB: 4ROC), but only involved in recognizing dinucleotides flanking the TATA box (PMID: 26638071). Redox sensing determines activation and repression of target genes
BRMS1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		BRMS1 functions as a corepressor by promoting binding of HDAC1 to RelA/p65, where it deacetylates lysine K310 on RelA/p65, which suppresses RelA/p65 transcriptional activity (PMID: 17000776)
BRPF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
BTAF1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Protein that uses ATP to dissociate TBP from the promoter
BTBD8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Probably annotated as TF based on presence of a BTB domain; however, these domains are not known to bind DNA
BTG2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional co-factor (PMID: 10617598)
BTK	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Involved in the regulation of ARID3A and NFAT in B lymphocyte development; has been thoroughly investigated, but there is no evidence to demonstrate DNA binding activity (see UniProt Q06187)
BTRC	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
BUD31	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included because GO says its DNA binding on the basis of (PMID: 7841202), a 1995 paper that only suggests DNA binding on the basis of the protein sequence. In fact, it is composed entirely of a G10 domain.
C14orf39	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
C1D	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		C1D has been shown to bind RNA (PMID: 17412707) and is associated with the exosome. C1D is also associated with DNA repair and has DNA-binding activitiy (PMID: 10362552)
C20orf194	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
C3orf33	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Some effect on DNA-binding of AP-1 (PMID: 20680465), but does no data supporting a role for C3orf33 as a DNA-binding factor itself
CACTIN	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein operates on a signaling cascade far upstream of NFKB (PMID: 20829348)
CAMK1D	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Functions in signalling cascade that leads to phosphorylation and activation of CREB (PMID: 16324104)
CAMK2A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CAPN15	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Basically an unknown protein - a likely protease that contains also znfRANBP-domains, so it could be a RNA-binding protein
CAPN3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because GO says positive regulation of NF-kappaB transcription factor activity. No indication of sequence specific DNA binding.
CARD11	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Plasma-membrane protein possibly functioning in upstream signaling of NFKB (PMID: 12154360)
CARD14	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CARF	Unknown	Yes	Known motif	1 Monomer or homomultimer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Transfac-only motif. Major evidence is found in (PMID: 11832226). Cloned by Y1H and binding demonstrated by gel-shift. Mutant probes do not compete. DNA binding ability seems solid but motif is sketchy.
CASP8AP2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Pfam DBD match is a likely false-positive - did not produce a motif in PBM experiments
CAT	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein that breaks down hydrogen peroxide
CBFA2T2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		CBFA2T2 oligomerizes to form a scaffold upon which PRDM14 and OCT4 are stabilized on chromatin (PMID: 27281218)
CBFA2T3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Co-repressor - does not contact DNA (PMID: 12559562; PMID: 15203199)
CBFB	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	CBFB augments the binding of RUNX to DNA, but does not itself bind DNA. Thus; it is a cofactor. Reviewed in (PMID:11105900). Two citations used by GO (PMID:8351518; PMID:9751756) do not demonstrate DNA binding.
CBL	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a ubiquitin ligase
CBLL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		E3-ubiquitin ligase involved in the regulation of cell adhesion (PMID: 11836526)
CC2D1A	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		(PMID: 17714190) states that human Freud-1L bound specifically to its dual repressor element in the 5-HT1A receptor gene in vitro
CC2D1B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		(PMID: 19423080) says it binds a known locus in vivo, although lack of canonical DBDs suggests indirect DNA-binding
CCDC71	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
CCNT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		General transcription machinery required to stimulate RNA pol II elongation (PMID: 16109377)
CCNT2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Has low or no sequence specificity (PMID: 27899659)
CD36	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CD40	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Cell surface receptor of TNF-family
CD40LG	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CDC6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CDK5RAP3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CDK7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CDK8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Mediator component
CDK9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Kinase protein. There is a structure with RNA (PDB: 5L1Z), where the CDK9 does not contact the RNA
CDKN1A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CDKN2A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein binds to and inactivates NFKB1 (PMID: 10353611)
CEBPZ	Unknown	Yes	Known motif	1 Monomer or homomultimer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain
CELF3	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Is a well established RBP
CENPA	Unknown	Yes	Likely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Histone like protein. Binds DNA in the crystal structure (PDB: 3AN2).
CENPS	Unknown	Yes	Likely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure (PDB: 4NDY) in heterodimeric complex with CENPX. Protein complex has many contacts with the backbone, but only a few with the bases.
CENPT	Unknown	Yes	Likely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Contains an archaeal histone-like fold (CBF_NFY). but at best would have low sequence specificity. Known role in centromere assembly and lack of known sequence specificity suggest that it is unlikely to be a sequence specific TF.
CENPX	Unknown	Yes	Likely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure (PDB: 4NDY) in heterodimeric complex with CENPS. Protein complex has many contacts with the backbone, but only a few with the bases.
CFLAR	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CGGBP1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Binds unstable triplet repeat 5-d(CGG)n-3 in the human FMR1 gene (PMID: 9201980)
CHCHD3	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Alias FLJ20420 can specially bind the hBAG-1 promoter region by EMSA and ChIP assays (PMID: 22567091)
CHD1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif	Has a putative AT-hook	(PMID: 22033927) discusses and presents a crystal structure with DNA. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. Recognizes backbone only, so it has low specificity.
CHD6	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		ATP dependent helicase (PMID: 17027977), so it has some affinity for DNA
CHD7	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Helicase and chromodomain
CHD9	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif	Has a putative AT-hook
CHP1	Unknown	No	ssDNA/RNA binding	3 Low specificity DNA-binding protein	No motif		According to EMSA, binds RNA strongly, and dsDNA weakly (PMID: 22727667)
CHRAC1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif
CHUK	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Kinase that operates upstream in the signalling cascade that leads to NFKB
CHURC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Most recent work has conclusively shown it does not bind DNA (PMID: 17610897), refuting a previous study (PMID: 14651851)
CIB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CIITA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Chromatin modifier
CIR1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CITED1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Known co-activator. GO says its sequence-specific DNA binding transcription factor activity NAS - PMID: 8901575 but this reference does not show this.
CITED2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CITED4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional co-factor
CIZ1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Presence of zf-C2H2_jaz domain suggests that its likely a dsRNA binding protein
CLU	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because GO says positive regulation of NF-kappaB transcription factor activity, but there is no DBD and no evidence of DNA binding.
CMKLR1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a G protein-coupled receptor for the chemoattractant adipokine chemerin
CNBP	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		CNBP has a specificity for single-stranded DNA (PMID: 2562787)
CNOT3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Part of complex that de-adenylates mRNA molecules (PMID: 27746116)
CNOT4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Regulates transcription through ubiquitination of TFIID (PMID:11823428). Only contains RRM domains, with no DBDs.
CNOT7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		(PMID:9820826) does not support DNA-binding
CNOT8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Deadenylase that probably regulates genes post-transcriptionally by controlling mRNA stability (PMID: 19605561)
COMMD1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
COMMD6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
COMMD7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
COPS2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
COPS3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Kinase that phosphorylates JUN and possibly other TFs
COPS4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CPEB1	Unknown	Yes	Known motif	1 Monomer or homomultimer	High-throughput in vitro		HT-SELEX motif could be an artefact of ssDNA binding activity, as CPEB1 is a well-characterized RNA-binding protein. Could not find evidence of CPEB1 DNA-binding activity in the literature
CREBBP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		CREBBP is a likely transcriptional co-activator based on its domains and previous experimental evidence. It has previously been shown to not bind DNA sequence-specifically (PMID: 21539536)
CREG1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Regulates transcription in tethering assays (PMID: 9710587). Unlikely to be a TF, based on the lack of a canonical DBD
CRTC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CRTC2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	CRTC2 binds CREB and does not make contacts with the DNA (PDB: 4HTM; PMID: 23213254)
CRTC3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Evidence showing that CRTC2, which resembles CERTC3, lacks DNA-binding acitvity. Its reasonable to speculate CRTC3 also lacks ability to bind to DNA
CSRNP1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)
CSRNP2	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)
CSRNP3	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)
CTBP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Transfac-only motif with no clear source. This is a known corepressor with a primary function in the Golgi.
CTBP2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CTH	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CTNNB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	This is beta catenin - acts as co-factor with TCF/LEF
CTNNBIP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CUL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Component of the E3-ubiquitin ligase complex (PMID: 11961546)
CUL2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CUL3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CUL4A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CUL4B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Structure (PDB: 4A0L) shows that CUL4B is recruited to DNA and does not make direct contact with it
CUL5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CYLD	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CYP1B1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
CYTL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DAB2IP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DACH1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif	Has a putative AT-hook	Binds with consensus AAWANAAAWAAWT and AATACAATTAAAT as strongest target sequences based on EMSA and SELEX (PMID: 20351289). Protein contains a winged helix structural domain (PMID: 12057194)
DACH2	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif	Has a putative AT-hook	Related to DACH1, which can bind DNA based on EMSA and SELEX (PMID: 20351289). Yet, the fly ortholog has been extensively studied and cannot bind DNA. (PMID: 8431945; PMID: 7821215)
DAP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein functions in apoptotic signaling
DAXX	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional co-repressor
DCP1A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DDB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		DDB1 does not contact the DNA in the structure (PDB: 4E5Z) - contact is mediated by DDB2
DDB2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DDB2 contacts the DNA in the (PDB: 4A0K) structure, albeit likely in a non sequence specific manner
DDN	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
DDR2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DDRGK1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DDX3X	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Protein is a RNA-helicase that can however bind both RNA and DNA (PMID: 21589879). The interaction is presumably nonspecific and a portion of the DNA has to be single-stranded
DDX5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional cofactor (PMID: 15298701)
DDX58	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DEK	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. (Entrez gene summary). So it must have some nonspecific DNA affinity.
DEPDC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Interacts with transcriptional corepressor ZNF224 (PMID: 20587513)
DEPDC1B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein does not have known DBDs and has been shown to function as an inhibitor of a RhoA-based signaling complex (PMID: 25458010)
DEPDC4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DEPDC5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DEPDC7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because Vasquerizas 2009 includes it with an x. No DBD and no other data to support being a TF.
DEPTOR	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DHX34	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DHX36	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds single stranded DNA in the structure (PDB: 2N21)
DISP3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DMAP1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Component of the NuA4 histone acetyltransferase (HAT) complex, which is involved in transcriptional activation of select genes, principally by acetylation of nucleosomal histones H4 and H2A (PMID: 14966270). (PMID: 20864525) shows DNA binding is sequence independent.
DMC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DMRTC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This particular DM protein lacks the DM DBD (PMID: 16488114)
DNA2	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Helicase involved in genome integrity. Binds single stranded DNA in the structure (PDB: 5EAN)
DNAJA3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein functions in a chaperone complex
DNAJC21	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Contains a single Matrin-type or U1-type C2H2 domain, which typically binds dsRNA. Its a known heat shock protein that may also be involved in rRNA processing.
DNMT3A	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).
DNMT3B	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).
DNMT3L	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).
DNTT	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds single stranded DNA in the structure (PDB: 4I27)
DPF2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		No evidence for DNA-binding activity - possible role in transcriptional regulation complex (PMID: 16785614)
DR1	Unknown	Yes	Likely to be sequence specific TF	2 Obligate heteromer	No motif		Binds DNA as a heterotrimeric complex of TBP, DR1, and DRAP1 (PDB: 1JFI)
DRAP1	Unknown	Yes	Likely to be sequence specific TF	2 Obligate heteromer	No motif		Based on structure (PDB: 1JFI), it forms the obligate heterodimer DR1-DRAP1 that furthermore contacts TBP. Only makes contact with the minor groove in a histone-like interaction, which is probably non-specific (PMID: 11461703)
DSP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DTX1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This protein is an E3 ligase that operates in the Notch pathway
DUSP12	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DVL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DVL2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		DVL2 does not have any known DBDs; or experimental evidence to suggest it is a TF.
DVL3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
DZIP1L	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Contains a weak ProSite match for a single C2H2 ZF (Uniprot) but not a Pfam match. No experimental evidence for DNA-binding exists
EAF2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		No convincing evidence that this protein binds DNA with any sequence specificity, or that this activity is required for its function. Thus at best the current evidence is that it is a cofactor of some sort cofactor (PMID: 12446457)
EDA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Cell surface protein that can be cleaved into a secreted one
EDA2R	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because GO says positive regulation of sequence-specific DNA binding transcription factor activity. Not DNA binding.
EDF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Known co-factor that binds DNA indirectly through interactions with TFs (PMID:12040021)
EDN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein that is processed into a secreted signaling peptide
EED	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Affects transcription by histone modification (PMID: 16357870)
EGLN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EID1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EID2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Associates with histone deacetylases (PMID: 12586827)
EIF2AK2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EIF2AK4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EIF3C	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EIF3CL	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EIF3K	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EME1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure (PDB: 4P0P) in a heterodimeric complex with MUS81.
ENO1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Enolase - DNA binding not shown to be direct
EP300	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	p300 is an archetype cofactor. It has many motifs, presumably because many TFs recruit it. Does not contact DNA in the structure (PDB: 3P57)
EP400	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif	Has a putative AT-hook	Protein is a nucleosome remodeling complex component with a role in depositing the H3.3 variant histone into promoter and enhancer regions (PMID: 26669263). Its MYB-like and helicase domains are likely non-specific DNA binding domains
EPHA5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
EPM2AIP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein that binds and regulates glycogen synthase allosterically (PMID: 24142699)
ERBIN	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ERC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ERCC3	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure (PDB: 5IY6). Protein is an ATP-dependent 3-5 DNA helicase, so likely non-specific.
ERCC4	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds ssDNA at splayed DNA (PDB: 2KN7)
EWSR1	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif
EXO1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Makes contact with ssDNA bases at DNA breaks (PDB: 3QE9)
EXOC2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Plasma-membrane protein functioning in targeting of exocytic vesicles
EXOG	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Endo/exonuclease (5-3), endonuclease G-like. Binds DNA in the crystal structure (PDB: 5T4I), presumably non-specifically
EZH1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Classic polycomb protein.
EZH2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This is a classic polycomb protein with no evidence of sequence specific DNA binding after years of intense study. I dont see anything in (PMID :15520282) that supports DNA binding.
FAAP24	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA backbone from the side of the minor groove in the crystal structure (PDB: 4BXO)
FAM153C	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FAM171B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
FAM200A	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Protein of unknown function that is conserved in animalia. Has similarities to transposases and zinc fingers, and thus could be a DNA binding protein although there is no evidence supporting this
FAN1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		FANCD2 and FANCI associated nuclease 1. Binds DNA in the crystal structure (PDB: 4REA), presumably non-specifically
FANCA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Involved in DNA repair (PMID: 8896564)
FANCD2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		DNA repair protein. Inconclusive data supporting sequence-specific binding. Binds NFKB target sites in EMSA using 293T expressing FANCD2 (PMID: 21912593). Since the protein is expressed in mammalian cells, it could still be NFKB mediated binding.
FANK1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Binds JUN to control its activity (PMID: 20978819), but there is no evidence that it binds DNA itself
FARSA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FARSB	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		tRNA synthetase
FBN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FBXO41	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FEN1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Involved in DNA replication. Binds DNA in the crystal structure (PDB: 3Q8K), presumably in a non-specific manner.
FER	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FGD1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FHL2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		LIM ZF proteins are unlikely to bind DNA. Experimental evidence does not support a role for FHL2 as a sequence-specific DNA-binding protein (PMID:10654935)
FLNA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Go annotation is based on (PMID: 15684392), which shows that it binds FOXC1 and PBX1 but doesnt show evidence for binding to DNA
FMNL2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FUBP1	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	ssDNA binding protein with crystal structure demonstrating binding to ssDNA (PDB: 1J4W). Its a KH domain protein - this is Levens protein, known to impact the Myc promoter.
FUBP3	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Can bind single stranded DNA in a sequence specific manner (PMID: 8940189). Contans KH domains and has direct evidence it is an RNA-binding protein (PMID: 21252297)
FUS	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		FUS is a well-established RNA-binding protein
FZD1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FZD2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transmembrane receptor protein that operates far upstream in the signalling cascade
FZD4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
FZD6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GABPB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Evidence exists showing that GABPB1 (E4TF1-47/53) has no DNA binding activity, but can assocaite with GABPA (E4TF1-60; Ets factor) (PMID: 8441384). Crystal structure of GAPBP1 with GABPA (PDB: 1AWC) clearly shows that the protein makes an extensive protein-protein interaction with GABPA, but does not bind DNA. Transfac PWM is a clear ETS-motif, so GABP1 is unlikely to contact DNA directly
GABPB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Obligate heteromer with GABPB1 (the alpha subunit) (PMID: 8810337), which together interact with GABPA (PMID: 8441384), but neither contacts the DNA
GADD45A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Doesnt have any DBDs - likely a co-factor
GAS6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GAS7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		(PMID: 9736752) only shows that it has a proline-rich domain similar to the one in Oct2. No evidence of DNA binding.
GCFC2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		There is some evidence that this protein is an RNA-binding protein (PMID: 24304693).
GEN1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Resolves Holliday junctions. Binds DNA in the crystal structure (PDB: 5T9J)
GLMP	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Binds GATCCGCCCGCTTGTGGCCAACTGGCTCCAGTCAC dsDNA based on EMSA (PMID: 18021396)
GOLGB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Golgi resident transmembrane protein that regulates glycosylation of other proteins (PMID: 27226319)
GON4L	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Prosite identifies a low-confidence Myb-like domain (e.g., cant decide between Myb, SANT, or no DBD), so its probably not a TF
GPATCH8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GPBP1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Solid data presented in (PMID: 14612417) Also known as Vasculin. (PMID: 26156556) also claims it has an extended AT hook.
GPBP1L1	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		Possible TF based on similarity to GPBP1. Despite its name, no available evidence for DNA binding. Could also be an RBP according to this screen (PMID: 22658674)
GPER1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GPR155	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GREM1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GRM6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GTF2A1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		General transcription factor. Binds DNA in the crystal structure (PDB: 5FUR). The protein contacts the DNA backbone as a heterotrimeric complex that also includes GTF2A2 and TBP. Has an extensive protein-protein interaction interface with the GTF2A2 (that does not contact the DNA) and will probably do nothing without it
GTF2A1L	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
GTF2A2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		GTF2A2 makes contacts with the DNA backbone (PDB:1NVP; PMID: 12972251), and thus is unlikely to be sequence-specific
GTF2B	Unknown	Yes	Known motif	3 Low specificity DNA-binding protein	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Contacts both DNA and TBP in the structure (PDB: 1C9B)
GTF2E2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		GTF2E2 weakly binds dsDNA (PMID: 10716934) - unlikely to be sequence-specific
GTF2F1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Does not contact DNA in the structure (PDB: 5IY6)
GTF2F2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		The protein contacts DNA in the structure (PDB: 5IY6), and could thus have some specificity; DNA is contacted by domain folded from RKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELK.
GTF2H1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		General transcription factor
GTF2H2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		GTF2H2 (p44) is part of the TFIIH complex, but does not contact the DNA based on structural evidence (PDB: 5IVW)
GTF2H2C	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a transcriptional co-regulator (PMID: 9880511)
GTF2H3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Pre-initiation complex component that does not contact DNA in the structure (PDB: 5IVW)
GTF2H4	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		General transcription factor
GTF3C1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Component of RNA polymerase III. Binds weakly to the A-box (PMID: 8164661)
GTF3C2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	GTF3C2 is a general transcription factor of RNA polymerase III and there is no evidence that it binds DNA in the preinitiation complex. Transfac motifs are suspect
H1F0	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Histone. Likely a false-positive Pfam match based on the similarity of Forkhead domains to H1 domains
H1FOO	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Variant linker histone protein that is expressed in oocytes
H1FX	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Histone component
HAVCR2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HCFC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is recruited to promoters by THAP11 and ZNF143 and probably does not bind DNA by itself (PMID: 26416877)
HCK	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Inhibits TP73-mediated transcription activation (PMID: 17535448)
HDAC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Histone deacetylase; likely to be a transcriptional cofactor. Transfac motif is dubious, and the GO annotation (PMID: 8646880) seems to be based on remote homology to a yeast TF
HDAC10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Histone deacetylase; likely to be a transcriptional cofactor
HDAC3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HDAC8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HDAC9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely to be a transcriptional cofactor
HELZ2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HIPK2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional cofactor that can act as a coactivator or corepressor. Phosphorylates many transcription factors. (UniProt Q9H2X6)
HIRA	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	Histone chaperone - TUP1 homolog.
HIST1H1A	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Histone component
HIST1H1B	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Linker histone. To my knowledge there has been no demonstration of sequence specificity of linker histones, so I think this one should be called unlikely.
HIST1H1C	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif
HIST1H1D	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Linker histone that binds DNA as heteromeric complex with the other histone proteins
HIST1H1E	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA as heteromultimeric complex
HIST1H1T	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif
HLA-DQB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HLA-DQB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HLA-DRB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HLA-DRB3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HLA-DRB5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HLTF	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	DNA repair protein. Even though it has 3 motifs, there is no compelling evidence that it really binds dsDNA - only single stranded DNA
HMOX1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Well characterized enzyme with no additional domains. Included only because GO lists it as a regulator of TFs. No support for DNA binding activity.
HNRNPA1	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds single stranded DNA in the structure (PDB: 1PGZ)
HNRNPA3	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Protein is a well established RBP
HNRNPAB	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		HNRNPAB proteins are involved in pre-mRNA splicing. However; RRM domains can also constitute ssDNA binding domains
HNRNPCL2	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Protein is a well established RBP
HNRNPD	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds single stranded DNA in the structure (PDB: 1WTB)
HNRNPDL	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Protein is a well established RBP
HNRNPK	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Protein is a well established RBP
HNRNPL	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		HNRNPL is a well-established RNA-binding protein; and the DNA-binding evidence was neither shown to be specific or direct (PMID: 11809897)
HNRNPU	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds pre-mRNA in vivo and binds both RNA and ssDNA in vitro (PMID: 1628625)
HP1BP3	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Histone H1-like protein. Binds in ChIP experiments (PMID: 27425409) and binds DNA (likely non-specifically) with HP1.
HR	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		JmjC domain is not a DBD, and GO annotation is based on homology to a zinc finger motif and not experimental DNA-binding evidence (PMID: 9445480)
HSBP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein that has been shown to bind to HSF1 leading to inhibition of its trimerization and DNA-binding( PMID: 9649501).
HSPA1A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
HSPA1B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ICAM1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IFI16	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Recognizes DNA without sequence specificity (PMID: 22618232; PMID: 18472023)
IFNB1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IGHM	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IKBKB	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IKBKG	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein binds to NFKB1 to regulate its activity
IL10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IL1B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IL1RAP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IL4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Extracellular signaling molecule. Included as a candidate only because it regulates STAT.
IL5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IL6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
INF2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook
ING4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Interacts physically with p53 (PMID: 12750254). Transfac motif is derived from ChIP-Chip data, so unclear if it can directly bind DNA
INS	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IRAK1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IRAK2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IRAK3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IRF2BP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ITCH	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ITGB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
ITGB3BP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
IZUMO2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		IZUMO is not considered to be a DNA-binding domain
JADE1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		FYVE and PHD zinc fingers are unlikely to specifically-bind DNA
JAK2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This is JAK from the classic JAK-STAT pathway. It is included only because GO lists it under positive regulation of sequence-specific DNA binding transcription factor activity. No evidence of sequence specificity - the STATs handle that.
JMY	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Coactivator protein that associates with p300 and TP53 (PMID: 10518217). There is no evidence that it contacts DNA itself. Functions also in actin nucleation (PMID: 19287377).
JUP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KANSL2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Protein is a component of the NSL chromatin remodelling complex
KAT2A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase
KAT2B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Interacts with TFs to modify histones (PMID: 9707565)
KAT5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone acetyltransferase
KAT6A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Histone deacetylase; likely a transcriptional cofactor
KAT6B	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Co-factor. Could possibly bind to DNA, as a helix- turn-helix DNA-binding motif is present within its MYST-type HAT domain.
KAT8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		No DBDs, no evidence of TF activity - looks like a chromatin protein. Included only because it has an x in Vaquerizas 2009.
KCNIP3	Unknown	Yes	Likely to be sequence specific TF	1 Monomer or homomultimer	No motif		There are multiple papers showing DREAM can bind DNA (PMID: 10078534, PMID: 11108959).
KDM1A	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Affects transcription by histone modification
KDM3A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Its a C6 zinc finger and Jumonji-type protein. No DBD.
KEAP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KIAA1549	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KIAA1683	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		No evidence to support a DNA binding function
KIAA1958	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KIT	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KNTC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Rod_C domain localizes to kinetochores but has not been shown to be DNA-binding
KRAS	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KRBOX1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		KRAB domain only - no DBD or evidence for independent DNA binding
KRTAP5-1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KRTAP5-9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
KRTAP9-9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Keratin-associated protein
LARP1	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Classic RNA binding protein
LARP1B	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif
LARP4	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Classic RNA binding protein
LARP4B	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Classic RNA binding protein
LARP6	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Classic RNA binding protein
LARP7	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Classic RNA binding protein
LGALS9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
LGR4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
LIG1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DNA ligase. Binds DNA in the crystal structure (PDB: 1X9N)
LIG3	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DNA ligase. Binds DNA in the crystal structure (PDB: 3L2P)
LMO2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Only known motifs are from Transfac or HocoMoco - origin is uncertain	Protein binds to bHLH TFs, which then bind to DNA (PMID: 9707419). Both transfac motifs are suspect - the bHLH motif likely resulted from an indirect interaction.
LMO4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
LPP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		znfLIM is probably not a DNA binding domain (PMID: 8506279). The protein has been reported to be coactivator for ETV4 (PMID: 16738319).
LRP5	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif
LRP6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Cell surface receptor that is in the beginning of the WNT signaling cascade. GO annotation has no evidence of DNA-binding activity (PMID: 14739301).
LRP8	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif
LRRFIP1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Seems to be included only because GO catalogs positive regulation of NF-kappaB transcription factor activity. Nothing that would indicate DNA binding.
LRRFIP2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Its paralog forms a complex with ETS1 that binds AGCCCCCGGCG sequences based on EMSA and SPR (PMID: 16199883). However, direct DNA binding by LRRFIP2 is not demonstrated, and it seems more likely that it is in the complex through protein-protein interactions.
LSR	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Cell plasma membrane resident protein that functions in cell-cell junctions (PMID: 25753034)
LTF	Unknown	Yes	Known motif	1 Monomer or homomultimer	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain
LTN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
LZTFL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Lactotransferrin - major iron-binding protein in milk. Two papers from the 1990s (PMID: 7854459; PMID: 1037119) demonstrate strong DNA binding.
LZTR1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
LZTS1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Does not contain a bZIP domain. (PMID: 10097140) does not examine TF activity or DNA binding - GO needs to be corrected.
MACC1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MACF1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because Vasquerizas 2009 includes it with an x. No DBD and no other data to support being a TF.
MAD2L2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Likely to be a DNA-binding protein that operates on DNA-repair (PMID: 25799990)
MALT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein that operates upstream of NFKB in a signaling cascade (PMID: 18223652)
MAML1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		MAML1 does not contact the DNA in the structure (PDB: 2F8X), but contacts RBPJ, which in turn binds DNA
MAML3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAP2K5	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Kinase that operates upstream in the signaling cascade that leads to NFKB
MAP3K10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAP3K13	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAP3K7	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a kinase
MAPK1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		MAP kinase; protein array paper evidence is not strong
MAPK10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein is a kinase
MAPK11	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAPK14	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Well characterized MAPK. Included because it as a regulator of several TFs and GO captures this.
MAPK3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAPK8	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MAPK9	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MATR3	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		An RBP that recognizes MAUCUUR-site based on Ray et al 2013 (PMID: 23846655)
MAVS	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Operates upstream in the signaling cascade that activates innate immunity response for viruses through NFLB and IRF3 TFs
MB21D1	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA with backbone contacts and one minor groove inserting Arginine in the crystal structure (PDB: 4LEY)
MBTPS2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		GO annotation has no evidence of DNA-binding activity, only modulation of TF activity (PMID: 11163209)
MDFI	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		MDF1 is a co-repressor that inhibits DNA-binding (PMID: 8797820)
MDM2	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif
MDM4	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Protein binds to, and inhibits, p53 (PMID: 9226370)
MED1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This is a component of Mediator.
MED12	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED13	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED13L	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED14	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED15	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED16	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		This is a component of Mediator.
MED17	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED21	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Does not contact DNA in the structure of the yeast mediator complex (PDB: 5SVA)
MED23	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED24	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MED6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Does not bind anywhere near DNA on crystal structure (PDB: 4V1O)
MEN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Interacts with NFKB1 (PMID: 11526476), JUN, JUND, and ELK1 and represses their activities with a mechanism that is at least for JUN and JUND dependent on their phosphorylation
MET	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Its a cell surface receptor and kinase - included only because Vasquerizas 2009 included it with an x.
MGMT	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents (PMID: 15964013); structure (PDB: 1YFH) is with cytosine alkylated DNA
MID2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		GO citation (PMID: 23077300) has no evidence of DNA-binding activity
MINK1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MKL1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional co-factor
MKL2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MKRN3	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Likely E3 ubiquitin ligase. Contains a RING (C3HC4) zinc finger motif and several C3H zinc finger motifs
MLLT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		X-ray structure indicates histone binding (PDB: 4TMP)
MLLT10	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	No evidence showing MLLT10 can bind to DNA in a sequence-specific manner (PMID: 7888665)
MLLT11	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MLLT3	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcription elongation factor [PMID: 20159561; PMID: 20471948]
MLLT6	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	Likely to be a transcriptional cofactor based on presence of PHD domains and (PMID: 15588942)
MN1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Evidence for DNA binding not strong in (PMID: 12569362)
MNAT1	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MPG	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		DNA error repair enzyme that excises alkylation-damaged purine bases. Binds dsDNA in the crystal structure (PDB: 1BNK)
MRPL28	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Included only because it has an X in Vaquerizas 2009
MRRF	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MSH2	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA that has a base mismatch as a heterodimer with MSH6. Binds DNA in the crystal structure (PDB: 2O8B)
MSH3	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Involved in mismatch repair - binds dsDNA with indels (PDB: 3THZ) and changes DNA shape
MSH6	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA that has base mismatches as a heterodimer with MSH2. Binds DNA in the crystal structure (PDB: 2O8B)
MSL3	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		Binds DNA in the crystal structure (PDB: 3OA6). Contacts only the backbone and doesnt cause large changes in the DNA shape
MSRB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		The paper cited by GO (PMID:10375640) called MSRB2 a TF based on amino acid sequence analysis, but did not provide any direct evidence
MST1R	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MTDH	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MTF2	Unknown	Yes	Known motif	1 Monomer or homomultimer	High-throughput in vitro		Recent study (PMID: 28869966) demonstrates direct, specific DNA binding to CG-rich sequences through PBMs, and crystal structure in complex with DNA
MTPN	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		No DBD; no evidence for DNA binding - only included because GO says its a positive regulator of NFkappaB.
MUS81	Unknown	No	Unlikely to be sequence specific TF	3 Low specificity DNA-binding protein	No motif		MUS81 is a structure-specific endonuclease subunit. It binds DNA in the crystal structure (PDB: 4P0P) in a heterodimeric complex with EME1.
MYBBP1A	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif	Has a putative AT-hook	Protein that activates TP53 (PMID: 24375404) and binds to MYB (PMID: 24375404); however, there is no evidence of direct binding to DNA
MYCBP	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif
MYD88	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Operates upstream in the signaling cascade (PMID: 22155231)
MYEF2	Unknown	No	ssDNA/RNA binding	4 Not a DNA binding protein	No motif		Binds single-stranded DNA and can regulate transcription in transfection reporter assays
MYOCD	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Transcriptional cofactor (PMID: 12640126)
NAB2	Unknown	No	Unlikely to be sequence specific TF	4 Not a DNA binding protein	No motif		Well characterized transcriptional co-repressor of e.g. EGR1 (PMID: 12427750)

NR0B1

Unknown

Yes

Known motif

2 Obligate heteromer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

AATF

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely does not bind to bind to DNA (PMID: 17634135).

ABL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ABRA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The Costars domain in this protein is an atypical winged helix protein that does not bind DNA but to other proteins (PMID: 21082705)

AC020915.1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ACOD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ACTR3B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ACTR3C

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pfam match to an APSES domain - this is likely a false positive, as these domains are mostly present in bacteria and fungi

ADAM8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ADAMTS17

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ADAMTS19

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

ADAR

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

PMID: 21728134 shows the ADAR protein bind to ds RNA and Z DNA. At best it would be a non-sequence specific DNA binding protein. But, it has a well established role as a dsRNA binding protein, so it is unlikely to be a TF.

ADGRA1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ADGRG3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

AEBP1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

This is a protease, but its ability to bind DNA is supported by both gel-shift (PMID: 15654748) and ChIP (PMID: 22723309).

AES

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely a transcriptional co-factor

AFAP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

There is no evidence suggesting DNA-binding activity

AFF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

MLL fusion partner

AFF3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 8555498) only says that In vitro-translated LAF-4 was able to bind strongly to double-stranded DNA cellulose - thats more consistent with nonspecific DNA binding. The key issue is whether the Transcription factor AF4/FMR2 (IPR007797) domain really is sequence specific. Most of the work has been done on the one Drosophila ortholog, lilliuputian. I see no evidence of DNA binding. Recent work on this family in human indicate that it functions in coactivation (PMID: 27899651; PMID: 261712

AFF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 8555498) only says that In vitro-translated LAF-4 was able to bind strongly to double-stranded DNA cellulose - thats more consistent with nonspecific DNA binding. The key issue is whether the Transcription factor AF4/FMR2 (IPR007797) domain really is sequence specific. Most of the work has been done on the one Drosophila ortholog, lilliuputian. I see no evidence of DNA binding. Recent work on this family in human indicate that it functions in coactivation (PMID: 27899651; PMID: 261712

AGER

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Contacts DNA in the structure (PDB: 4OI7)

AGT

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

AIM2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Based on (PDB: 3RN2), the protein binds DNA but contacts only the backbone; AIM2 binds cytrosolic dsDNA in the innate immune response

AKT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ALK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates far upstream in the signaling cascade

ALKBH2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Binds DNA in the crystal structure (PDB: 3BTX)

AMH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ANAPC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Scaffolding protein that associates with ubiquitin ligase complexes

ANKRD30A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

GO citation (PMID: 11280766) has no evidence of DNA-binding activity and was based on homology

ANXA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein operates far upstream on the signaling cascade.

ANXA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

AP5Z1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

May have helicase activity and play a role in DNA repair (PMID: 20613862)

APBB3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

APEX1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

The structure (PDB:1DEW) is with abasic DNA - the protein is a base excision repair enzyme that cleaves off abasic bases

APOBEC3A

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds ssDNA (PDB: 5KEG)

APOBEC3B

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds ssDNA (PDB: 5TD5)

APOBEC3G

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Restriction factor of HIV-1 that binds ssDNA (PDB: 5K83)

APTX

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds and fixes DNA-RNA hybrids/ APTX efficiently repairs adenylated RNA-DNA and acts in the RNA-DNA damage response (PMID: 24362567)

ARHGAP35

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds DNA specifically based on EMSA and nuclease protection assay data (PMID: 1894621), despite lacking any clear DBDs.

ARHGEF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ARHGEF5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO annotation provides no evidence of DNA-binding activity (PMID: 15601624)

ARRB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ChIP data available, but unclear if it can bind to DNA directly (PMID: 16325578)

ARRB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ASCC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a coactivator that is reported to bind to SRF, NFKB1, and JUN (PMID: 12077347)

ATF7IP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Murine homolog involved in H4K9 trimethylation by SETDB1 (PMID: 14536086)

ATM

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase protein that binds to and activates certain TFs

ATR

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ATRX

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ATRX does not contain any canonical sequence-specific DBDs but it does contain a non-specific DNA binding helicase that allows it to bind repeat sequences (PMID:21029860) and telomeres (PMID:20651253). ATRX is involved in multiple processes (transcription, replication), and is associated with multiple complexes (Swi/Snf, histone chaperones, and repressive complexes including TRIM 28 (PMID:27029610)), and as such does affect transcription. Given the lack of sequence-specific binding it is unlikel

ATXN7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ATXN7 SCA7 domain facilitates interactions with histone dimers (PMID: 20634802)

BAG1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Antiapoptotic BCL-protein

BANF1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure, contacting only the backbone from the side of the minor groove (PDB: 2BZF)

BANP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

BANP has no DBD and is known to bind other TFs; likely that the Transfac motif is from one of its binding partners

BCL10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Apoptosis associated protein that operates upstream on a cascade that includes NFKB

BCL3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

No DBD - instead, this is a known cofactor of NF-kappaB. The Transfac motif is the NFKB1 motif. GO cites only electronic annotation and needs to be fixed.

BCLAF1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

No DBD. Only weak evidence is available for indirect binding (PMID: 10330179). Suspect motif - it is a clear ETS-site. (PMID: 10330179) shows that the protein binds DNA in filter binding assay, but not that it is sequence specific.

BCOR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-repressor that associates with BCL6 (PMID: 10898795)

BDP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BEX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely a cofactor- (PMID: 16314316) shows results for related BEX2

BIN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BLM

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Helicase involved in DNA replication and repair (PDB: 4CGZ)

BLZF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is a golgi protein with no evidence for DNA binding.

BMI1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BMI1 binds to nucleosomes as part of the PRC1 complex but does not contact the DNA directly (PDB: 4R8P)

BMP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BMP4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely a cofactor.

BMP7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BMPR1A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BOD1L1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

BOLA1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BOLA2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BOLA2B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BOLA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

E. Coli homologue of the BOLA binds DNA; however there is no evidence in the mammalian proteins

BPNT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BPTF

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain; Has a putative AT-hook

(PMID: 10575013) obtained a motif by SELEX and showed that mutating the sequence diminished binding in vitro. Unusual for a PHD/Ring finger, but its there in the literature.

BRCA1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

In vivo/Misc source

BRCA1 likely binds to DNA without DNA sequence specificity (PMID: 11353843)

BRD4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Binds acetylated histones

BRD7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BRD8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

TF-coactivator

BRD9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Evidence ony for interaction with histones (PMID: 22464331)

BRF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

GTF - Pol III - TRANSFAC has a motif but its likely not for this protein, but for the complex as a whole

BRF2

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Makes backbone and sequence-specific interactions with DNA (PDB: 4ROC), but only involved in recognizing dinucleotides flanking the TATA box (PMID: 26638071). Redox sensing determines activation and repression of target genes

BRMS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BRMS1 functions as a corepressor by promoting binding of HDAC1 to RelA/p65, where it deacetylates lysine K310 on RelA/p65, which suppresses RelA/p65 transcriptional activity (PMID: 17000776)

BRPF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

BTAF1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein that uses ATP to dissociate TBP from the promoter

BTBD8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Probably annotated as TF based on presence of a BTB domain; however, these domains are not known to bind DNA

BTG2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-factor (PMID: 10617598)

BTK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Involved in the regulation of ARID3A and NFAT in B lymphocyte development; has been thoroughly investigated, but there is no evidence to demonstrate DNA binding activity (see UniProt Q06187)

BTRC

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

BUD31

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included because GO says its DNA binding on the basis of (PMID: 7841202), a 1995 paper that only suggests DNA binding on the basis of the protein sequence. In fact, it is composed entirely of a G10 domain.

C14orf39

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

C1D

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

C1D has been shown to bind RNA (PMID: 17412707) and is associated with the exosome. C1D is also associated with DNA repair and has DNA-binding activitiy (PMID: 10362552)

C20orf194

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

C3orf33

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Some effect on DNA-binding of AP-1 (PMID: 20680465), but does no data supporting a role for C3orf33 as a DNA-binding factor itself

CACTIN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein operates on a signaling cascade far upstream of NFKB (PMID: 20829348)

CAMK1D

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Functions in signalling cascade that leads to phosphorylation and activation of CREB (PMID: 16324104)

CAMK2A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CAPN15

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Basically an unknown protein - a likely protease that contains also znfRANBP-domains, so it could be a RNA-binding protein

CAPN3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because GO says positive regulation of NF-kappaB transcription factor activity. No indication of sequence specific DNA binding.

CARD11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Plasma-membrane protein possibly functioning in upstream signaling of NFKB (PMID: 12154360)

CARD14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CARF

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Transfac-only motif. Major evidence is found in (PMID: 11832226). Cloned by Y1H and binding demonstrated by gel-shift. Mutant probes do not compete. DNA binding ability seems solid but motif is sketchy.

CASP8AP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pfam DBD match is a likely false-positive - did not produce a motif in PBM experiments

CAT

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that breaks down hydrogen peroxide

CBFA2T2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CBFA2T2 oligomerizes to form a scaffold upon which PRDM14 and OCT4 are stabilized on chromatin (PMID: 27281218)

CBFA2T3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Co-repressor - does not contact DNA (PMID: 12559562; PMID: 15203199)

CBFB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

CBFB augments the binding of RUNX to DNA, but does not itself bind DNA. Thus; it is a cofactor. Reviewed in (PMID:11105900). Two citations used by GO (PMID:8351518; PMID:9751756) do not demonstrate DNA binding.

CBL

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiquitin ligase

CBLL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

E3-ubiquitin ligase involved in the regulation of cell adhesion (PMID: 11836526)

CC2D1A

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

(PMID: 17714190) states that human Freud-1L bound specifically to its dual repressor element in the 5-HT1A receptor gene in vitro

CC2D1B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 19423080) says it binds a known locus in vivo, although lack of canonical DBDs suggests indirect DNA-binding

CCDC71

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

CCNT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

General transcription machinery required to stimulate RNA pol II elongation (PMID: 16109377)

CCNT2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Has low or no sequence specificity (PMID: 27899659)

CD36

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CD40

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Cell surface receptor of TNF-family

CD40LG

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CDC6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CDK5RAP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CDK7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CDK8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Mediator component

CDK9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase protein. There is a structure with RNA (PDB: 5L1Z), where the CDK9 does not contact the RNA

CDKN1A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CDKN2A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein binds to and inactivates NFKB1 (PMID: 10353611)

CEBPZ

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

CELF3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Is a well established RBP

CENPA

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone like protein. Binds DNA in the crystal structure (PDB: 3AN2).

CENPS

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4NDY) in heterodimeric complex with CENPX. Protein complex has many contacts with the backbone, but only a few with the bases.

CENPT

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Contains an archaeal histone-like fold (CBF_NFY). but at best would have low sequence specificity. Known role in centromere assembly and lack of known sequence specificity suggest that it is unlikely to be a sequence specific TF.

CENPX

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4NDY) in heterodimeric complex with CENPS. Protein complex has many contacts with the backbone, but only a few with the bases.

CFLAR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CGGBP1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds unstable triplet repeat 5-d(CGG)n-3 in the human FMR1 gene (PMID: 9201980)

CHCHD3

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Alias FLJ20420 can specially bind the hBAG-1 promoter region by EMSA and ChIP assays (PMID: 22567091)

CHD1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Has a putative AT-hook

(PMID: 22033927) discusses and presents a crystal structure with DNA. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. Recognizes backbone only, so it has low specificity.

CHD6

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ATP dependent helicase (PMID: 17027977), so it has some affinity for DNA

CHD7

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Helicase and chromodomain

CHD9

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Has a putative AT-hook

CHP1

Unknown

No

ssDNA/RNA binding

3 Low specificity DNA-binding protein

No motif

According to EMSA, binds RNA strongly, and dsDNA weakly (PMID: 22727667)

CHRAC1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

CHUK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase that operates upstream in the signalling cascade that leads to NFKB

CHURC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Most recent work has conclusively shown it does not bind DNA (PMID: 17610897), refuting a previous study (PMID: 14651851)

CIB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CIITA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Chromatin modifier

CIR1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CITED1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known co-activator. GO says its sequence-specific DNA binding transcription factor activity NAS - PMID: 8901575 but this reference does not show this.

CITED2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CITED4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-factor

CIZ1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Presence of zf-C2H2_jaz domain suggests that its likely a dsRNA binding protein

CLU

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because GO says positive regulation of NF-kappaB transcription factor activity, but there is no DBD and no evidence of DNA binding.

CMKLR1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a G protein-coupled receptor for the chemoattractant adipokine chemerin

CNBP

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

CNBP has a specificity for single-stranded DNA (PMID: 2562787)

CNOT3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Part of complex that de-adenylates mRNA molecules (PMID: 27746116)

CNOT4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Regulates transcription through ubiquitination of TFIID (PMID:11823428). Only contains RRM domains, with no DBDs.

CNOT7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID:9820826) does not support DNA-binding

CNOT8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Deadenylase that probably regulates genes post-transcriptionally by controlling mRNA stability (PMID: 19605561)

COMMD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

COMMD6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

COMMD7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

COPS2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

COPS3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase that phosphorylates JUN and possibly other TFs

COPS4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CPEB1

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

HT-SELEX motif could be an artefact of ssDNA binding activity, as CPEB1 is a well-characterized RNA-binding protein. Could not find evidence of CPEB1 DNA-binding activity in the literature

CREBBP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CREBBP is a likely transcriptional co-activator based on its domains and previous experimental evidence. It has previously been shown to not bind DNA sequence-specifically (PMID: 21539536)

CREG1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Regulates transcription in tethering assays (PMID: 9710587). Unlikely to be a TF, based on the lack of a canonical DBD

CRTC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CRTC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

CRTC2 binds CREB and does not make contacts with the DNA (PDB: 4HTM; PMID: 23213254)

CRTC3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Evidence showing that CRTC2, which resembles CERTC3, lacks DNA-binding acitvity. Its reasonable to speculate CRTC3 also lacks ability to bind to DNA

CSRNP1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)

CSRNP2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)

CSRNP3

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

All three paralogs (CSRNP1, CSRNP2, and CSRNP3) bind an AGAGTG consensus based on SELEX experiments (PMID: 17726538)

CTBP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Transfac-only motif with no clear source. This is a known corepressor with a primary function in the Golgi.

CTBP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CTH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CTNNB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

This is beta catenin - acts as co-factor with TCF/LEF

CTNNBIP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CUL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Component of the E3-ubiquitin ligase complex (PMID: 11961546)

CUL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CUL3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CUL4A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CUL4B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Structure (PDB: 4A0L) shows that CUL4B is recruited to DNA and does not make direct contact with it

CUL5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CYLD

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CYP1B1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

CYTL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DAB2IP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DACH1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Has a putative AT-hook

Binds with consensus AAWANAAAWAAWT and AATACAATTAAAT as strongest target sequences based on EMSA and SELEX (PMID: 20351289). Protein contains a winged helix structural domain (PMID: 12057194)

DACH2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Has a putative AT-hook

Related to DACH1, which can bind DNA based on EMSA and SELEX (PMID: 20351289). Yet, the fly ortholog has been extensively studied and cannot bind DNA. (PMID: 8431945; PMID: 7821215)

DAP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein functions in apoptotic signaling

DAXX

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-repressor

DCP1A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DDB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DDB1 does not contact the DNA in the structure (PDB: 4E5Z) - contact is mediated by DDB2

DDB2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DDB2 contacts the DNA in the (PDB: 4A0K) structure, albeit likely in a non sequence specific manner

DDN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

DDR2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DDRGK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DDX3X

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a RNA-helicase that can however bind both RNA and DNA (PMID: 21589879). The interaction is presumably nonspecific and a portion of the DNA has to be single-stranded

DDX5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor (PMID: 15298701)

DDX58

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DEK

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

This protein binds to cruciform and superhelical DNA and induces positive supercoils into closed circular DNA, and is also involved in splice site selection during mRNA processing. (Entrez gene summary). So it must have some nonspecific DNA affinity.

DEPDC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Interacts with transcriptional corepressor ZNF224 (PMID: 20587513)

DEPDC1B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein does not have known DBDs and has been shown to function as an inhibitor of a RhoA-based signaling complex (PMID: 25458010)

DEPDC4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DEPDC5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DEPDC7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because Vasquerizas 2009 includes it with an x. No DBD and no other data to support being a TF.

DEPTOR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DHX34

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DHX36

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 2N21)

DISP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DMAP1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Component of the NuA4 histone acetyltransferase (HAT) complex, which is involved in transcriptional activation of select genes, principally by acetylation of nucleosomal histones H4 and H2A (PMID: 14966270). (PMID: 20864525) shows DNA binding is sequence independent.

DMC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DMRTC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This particular DM protein lacks the DM DBD (PMID: 16488114)

DNA2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Helicase involved in genome integrity. Binds single stranded DNA in the structure (PDB: 5EAN)

DNAJA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein functions in a chaperone complex

DNAJC21

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Contains a single Matrin-type or U1-type C2H2 domain, which typically binds dsRNA. Its a known heat shock protein that may also be involved in rRNA processing.

DNMT3A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).

DNMT3B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).

DNMT3L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DNMT3A and DNMT3B are de novo methyltransferases that are activated by enzymatically inactive paralog DNMT3L. Besides the C-terminal catalytic core, the PWWP domain of 3A and 3B can also bind to DNA. Presumably there is no sequence specificity and instead the de novo methylation complexes are recruited by histone modifications on the N-terminal tail of H3. Reviewed in (PMID: 27826835).

DNTT

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 4I27)

DPF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No evidence for DNA-binding activity - possible role in transcriptional regulation complex (PMID: 16785614)

DR1

Unknown

Yes

Likely to be sequence specific TF

2 Obligate heteromer

No motif

Binds DNA as a heterotrimeric complex of TBP, DR1, and DRAP1 (PDB: 1JFI)

DRAP1

Unknown

Yes

Likely to be sequence specific TF

2 Obligate heteromer

No motif

Based on structure (PDB: 1JFI), it forms the obligate heterodimer DR1-DRAP1 that furthermore contacts TBP. Only makes contact with the minor groove in a histone-like interaction, which is probably non-specific (PMID: 11461703)

DSP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DTX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This protein is an E3 ligase that operates in the Notch pathway

DUSP12

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DVL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DVL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DVL2 does not have any known DBDs; or experimental evidence to suggest it is a TF.

DVL3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DZIP1L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contains a weak ProSite match for a single C2H2 ZF (Uniprot) but not a Pfam match. No experimental evidence for DNA-binding exists

EAF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No convincing evidence that this protein binds DNA with any sequence specificity, or that this activity is required for its function. Thus at best the current evidence is that it is a cofactor of some sort cofactor (PMID: 12446457)

EDA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Cell surface protein that can be cleaved into a secreted one

EDA2R

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because GO says positive regulation of sequence-specific DNA binding transcription factor activity. Not DNA binding.

EDF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known co-factor that binds DNA indirectly through interactions with TFs (PMID:12040021)

EDN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that is processed into a secreted signaling peptide

EED

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Affects transcription by histone modification (PMID: 16357870)

EGLN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EID1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EID2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Associates with histone deacetylases (PMID: 12586827)

EIF2AK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EIF2AK4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EIF3C

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EIF3CL

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EIF3K

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EME1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4P0P) in a heterodimeric complex with MUS81.

ENO1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Enolase - DNA binding not shown to be direct

EP300

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

p300 is an archetype cofactor. It has many motifs, presumably because many TFs recruit it. Does not contact DNA in the structure (PDB: 3P57)

EP400

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Has a putative AT-hook

Protein is a nucleosome remodeling complex component with a role in depositing the H3.3 variant histone into promoter and enhancer regions (PMID: 26669263). Its MYB-like and helicase domains are likely non-specific DNA binding domains

EPHA5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

EPM2AIP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that binds and regulates glycogen synthase allosterically (PMID: 24142699)

ERBIN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ERC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ERCC3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 5IY6). Protein is an ATP-dependent 3-5 DNA helicase, so likely non-specific.

ERCC4

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds ssDNA at splayed DNA (PDB: 2KN7)

EWSR1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

EXO1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Makes contact with ssDNA bases at DNA breaks (PDB: 3QE9)

EXOC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Plasma-membrane protein functioning in targeting of exocytic vesicles

EXOG

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Endo/exonuclease (5-3), endonuclease G-like. Binds DNA in the crystal structure (PDB: 5T4I), presumably non-specifically

EZH1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Classic polycomb protein.

EZH2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is a classic polycomb protein with no evidence of sequence specific DNA binding after years of intense study. I dont see anything in (PMID :15520282) that supports DNA binding.

FAAP24

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA backbone from the side of the minor groove in the crystal structure (PDB: 4BXO)

FAM153C

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FAM171B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

FAM200A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein of unknown function that is conserved in animalia. Has similarities to transposases and zinc fingers, and thus could be a DNA binding protein although there is no evidence supporting this

FAN1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

FANCD2 and FANCI associated nuclease 1. Binds DNA in the crystal structure (PDB: 4REA), presumably non-specifically

FANCA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Involved in DNA repair (PMID: 8896564)

FANCD2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

DNA repair protein. Inconclusive data supporting sequence-specific binding. Binds NFKB target sites in EMSA using 293T expressing FANCD2 (PMID: 21912593). Since the protein is expressed in mammalian cells, it could still be NFKB mediated binding.

FANK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Binds JUN to control its activity (PMID: 20978819), but there is no evidence that it binds DNA itself

FARSA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FARSB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

tRNA synthetase

FBN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FBXO41

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FEN1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in DNA replication. Binds DNA in the crystal structure (PDB: 3Q8K), presumably in a non-specific manner.

FER

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FGD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FHL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LIM ZF proteins are unlikely to bind DNA. Experimental evidence does not support a role for FHL2 as a sequence-specific DNA-binding protein (PMID:10654935)

FLNA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Go annotation is based on (PMID: 15684392), which shows that it binds FOXC1 and PBX1 but doesnt show evidence for binding to DNA

FMNL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FUBP1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

ssDNA binding protein with crystal structure demonstrating binding to ssDNA (PDB: 1J4W). Its a KH domain protein - this is Levens protein, known to impact the Myc promoter.

FUBP3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Can bind single stranded DNA in a sequence specific manner (PMID: 8940189). Contans KH domains and has direct evidence it is an RNA-binding protein (PMID: 21252297)

FUS

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

FUS is a well-established RNA-binding protein

FZD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FZD2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transmembrane receptor protein that operates far upstream in the signalling cascade

FZD4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

FZD6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GABPB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Evidence exists showing that GABPB1 (E4TF1-47/53) has no DNA binding activity, but can assocaite with GABPA (E4TF1-60; Ets factor) (PMID: 8441384). Crystal structure of GAPBP1 with GABPA (PDB: 1AWC) clearly shows that the protein makes an extensive protein-protein interaction with GABPA, but does not bind DNA. Transfac PWM is a clear ETS-motif, so GABP1 is unlikely to contact DNA directly

GABPB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Obligate heteromer with GABPB1 (the alpha subunit) (PMID: 8810337), which together interact with GABPA (PMID: 8441384), but neither contacts the DNA

GADD45A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Doesnt have any DBDs - likely a co-factor

GAS6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GAS7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 9736752) only shows that it has a proline-rich domain similar to the one in Oct2. No evidence of DNA binding.

GCFC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

There is some evidence that this protein is an RNA-binding protein (PMID: 24304693).

GEN1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Resolves Holliday junctions. Binds DNA in the crystal structure (PDB: 5T9J)

GLMP

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds GATCCGCCCGCTTGTGGCCAACTGGCTCCAGTCAC dsDNA based on EMSA (PMID: 18021396)

GOLGB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Golgi resident transmembrane protein that regulates glycosylation of other proteins (PMID: 27226319)

GON4L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Prosite identifies a low-confidence Myb-like domain (e.g., cant decide between Myb, SANT, or no DBD), so its probably not a TF

GPATCH8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GPBP1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Solid data presented in (PMID: 14612417) Also known as Vasculin. (PMID: 26156556) also claims it has an extended AT hook.

GPBP1L1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Possible TF based on similarity to GPBP1. Despite its name, no available evidence for DNA binding. Could also be an RBP according to this screen (PMID: 22658674)

GPER1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GPR155

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GREM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GRM6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GTF2A1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

General transcription factor. Binds DNA in the crystal structure (PDB: 5FUR). The protein contacts the DNA backbone as a heterotrimeric complex that also includes GTF2A2 and TBP. Has an extensive protein-protein interaction interface with the GTF2A2 (that does not contact the DNA) and will probably do nothing without it

GTF2A1L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GTF2A2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

GTF2A2 makes contacts with the DNA backbone (PDB:1NVP; PMID: 12972251), and thus is unlikely to be sequence-specific

GTF2B

Unknown

Yes

Known motif

3 Low specificity DNA-binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Contacts both DNA and TBP in the structure (PDB: 1C9B)

GTF2E2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

GTF2E2 weakly binds dsDNA (PMID: 10716934) - unlikely to be sequence-specific

GTF2F1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5IY6)

GTF2F2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

The protein contacts DNA in the structure (PDB: 5IY6), and could thus have some specificity; DNA is contacted by domain folded from RKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELK.

GTF2H1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

General transcription factor

GTF2H2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GTF2H2 (p44) is part of the TFIIH complex, but does not contact the DNA based on structural evidence (PDB: 5IVW)

GTF2H2C

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a transcriptional co-regulator (PMID: 9880511)

GTF2H3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pre-initiation complex component that does not contact DNA in the structure (PDB: 5IVW)

GTF2H4

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

General transcription factor

GTF3C1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Component of RNA polymerase III. Binds weakly to the A-box (PMID: 8164661)

GTF3C2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

GTF3C2 is a general transcription factor of RNA polymerase III and there is no evidence that it binds DNA in the preinitiation complex. Transfac motifs are suspect

H1F0

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone. Likely a false-positive Pfam match based on the similarity of Forkhead domains to H1 domains

H1FOO

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Variant linker histone protein that is expressed in oocytes

H1FX

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone component

HAVCR2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HCFC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is recruited to promoters by THAP11 and ZNF143 and probably does not bind DNA by itself (PMID: 26416877)

HCK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Inhibits TP73-mediated transcription activation (PMID: 17535448)

HDAC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Histone deacetylase; likely to be a transcriptional cofactor. Transfac motif is dubious, and the GO annotation (PMID: 8646880) seems to be based on remote homology to a yeast TF

HDAC10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Histone deacetylase; likely to be a transcriptional cofactor

HDAC3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HDAC8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HDAC9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely to be a transcriptional cofactor

HELZ2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HIPK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor that can act as a coactivator or corepressor. Phosphorylates many transcription factors. (UniProt Q9H2X6)

HIRA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Histone chaperone - TUP1 homolog.

HIST1H1A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone component

HIST1H1B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Linker histone. To my knowledge there has been no demonstration of sequence specificity of linker histones, so I think this one should be called unlikely.

HIST1H1C

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

HIST1H1D

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Linker histone that binds DNA as heteromeric complex with the other histone proteins

HIST1H1E

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA as heteromultimeric complex

HIST1H1T

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

HLA-DQB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HLA-DQB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HLA-DRB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HLA-DRB3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HLA-DRB5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HLTF

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

DNA repair protein. Even though it has 3 motifs, there is no compelling evidence that it really binds dsDNA - only single stranded DNA

HMOX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Well characterized enzyme with no additional domains. Included only because GO lists it as a regulator of TFs. No support for DNA binding activity.

HNRNPA1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 1PGZ)

HNRNPA3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a well established RBP

HNRNPAB

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

HNRNPAB proteins are involved in pre-mRNA splicing. However; RRM domains can also constitute ssDNA binding domains

HNRNPCL2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a well established RBP

HNRNPD

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 1WTB)

HNRNPDL

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a well established RBP

HNRNPK

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a well established RBP

HNRNPL

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

HNRNPL is a well-established RNA-binding protein; and the DNA-binding evidence was neither shown to be specific or direct (PMID: 11809897)

HNRNPU

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds pre-mRNA in vivo and binds both RNA and ssDNA in vitro (PMID: 1628625)

HP1BP3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone H1-like protein. Binds in ChIP experiments (PMID: 27425409) and binds DNA (likely non-specifically) with HP1.

HR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

JmjC domain is not a DBD, and GO annotation is based on homology to a zinc finger motif and not experimental DNA-binding evidence (PMID: 9445480)

HSBP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that has been shown to bind to HSF1 leading to inhibition of its trimerization and DNA-binding( PMID: 9649501).

HSPA1A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

HSPA1B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ICAM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IFI16

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Recognizes DNA without sequence specificity (PMID: 22618232; PMID: 18472023)

IFNB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IGHM

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IKBKB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IKBKG

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein binds to NFKB1 to regulate its activity

IL10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IL1B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IL1RAP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IL4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Extracellular signaling molecule. Included as a candidate only because it regulates STAT.

IL5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IL6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

INF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

ING4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Interacts physically with p53 (PMID: 12750254). Transfac motif is derived from ChIP-Chip data, so unclear if it can directly bind DNA

INS

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IRAK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IRAK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IRAK3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IRF2BP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ITCH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ITGB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ITGB3BP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IZUMO2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

IZUMO is not considered to be a DNA-binding domain

JADE1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

FYVE and PHD zinc fingers are unlikely to specifically-bind DNA

JAK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is JAK from the classic JAK-STAT pathway. It is included only because GO lists it under positive regulation of sequence-specific DNA binding transcription factor activity. No evidence of sequence specificity - the STATs handle that.

JMY

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Coactivator protein that associates with p300 and TP53 (PMID: 10518217). There is no evidence that it contacts DNA itself. Functions also in actin nucleation (PMID: 19287377).

JUP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KANSL2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein is a component of the NSL chromatin remodelling complex

KAT2A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase

KAT2B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Interacts with TFs to modify histones (PMID: 9707565)

KAT5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone acetyltransferase

KAT6A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone deacetylase; likely a transcriptional cofactor

KAT6B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Co-factor. Could possibly bind to DNA, as a helix- turn-helix DNA-binding motif is present within its MYST-type HAT domain.

KAT8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBDs, no evidence of TF activity - looks like a chromatin protein. Included only because it has an x in Vaquerizas 2009.

KCNIP3

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

There are multiple papers showing DREAM can bind DNA (PMID: 10078534, PMID: 11108959).

KDM1A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Affects transcription by histone modification

KDM3A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Its a C6 zinc finger and Jumonji-type protein. No DBD.

KEAP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KIAA1549

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KIAA1683

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No evidence to support a DNA binding function

KIAA1958

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KIT

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KNTC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Rod_C domain localizes to kinetochores but has not been shown to be DNA-binding

KRAS

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KRBOX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KRAB domain only - no DBD or evidence for independent DNA binding

KRTAP5-1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KRTAP5-9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

KRTAP9-9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Keratin-associated protein

LARP1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Classic RNA binding protein

LARP1B

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

LARP4

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Classic RNA binding protein

LARP4B

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Classic RNA binding protein

LARP6

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Classic RNA binding protein

LARP7

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Classic RNA binding protein

LGALS9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LGR4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LIG1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA ligase. Binds DNA in the crystal structure (PDB: 1X9N)

LIG3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA ligase. Binds DNA in the crystal structure (PDB: 3L2P)

LMO2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Protein binds to bHLH TFs, which then bind to DNA (PMID: 9707419). Both transfac motifs are suspect - the bHLH motif likely resulted from an indirect interaction.

LMO4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LPP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

znfLIM is probably not a DNA binding domain (PMID: 8506279). The protein has been reported to be coactivator for ETV4 (PMID: 16738319).

LRP5

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

LRP6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Cell surface receptor that is in the beginning of the WNT signaling cascade. GO annotation has no evidence of DNA-binding activity (PMID: 14739301).

LRP8

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

LRRFIP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Seems to be included only because GO catalogs positive regulation of NF-kappaB transcription factor activity. Nothing that would indicate DNA binding.

LRRFIP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Its paralog forms a complex with ETS1 that binds AGCCCCCGGCG sequences based on EMSA and SPR (PMID: 16199883). However, direct DNA binding by LRRFIP2 is not demonstrated, and it seems more likely that it is in the complex through protein-protein interactions.

LSR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Cell plasma membrane resident protein that functions in cell-cell junctions (PMID: 25753034)

LTF

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

LTN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LZTFL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Lactotransferrin - major iron-binding protein in milk. Two papers from the 1990s (PMID: 7854459; PMID: 1037119) demonstrate strong DNA binding.

LZTR1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LZTS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contain a bZIP domain. (PMID: 10097140) does not examine TF activity or DNA binding - GO needs to be corrected.

MACC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MACF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because Vasquerizas 2009 includes it with an x. No DBD and no other data to support being a TF.

MAD2L2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Likely to be a DNA-binding protein that operates on DNA-repair (PMID: 25799990)

MALT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that operates upstream of NFKB in a signaling cascade (PMID: 18223652)

MAML1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAML1 does not contact the DNA in the structure (PDB: 2F8X), but contacts RBPJ, which in turn binds DNA

MAML3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAP2K5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase that operates upstream in the signaling cascade that leads to NFKB

MAP3K10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAP3K13

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAP3K7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a kinase

MAPK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAP kinase; protein array paper evidence is not strong

MAPK10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a kinase

MAPK11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAPK14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Well characterized MAPK. Included because it as a regulator of several TFs and GO captures this.

MAPK3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAPK8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MAPK9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MATR3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

An RBP that recognizes MAUCUUR-site based on Ray et al 2013 (PMID: 23846655)

MAVS

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates upstream in the signaling cascade that activates innate immunity response for viruses through NFLB and IRF3 TFs

MB21D1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA with backbone contacts and one minor groove inserting Arginine in the crystal structure (PDB: 4LEY)

MBTPS2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO annotation has no evidence of DNA-binding activity, only modulation of TF activity (PMID: 11163209)

MDFI

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MDF1 is a co-repressor that inhibits DNA-binding (PMID: 8797820)

MDM2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

MDM4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein binds to, and inhibits, p53 (PMID: 9226370)

MED1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is a component of Mediator.

MED12

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED13

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED13L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED15

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED16

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is a component of Mediator.

MED17

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED21

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure of the yeast mediator complex (PDB: 5SVA)

MED23

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED24

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MED6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not bind anywhere near DNA on crystal structure (PDB: 4V1O)

MEN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Interacts with NFKB1 (PMID: 11526476), JUN, JUND, and ELK1 and represses their activities with a mechanism that is at least for JUN and JUND dependent on their phosphorylation

MET

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Its a cell surface receptor and kinase - included only because Vasquerizas 2009 included it with an x.

MGMT

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents (PMID: 15964013); structure (PDB: 1YFH) is with cytosine alkylated DNA

MID2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO citation (PMID: 23077300) has no evidence of DNA-binding activity

MINK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MKL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-factor

MKL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MKRN3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Likely E3 ubiquitin ligase. Contains a RING (C3HC4) zinc finger motif and several C3H zinc finger motifs

MLLT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

X-ray structure indicates histone binding (PDB: 4TMP)

MLLT10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

No evidence showing MLLT10 can bind to DNA in a sequence-specific manner (PMID: 7888665)

MLLT11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MLLT3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcription elongation factor [PMID: 20159561; PMID: 20471948]

MLLT6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Likely to be a transcriptional cofactor based on presence of PHD domains and (PMID: 15588942)

MN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Evidence for DNA binding not strong in (PMID: 12569362)

MNAT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MPG

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA error repair enzyme that excises alkylation-damaged purine bases. Binds dsDNA in the crystal structure (PDB: 1BNK)

MRPL28

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because it has an X in Vaquerizas 2009

MRRF

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MSH2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA that has a base mismatch as a heterodimer with MSH6. Binds DNA in the crystal structure (PDB: 2O8B)

MSH3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in mismatch repair - binds dsDNA with indels (PDB: 3THZ) and changes DNA shape

MSH6

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA that has base mismatches as a heterodimer with MSH2. Binds DNA in the crystal structure (PDB: 2O8B)

MSL3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 3OA6). Contacts only the backbone and doesnt cause large changes in the DNA shape

MSRB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The paper cited by GO (PMID:10375640) called MSRB2 a TF based on amino acid sequence analysis, but did not provide any direct evidence

MST1R

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MTDH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MTF2

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

Recent study (PMID: 28869966) demonstrates direct, specific DNA binding to CG-rich sequences through PBMs, and crystal structure in complex with DNA

MTPN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD; no evidence for DNA binding - only included because GO says its a positive regulator of NFkappaB.

MUS81

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

MUS81 is a structure-specific endonuclease subunit. It binds DNA in the crystal structure (PDB: 4P0P) in a heterodimeric complex with EME1.

MYBBP1A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Protein that activates TP53 (PMID: 24375404) and binds to MYB (PMID: 24375404); however, there is no evidence of direct binding to DNA

MYCBP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

MYD88

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates upstream in the signaling cascade (PMID: 22155231)

MYEF2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single-stranded DNA and can regulate transcription in transfection reporter assays

MYOCD

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor (PMID: 12640126)

NAB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Well characterized transcriptional co-repressor of e.g. EGR1 (PMID: 12427750)

NABP2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 4OWW)

NACC2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds DNA as a homodimer, recognizing a TGTCRSWWYYGWC consensus based on SELEX experiments (PMID: 22926524)

NCOA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NCOA5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known coactivator with no DBD

NCOA6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a transcriptional co-regulator (PMID: 10681503)

NCOA7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known co-activator; included only because TF-cat documents this

NDN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NDP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because GO says positive regulation of sequence-specific DNA binding transcription factor activity. Not DNA binding.

NEIL1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA glycosylase 1. Binds DNA in the crystal structure (PDB: 5ITR)

NFAM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NFAM1 modulates B cell signaling through its immunoreceptor tyrosine-based activation motif, which regulates B cell development (PMID: 15143214)

NFE4

Unknown

Yes

Known motif

2 Obligate heteromer

In vivo/Misc source

NFE4 does not posess a DBD. It is a member of the SSP complex that regulates B-globin gene expression, and binds DNA as a heteromer with CP2, based on EMSA (PMID: 7828600; PMID: 15273251). A shorter isoform prevents CP2 binding (PMID: 16263792) and is involved in repression. No gel-shift experiments have been performed in the absence of its partner, CP2, thus its likely an obligate heteromer.

NFKBIA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is I kappa B alpha, which interacts with NFkappaB. No DBD, and evidence indicates that it is not a TF.

NFKBIB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

From (PMID: 12686541), it appears that the ternary complex is stabilized by an interaction with this protein, which suggests that this protein may offer a conducive electrostatic environment rather directly contributing to the binding event.

NFKBID

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NFKBIL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NFKBIZ

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NFRKB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a winged helix but cannot bind to the NFKB consensus.

NFYB

Unknown

Yes

Known motif

2 Obligate heteromer

In vivo/Misc source

Obligate heterotrimer of NFYA, NFYB, and NFYC

NFYC

Unknown

Yes

Known motif

2 Obligate heteromer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

PDB 4AWL is a very tightly intertwined heterotrimeric complex of NFYA, NFYB and NFYC with a plenty of protein-protein interactions. NFYA contains the recognition alpha-helix but there is no point considering any of the components separately as they are definitely complexed even in the solution and all contribute contacts with the DNA backbone.

NKRF

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds AATTTCCTCTGA based on EMSA (PMID: 11071890) and to AATTCCCTGA based on another EMSA (PMID: 16107696)

NLRC3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NLRC4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NLRC5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein inhibits NFKB activity

NLRP12

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NLRP2B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NLRP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates upstream in the signaling cascade

NME2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds to telomeres (PMID: 22135295). Binds specific sequences by gel-shift, and binding is impacted by a SNP (PMID: 23368879)

NOC3L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No evidence to support a DNA binding function

NOC4L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is associated with ribosome synthesis (PMID: 27798105)

NOCT

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Deadenylase protein that probably regulates genes post-transcriptionally (PMID: 22073225)

NOD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NOD-proteins function in signaling cascades that report bacterial peptidoglycans. They activate kinases that in turn activate NFKB proteins etc. Reviewed in (PMID: 25526305)

NOD2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NODAL

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a secreted signaling molecule

NONO

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RBP with RRM domains

NOP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

NOTCH1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

A transmembrane protein that inhibits MEF2C activation (PMID: 10082551). NOTCH1 does not bind DNA in the structure, and is not required for DNA binding, since RBPJ is bound without it in (PDB:4J2X).

NOTCH2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transmembrane receptor protein that operates far upstream in the signaling cascade

NOTCH3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Fragment of NOTCH. Is a coactivator.

NPM1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

No evidence for sequence-specific DNA-binding (PMID: 2223875)

NR0B2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcription cofactor - lacks a conventional DNA binding domain and represses the transcriptional activity of various nuclear receptors (PMID: 14752053)

NRF1

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

NRG1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Cell surface receptor - does not have predicted DBDs

NRIP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor

NRIP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Binds indirectly to DNA through interactions with NHR TFs (PMID: 10860982)

NRK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a kinase

NSD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a histone methyltransferase with H3K36 and H4K20 methylation activities (PMID: 12805229)

NTRK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Membrane bound receptor protein

NUCKS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contains a GRP core, which is similar to an AT-hook. But, the amino acids flanking the core are quite different from an AT-hook. Could non-specifically bind to DNA, but lacks compelling evidence.

NUP98

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

OGG1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA error repairing enzyme. Binds DNA in the crystal structure (PDB: 1EBM), presumably without specificity

OPRD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transmembrane protein

OTOP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

OTULIN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PA2G4

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds CGGCAAAAAGG repeats based on EMSA performed with recombinant E.Coli expressed protein (PMID: 1507318)

PABPN1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

PARK7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates upstream in the signaling cascade

PARP1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

In vivo/Misc source

DNA repair protein that binds dsDNA non-specifically (PMID: 21183686; PMID: 21262234). The Transfac motifs are likely NFAT target sites

PARP10

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Contains two RRM domains, so likely an RNA-binding protein. Myc-interacting factor capable of ADP-ribosylating itself and core histones (PMID: 15674325).

PAWR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that binds to several TFs such as PITX2 (PMID: 19801652) and appears to inactivate them

PAXBP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has been shown to associate with PAX3 and PAX7, and recruits H3K4 methyltransferase complex (PMID: 22862948). Has a putative DNA-binding domain, so it could contribute to specificity or even function as an independent TF

PAXIP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional coactivator that associates with PAX2 (PMID: 10908331)

PCBD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Coactivator for HNF1A-dependent transcription. Regulates the dimerization of homeodomain protein HNF1A and enhances its transcriptional activity (UniProt: P61457)

PCBP1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Crystal structure shows it binds ssDNA (PDB: 1ZTG).

PCBP2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is an RBP. Structure (PDB:2PQU) is with single stranded DNA

PCBP3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

KH domain suggests that this is an RNA-binding protein

PCGF2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

(PMID: 8521824) shows via SELEX and EMSA that the recombinant PCGF2 protein binds GACT repeats

PCGF6

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds GACTNGACT based on SELEX and EMSA performed in (PMID: 8521824)

PCNA

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 5L7C). Protein barely contacts the DNA at all

PCSK6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PDCD7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD. No evidence for sequence-specific DNA binding. Included only because TFcat says its a cofactor.

PDS5B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

PELI1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Ubiquitin ligase

PER1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that associates with CLOCK-ARNTL heterodimers to silence the expression of their target genes (PMID: 16987893)

PER2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that operates in the circadian clock through binding to and inhibiting the ARNTL-CLOCK heterodimer. Does not bind DNA itself )PMID: 16987893)

PER3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PEX14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PFDN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PGBD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PiggyBac Transposable Element Derived 1. Contains a SCAN domain and interacts with other SCAN proteins (see Q96JS3). Interpro also lists without ref that it has sequence specific DNA binding activity (IEA code). No concrete evidence available.

PGS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PHB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is likely a mitochondrial chaperone and thus its roles associated with transcription are likely to be very indirect (PMID: 10835343)

PHB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein has been shown to bind to TFs and function as a co-repressor. There appears to be no evidence for direct DNA-binding activity (PMID: 18629613)

PHF1

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

Recent study (PMID: 28869966) demonstrates direct, specific DNA binding to CG-rich sequences through PBMs, and crystal structure in complex with DNA

PHF19

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Recent study (PMID: 28869966) demonstrates direct, specific DNA binding to CG-rich sequences of related proteins through PBMs, and crystal structure in complex with DNA

PHF5A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

This is a known spliceosomal protein with a PhD domain. I dont see the evidence that it binds the GJA1/Cx43 promoter, as listed on GeneCards. The reference cited does not mention this protein as far as I can see. In any case, binding could be indirect - the most likely role in transcription for a PHD domain protein would be as a cofactor.

PHTF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Despite its name, does not have a detectable Homeodomain. No available evidence for DNA binding.

PHTF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contains a Transcription factor homeodomain, male germ-cell domain (INTERPRO:IPR021980, PFAM:PF12129) that does not have any known DNA-binding activity. Its name comes from a fly ortholog that does contain a homeobox; but, the human gene does not.

PIAS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The protein contains a SAP motif, which has been annotated as a putative DNA-binding motif without supporting experimental evidence (PMID:10694879)

PIAS2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Sumoylates transcription factors to modulate their activities (PMID: 22406621; PMID: 15976810; PMID: 15920481)

PIAS3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PIAS-proteins regulate transcription factors by sumoylating them (PMID: 12077349)

PIAS4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD. No evidence of DNA binding - its a known cofactor

PIDD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates upstream in the NFKB signaling cascade

PIKFYVE

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because its in Vasquerizas 2009 with an x. No DBD and no other evidence of DNA binding.

PIM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Affects transcription by phosphorylating TFs (PMID: 18593906)

PINK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PKHD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The TIG domain is potentially DNA-binding but there is no literature evidence to suggest that PKHD1 is a TF. Membrane protein that operates upstream in the signaling cascade leading to NFKB (PMID: 21300060)

PKHD1L1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Membrane receptor (PMID: 12620974)

PLA2G10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLA2G1B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLEK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The DEP-domain is a winged helix-turn-helix protein domain, and thus it is related to ETS, RFX, and FOX domains. However, there is no evidence for DNA-binding activity and it has been shown to operate in G-protein signalling upstream of TFs

PLEK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLEKHA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

No DBDs; no indication of DNA binding - included only because Vasquerizas 2009 included it with an x.

PLPP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLSCR1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

PLSCR1 has been demonstrated to bind a GTAACCATGTGGA sequence in the IP3R1 promoter (PMID:16091359), mediated by a specific portion of the protein.

PLXNA1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PLXNA2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PLXNA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PLXNA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade (PMID: 12591607).

PLXNB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PLXNB2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLXNB3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PLXNC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PLXND1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a semaphorin receptor that operates far upstream on the signaling cascade.

PML

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely a transcriptional cofactor. Does not have any clear DBDs. RING-fingers are more typically protein-protein interaction domains

PNKP

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 3ZVN)

POGZ

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Has a potential DBD that is similar to Drosophila Brinker but no other data suggesting TF function. Likely co-factor.

POLA1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4Q5V)

POLB

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase that participates in base excision repair. Binds DNA in the crystal structure (PDB: 1BPX)

POLE3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

POLE4

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone-like subunit of DNA polymerase epsilon

POLG

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4ZTU)

POLH

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase. Binds DNA in the crystal structure (PDB: 3JAA)

POLI

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase. Binds DNA in the crystal structure (PDB: 1T3N)

POLK

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase. Binds DNA in the crystal structure (PDB: 2OH2)

POLL

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase. Binds DNA in the crystal structure (PDB: 1RZT)

POLM

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase that operates on non-homologous end joining. Binds DNA in the crystal structure (PDB: 2IHM)

POLN

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4XVI)

POLQ

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4X0P)

POLR1B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

General Transcription Factor

POLR2A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Contacts DNA in the structure (PDB: 5FLM)

POLR2B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Contacts DNA in the structure (PDB: 5FLM)

POLR2E

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

RNA-polymerase subunit. Binds DNA in the crystal structure (PDB: 5IY6)

POLR2J

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FLM)

POLR2K

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FLM)

POLR2L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FLM)

POLR3A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Transfac motifs are dubious, and do not appear to be similar to any known motifs.

POLRMT

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 4BOC)

POT1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 1XJV)

POU2AF1

Unknown

Yes

Known motif

2 Obligate heteromer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Requires POU2F1 to bind DNA. In the crystal structure (PDB:1CQT), POU2AF1 contacts both the POU2F1 and DNA major groove

PPARGC1A

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

PPARGC1B

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Contains a single RRM domain, so could possibly be an RNA binding protein

PPP1R13L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PPP2R3B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PPP2R5B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PPP3CA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PPRC1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

PQBP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a WW domain. May interact with Pol II, but no indication of sequence specific DNA binding

PRAM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRAP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRB3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Human salivary glycoprotein

PRDM7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only has KRAB and SET domains - no C2H2 ZFs.

PRDX3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PREB

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

In vitro gel-shift experiments show that PREB binds specific promoter sequences (PMID: 10194769; PMID: 19426980) without the presence of a canonical DBD

PREX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because Vasquerizas 2009 includes it with an x. No DBD and no other data to support being a TF.

PREX2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRH2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRIM2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds DNA-RNA hybrid in the structure (PDB: 5F0Q)

PRIMPOL

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in DNA replication. Binds DNA in the crystal structure (PDB: 5L2X), presumably non-specifically.

PRKCB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRKCH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a kinase that activates another kinase leading to degradation of NFKB inhibitor NFKBIA (PMID: 21820409)

PRKCI

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase that operates upstream in the signaling cascade that leads to NFKB

PRKCQ

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRKCZ

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRKD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRKD2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRKN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiquitin ligase

PRMT2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PRNP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PSMA6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PSMC5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PSMD10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO annotation has no evidence of DNA-binding activity; only modulation of NF-kappaB activity (PMID: 18040287)

PSMD11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PSMD12

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PSPC1

Unknown

No

ssDNA/RNA binding

3 Low specificity DNA-binding protein

No motif

Contains RRMs and no DBDs. Mouse orhtolog has been found in androgen receptor complexes (PMID: 16641145) but no DNA-binding activity has been shown.

PTCH1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PTEN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PTGIS

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

It is a cytochrome p450 enzyme

PTH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PTTG1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO annotation has no evidence for DNA-binding activity (PMID:9811450), only transcriptional activation in reporter experiments

PUM3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds dsDNA in the crystal structure (PDB: 4WZW). Makes extensive contacts with the backbone that cause shape changes and could possibly lead to specificity.

PURA

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Binds dsDNA (PMID: 15282343) and ssDNA (PMID: 1448097) specifically

PURB

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds dsDNA (PMID: 15282343) and ssDNA (PMID: 1448097) specifically

PURG

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Paralogs PURA and PURB bind dsDNA (PMID: 15282343) and ssDNA (PMID: 1448097) specifically.

PYCARD

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PYDC1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

PYDC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that regulates NFKB activity

QRICH1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RAB7B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein activates NFKB (PMID: 20953574)

RAD21

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Motifs are suspicious; protein is a component of the cohesin complex and there is no evidence for direct binding to DNA.

RAD51

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Functions in homologous recombination DNA-repair. Binds DNA with low specificity (PMID:10390347)

RAG1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds DNA specifically (PMID: 10066757)

RAI1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Chromatin remodeler

RAPGEF3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD and no evidence its a TF - included only because it has an x in Vaquerizas 2009

RAPGEF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RAPGEF5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Classic co-factor

RBBP7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RBCK1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Fairly well-studied E3 ubiquitin-protein ligase. But EMSA data exist demonstrating binding to TGG-containing DNA (PMID: 9514928)

RBL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RBL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-repressor

RBM10

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA-binding protein

RBM20

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Likely an RNA-binding protein

RBM22

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA binding protein (PMID: 17045351)

RBM26

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA-binding protein (PMID: 22681889; PMID: 22658674)

RBM27

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Likely an RNA-binding protein

RBM5

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA-binding protein that binds RNA with two RRM-domains and regulates splicing (PMID: 24486491)

RBM6

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA-binding protein that binds RNA with two RRM-domains and regulates splicing (PMID: 24332178)

RCAN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SH3 domain protein that interacts with calcineurin. GO annotation and abstract in (PMID: 8595418) appear erroneous - mentions a binding domain in the abstract, but no evidence is provided in the paper.

RECQL

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ATP dependent DNA helicase. Binds DNA in the crystal structure (PDB: 2WWY)

RELL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RELN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a large secreted extracellular matrix protein

REV1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA polymerase. Binds DNA in the crystal structure (PDB: 3GQC)

REXO4

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

REXO4 (hPMC2) has been shown to bind ERE containing sequences in gel-shift experiments (PMID: 10908561) in complex with ERbeta. However, figures containing the gel-shifts have been cropped to exclude the unshifted free DNA band so it is hard to judge the evidence.

RFC1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA-dependent ATPase. Binds DNA (contact with major groove and backbone) in the crystal structure (PDB: 2K7F)

RFXANK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

AKA RFX-B. No DBD, no motifs produced when tested, no evidence of independent DNA binding. (PMID: 9806546) shows that its interaction with RFX5 and RFXAP is essential for binding of the RFX complex to MHC-II promoters, but it does not bind DNA on its own.

RFXAP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included because TF-CAT calls it a cofactor and GO erroneously calls it sequence-specific DNA binding.

RGCC

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RGS11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

RGS6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RGS7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RGS9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RHEBL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RING1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RING1 is a well-characterized member of the Polycomb complex. No reference to DNA-binding in literature search on EntrezGene

RIOK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RIPK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RIPK2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein activates NFKB through its kinase activity

RIPK3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase protein

RIPK4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RLIM

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

LIM ZF proteins are unlikely to bind DNA

RNASE2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RNASEH1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Ribonuclease H1. Binds DNA-RNA hybrid in structure (PDB: 2QKB)

RNF114

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RNF125

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiguitin ligase

RNF138

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

DNA repair protein. RNF138 is recruited to DNA damage sites through zinc fingers that have a strong preference for DNA with 5- or 3-single-stranded overhangs. (PMID: 26502055)

RNF14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor

RNF166

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiquitin ligase (PMID: 26456228)

RNF2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Forms non-specific DNA contacts according to crystal structure (PMID: 25355358)

RNF25

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Probably a co-regulator; no clear evidence for direct binding to DNA

RNF31

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiquitin ligase (PMID: 18408734)

RNF41

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiquitin ligase

RPA2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RPA4

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

ssDNA binding protein involved in DNA repair (PMID: 7760808)

RPL7

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA by filter binding (PMID: 8441630), but competition assays suggest it is non-specific. A specific dsRNA structure is thought to be the preferred substrate. RNA-binding has been demonstrated by gel-shift experiments (PMID: 10329420).

RPL7A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RPS27A

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RPS6KA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RPS6KA5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD - its a kinase. Included only because GO says its an upstream regulator of CREB and NF-kappaB

RRN3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RUNX1T1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

RWDD3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included because GO says negative regulation of NF-kappaB transcription factor activity. No DBD, no motif, etc

RYBP

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Contains RanBP ZFs, so likely an RNA-binding protein

S100A12

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

S100A8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

S100A9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SAFB

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Based on this review the protein is likely to bind AT-rich DNA in a non-sequence specific manner (PMID: 27888239)

SAFB2

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Bind AT-rich DNA elements and RNA (PMID: 27888239)

SAV1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SCAND1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SCAND2P

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pseudogene

SCAPER

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Involved in cell cycle regulation in the cytoplasm (PMID: 17698606)

SCMH1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Has a SLED domain (IPR021987). (PMID: 24727478) claims, based on NMR, that SLED is a sequence-specific DBD with relatively high specificity

SCML1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Homologous to polycomb proteins, so likely a transcriptional cofactor (PMID: 9570953). Has putative roles in the testis development and spermatogenesis (PMID:18601738). Reference cited by GO provides no evidence of DNA-binding activity (PMID: 9570953).

SCML2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Part of the polycomb repressor complex that functions in male, establishing the male germline epigenome through regulation of histone H2A ubiquitination (PMID: 25703348)

SEMA4A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SERTAD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-factor; no evidence for DNA-binding activity

SERTAD2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor that associates with E2F/TFDP heterodimers (PMID: 19152710). Does not contain any DBDs

SETD6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Methyltransferase to the NF-kappaB complex (PMID: 21131967) and histones (PMID: 23324626)

SF3A2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Functions in splicing

SF3A3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

RNA-binding protein

SFPQ

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Splicing factor - contains 2 RRM domains

SFRP4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SFRP5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SFTPB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SGK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SGK3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein kinase that operates upstream in the signaling cascade

SHH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SHPRH

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SIGIRR

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SIK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SIN3A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Motifs are suspect and probably reflect DNA binding specificities of SIN3 contacted TFs. SIN3 does not have any DBDs and is thought to function as a scaffold protein that connects TFs to HDAC complexes. Reviewed in (PMID: 19505602)

SIN3B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Can be tethered to DNA by Mad-Max, but does not appear to have any specificity (PMID: 7889570)

SIRT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SIRT2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SIRT3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a histone de-acetylase

SIRT6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

No canonical DBD, but it does bind at least one sequence-specific DNA binding protein (TRF2). Seems more likely to be a cofactor.

SIVA1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Affects transcription through interactions with NF-kappaB (PMID: 16491128)

SKI

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Conflicting evidence. Binds specifically to GTCTAGAC via EMSA in one study (PMID: 9452486). But, needs to form complexes with other proteins, such as NFI, to bind to DNA in another (PMID: 9380514). Related to SKIL, which also has evidence for DNA binding (PMID: 9824161)

SKIDA1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SKIL

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Homodimerizes on GTCTAGAC sequence (EMSA) (PMID: 9824161)

SKOR1

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

SLC22A4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a transmembrane protein of the plasmamembrane

SLC26A10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SLC26A3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included as a candidate only because GO cites a 1993 paper where sequence analysis identified a homeodomain. But, there seems to be no homeodomain.

SLC30A9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SLC39A10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SLC4A10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SMARCA2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

No clear DBD, and its a known cofactor

SMARCA4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

(PMID: 24752179) shows via ChIP that it has DNA mediated regulatory activity, but unknown if this is direct or indirect binding. No clear DBD present in the protein.

SMARCAL1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Is a DNA binding helicase

SMARCB1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Alias INI1 is a minor groove DNA-binding protein (PMID: 19398554)

SMARCD1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

It is an active ATP-utilizing chromatin remodeling protein (PMID: 25818293)

SMARCD2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Transcriptional cofactor (PMID: 8804307)

SMARCD3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Chromatin remodelling complex component

SMC3

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Binds and compacts DNA as a SMC1-SMC3 heterodimer that is part of the cohesin complex (PMID: 23620281). Transfac motifs likely reflect the binding of other TFs such as CTCF that associate with cohesin

SMO

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The protein is a G-protein coupled receptor

SMUG1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in DNA mismatch repair. Xenopus homolog binds dsDNA in the crystal structure (PDB: 1OE4)

SMYD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SMYD3

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds GGAGGG elements based on SELEX performed using GST fusion protein (PMID: 15235609)

SNAPC2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Recognizes the PSE-element, which is located in the core promoters of snRNA genes, and helps to recruit TBP (PMID: 8633057)

SNAPC5

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds specifically to the PSE (PMID: 9732265)

SNRPC

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Component of the spliceosomal U1 snRNP

SNURF

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely a TF co-factor

SNW1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SOGA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contain any likely DBDs.

SON

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

The protein has been reported to bind a GAKANSRCC consensus based on SELEX experiments. Recognizes a matching GAGACCACC sequence in a hepatitis B virus regulatory element (PMID: 11306577)

SORBS2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SPEN

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Has a putative AT-hook

Data inconclusive. Contains RRM domains, suggesting RNA binding activity. Gel-shift experiments demonstrate that SPEN (aka MINT) binds ss and dsDNA G- and T-rich elements (PMID: 10451362), but in another system SPEN does not bind DNA directly and is recruited (PMID: 15778499). RNA-binding activities have also been documented (PMID: 24748666).

SPHK1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SPZ1

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Binds to E-boxes (EMSA) (PMID: 15226296)

SSB

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds to the 3 poly(U) terminus of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation (PMID: 3192525; PMID: 2470590]

SSBP2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in DNA damage response. Has domain IPR008116 Sequence-specific single-strand DNA-binding protein

SSBP3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Single stranded DNA binding protein. There is no evidence for sequence specificity, although it can operate as a transcriptional co-regulator (PMID: 26495868)

SSBP4

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

(PMID:9531483) shows that the SSDP_DNA-bd domain has sequence-specific single-stranded DNA-binding activity.

SSH1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SSH2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SSH3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SSX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

STAG1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Part of the cohesin complex

STK16

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

STK3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Kinase - included only because GO says it regulates TFs

STK36

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

STRN

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

STRN3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

GO annotation has no evidence for DNA-binding activity (PMID: 11570823), and STRN3 lacks a canonical DBD

SUB1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

The structure (PDB: 2C62) demonstrates binding to single stranded DNA

SUFU

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SUMO1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

SUPT16H

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Component of the FACT histone remodeling complex, which functions in transcriptional elongation (PMID: 12934006). (PDB: 4Z2M) shows that the protein contacts H3 and H4 proteins, but it could also contact DNA

SUPT4H1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Involved in transcription elongation (PMID: 9450929)

SUPT5H

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein that regulates transcriptional elongation (PMID: 9450929)

SUPT6H

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

SPT6 is an elongation factor, not a TF. GO needs to be corrected - (PMID: 8786132) does not demonstrate sequence specificity or DNA binding.

SUV39H1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a histone methyltransferase that trimethylates lysine 9 of histone H3

SUV39H2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Histone (H3K9) methyltransferase. Also directs DNA methylation (UniProt: Q9H5I1) (PMID: 14765126)

SUZ12

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein is a component of the PRC2 repressor complex, which silences DNA through histone methylation. The protein has two znf C2H2-like domains that appear to be used in association with chromatin (PMID: 24100017)

SYK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known co-factor

TAB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TAB2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Works as a protein-protein interaction adapter to recruit TAK1-kinase (PMID: 10882101). Could also work as an RBP, based on presence of a zf-RanBP domain

TAB3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

TADA3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Paper cited by GO annotation has no evidence of specific DNA-binding activity (PMID: 9674425), and is based on experiments using an entire complex

TAF1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

Contacts DNA in the structure (PDB: 5FUR). Transfac motifs are suspect, and are probably in vivo signals derived from promoter binding TFs (e.g. YY1 and ETS)

TAF10

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

General transcription factor

TAF11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not interact with DNA (PMID: 15657423)

TAF12

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

(PMID: 15601843) shows it has DNA binding activity in a complex with TAF4b.

TAF13

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Forms heterodimer TAF11:TAF13, which has a histone-fold like structure and could thus bind DNA in a non- or low specific manner (PMID: 9695952)

TAF1A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

General TF. Directly binds to DNA, likely in a non sequence-specific manner (PMID: 15970593), although it is possible it might have some specificity.

TAF1B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Pol I TAF that contacts the rDNA promoter in conjunction with TBP and UBF (PMID: 7491500). No clear evidence that it directly confers sequence specificity.

TAF1C

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC.

TAF1L

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in preinitiation complex assembly (general transcriptional machinery. Is a paralog of TAF1, which binds DNA based on the structure (PDB: 5FUR)

TAF2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Directly contact with DNA in TFIID complex (PMID: 27096372), and mediate major interactions with the downstream promoter together with TAF1. Contacts DNA in the structure (PDB: 5FUR)

TAF3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contacts chromatin through modified histones and TFs such as TP53 (PMID: 18549481)

TAF4

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

The TAF4 domain interacts with TAF12 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function for of a subset of genes (PMID: 19635797; PMID: 12237304)

TAF4B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Histone-like protein that binds DNA as an obligate heterodimeric complex with TAF12 (PMID: 19635797). Target sequence needs to be over 70 bases long and doesnt appear to have sequence specificity

TAF5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TAF5L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Paralog of TAF5 that is unlikely to contact DNA (PMID: 17227857)

TAF6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FUR)

TAF6L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Part of the PCAF Histone Acetylase Complex (PMID: 9674425). Structurally similar to TAF6, which does not contact DNA directly

TAF7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FUR)

TAF7L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TAF8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contact DNA in the structure (PDB: 5FUR)

TAF9

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Related to histone H3. (PMID: 15601843) shows DNA binding activity in complex with TAF4b, but does not demonstrate intrinsic sequence specificity. May contact promoter DNA (PMID: 23292512)

TAF9B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TARDBP

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Is an RNA-binding protein that can also bind single stranded DNA, as in the structure (PDB: 3D2W)

TAX1BP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TBL1Y

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD. Included as a candidate only because TFcat lists it as a putative coactivator.

TCEA2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Likely binds RNA based on similarity to TCEA1

TCEAL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TCEAL7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Modulates transcription, but there is no evidence for DNA binding (PMID: 19966855)

TCEAL8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Lacks a canonical DBD

TCF19

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Previous evidence (PMID: 1868030) for TF activity is based on sequence analysis (high proline content), and presence of an FHA domain. However, neither prove ability to bind DNA in a sequence-specific manner

TCF20

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

(PMID: 7760812) identified this protein in a library screen and demonstrated DNA binding of an IVT product to an enhancer of interest. They also identified a putative bZIP domain that is not detected by Pfam or SMART. (PMID:10995766) subsequently mapped the strongest DNA binding site.

TCF25

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only evidence is based on (PMID:16574069), which claims that hnulp1 (TCF25) contains a possible bHLH domain and that it represses transcription in a Gal4-forced recruitment assay.

TDG

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

TDG is specific for G/T mispairs in DNA (PDB: 2RBA; PMID: 18587051). Some evidence exists for TDG affecting transcription through interactions with NHR TFs (PMID: 9694815), suggesting it could also be a transcriptional co-factor

TDP1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 1NOP)

TDP2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds single stranded DNA in the structure (PDB: 4F1H)

TET2

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Binds DNA in the crystal structure (PDB: 4NM6). Oxidizes 5-methylcytosine (5mC).

TGFB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TGFB1I1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Available evidence suggests that it acts as a co-factor

TGS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is an RNA-modifying enzyme (PMID: 19307714)

THRAP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

THYN1

Unknown

Yes

Likely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure (PDB: 5J3E). Recognizes 5mC containing DNA. Contacts the DNA backbone from the side of the minor groove and has an arginine that inserts into the minor groove.

TIA1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Has an RRM domain. Binds single stranded DNA in the structure (PDB: 5ITH)

TICAM1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TIPARP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TIRAP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TLE1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-factor

TLE2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TLE3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Protein is a transcriptional co-regulator (PMID: 21459326)

TLE4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TLE4 is a Groucho protein (co-repressor)

TLE6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional cofactor that associates with FOXG1 (PMID: 16314515)

TLR2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Upstream of NFKB and not involved in DNA-binding

TLR3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Binds dsRNA (PMID: 16111635)

TLR4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TLR9

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Protein is a nonmethylated CpG dsDNA recognizing protein that operates in the innate immune response to pathogen invasion of the cell. It isnt a TF, but it binds pathogenic DNA (PMID: 11564765). Binds single-stranded DNA in the structure (PDB: 3WPC)

TMEM235

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transmembrane protein

TMF1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

Bacterially-expressed protein binds specifically to the TATA element to compete with TBP, based on EMSA (PMID: 1409643)

TNF

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

The protein is a secreted cytokine and operates far upstream in the signaling cascade

TNFAIP3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Inhibits NFKB-activation. No evidence for direct binding to DNA

TNFRSF11A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TNFRSF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates far upstream in the signaling cascade

TNFSF11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TNFSF18

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a cytokine

TNFSF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Extracellular signaling molecule. Included only because it regulates TFs.

TONSL

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds to the N-terminal tail of Histone H4 (PMID: 27338793, PDB: 5JA4). It is likely a histone chaperone (PMID: 26527279) and thus probably forms nonspecific contacts with DNA.

TOP1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA topoisomerase. Binds DNA in the crystal structure (PDB: 1A31).

TOP2A

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA topoisomerase. Binds DNA in the crystal structure (PDB: 4FM9).

TOP2B

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

DNA topoisomerase. Binds DNA in the crystal structure (PDB: 3QX3).

TOPORS

Unknown

Yes

Known motif

1 Monomer or homomultimer

In vivo/Misc source

Only known motifs are from Transfac or HocoMoco - origin is uncertain

TP53BP1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

TRADD

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Regulates transcription by binding to the adaptor protein TRAF2, leading to reduction of recruitment of inhibitor-of-apoptosis proteins. No evidence for binding DNA (PMID: 18309324)

TRAF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRAF1 is an NF-kappaB interactor (PMID: 10692572), and is unlikely to have DNA-binding activity

TRAF2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Does not contain any canonical DBDs

TRAF3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRAF4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates far upstream in the signaling cascade

TRAF5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates far upstream in the signaling cascade

TRAF6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRAPPC9

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TREX1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Has weak exonuclease activity for GAG, ACA, and CTGC DNA sequences (PMID: 17355961)

TRIB1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Associates with CEBPB and CEBPA and inhibits their activities (PMID: 17724128). This is probably achieved through control of their proteosomal degradation (PMID: 17576771)

TRIB3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Disabled kinase - binds NFkappaB and ATF4, but no evidence for direct sequence specific DNA binding.

TRIM13

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Operates far upstream in the signaling cascade. Ring fingers usually operate in protein-protein interactions

TRIM14

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM15

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM21

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM22

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM23

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM24

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Known cofactor. Included because TF-CAT documents this. Does not have any canonical DBDs.

TRIM25

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM26

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM27

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Evidence presented in (PMID: 1437549) for DNA-binding of alias RFP is not strong - if anything, this is likely a non-specific DNA binder

TRIM28

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Only known motifs are from Transfac or HocoMoco - origin is uncertain

This protein a well-known co-repressor and is recruited to DNA by KRAB-domain containing TFs. Transfac motifs are likely from interacting proteins

TRIM29

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Previous evidence for TF activity (PMID: 8188213) is based on sequence analysis and does not provide DNA-binding evidence. Based on EntrezGene information, its likely a transcriptional co-factor

TRIM3

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Contains multiple NHL domains, which bind RNA (see, for example, LRP8).

TRIM31

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM32

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

TRIM33

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM34

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM37

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Included only because GO says it is a regulator of NFkappaB. No evidence for DNA binding, and no canonical DBD.

TRIM38

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIM40

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein that promotes post-translational modification of an NBKB-inhibitor protein (PMID: 21474709)

TRIM5

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBD and no evidence for DNA binding. Included as a candidate only because GO says its a regulator.

TRIM52

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Established ubiquitin ligase that targets at least one viral protein (NS2A) of Japanese Encephalitis Virus to proteosomal degradation (PMID: 27667714)

TRIM62

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a ubiguitin ligase (PMID: 23402750)

TRIM8

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRIP11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Structural component of the Golgi-apparatus (PMID: 19112494)

TRIT1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Protein is a tRNA modifying enzyme (PMID: 15870694)

TRMT1L

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TRRAP

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a component of histone acetyltransferase complexes

TSC2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TSC22D1

Unknown

Yes

Likely to be sequence specific TF

1 Monomer or homomultimer

No motif

TSC22D1 appears to homo- and heterodimerize with other TFs to affect transcription (PMID: 10488076). In vitro, it has been shown to bind GC-rich DNA sequences (PMID: 9022669)

TSC22D2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

There is some evidence that a related protein (TSC22D1) binds DNA specifically - thus, it is possible this is also a TF.

TSC22D3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

There is some evidence that a related protein (TSC22D1) binds DNA specifically - thus, it is possible this is also a TF.

TSC22D4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

There is some evidence that a related protein (TSC22D1) binds DNA specifically - thus, it is possible this is also a TF.

TSN

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Based on (PMID: 20450889) and (PMID: 12484770), this protein binds repetitive DNA sequences as multimeric complexes that may contain partner protein TSNAX

TSSK4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

TUB

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

The Tubby C-terminal domain (IPR000007; PF01167) has been shown to impart nuclear localization and bind select dsDNA sequences in gel-shift experiments (PMID: 10591637). This article hypothesized that this domain constitutes a bona fide sequence specific TF, but no concrete evidence for this exists to date

TULP4

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

(PMID: 10591637) shows that it binds dsDNA. All other research, however, supports phosphoinositide-binding as the major function of the tubby domain.

TUT1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

TXK

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Experimental evidence for DNA-binding was performed with nuclear extract - thus, the apparent specific-binding of TXK could be due to indirect binding (PMID: 11859127). In addition a whitepaper suggests that this interaction could not be replicated (Miskimins, Beth)

U2AF1

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Well-established RNA binding protein

U2AF1L4

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Related to U2AF1, so likely also an RNA binding protein.

UBA52

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBB

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBC

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBE2K

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBE2N

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBE2V1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Ubiquitin ligase

UBN1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Interacts with bZIP transcription factors (PMID: 10725330)

UBR4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UBTFL6

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pseudogene

According to ENSEMBL this is a Pseudogene, and it is of uncertain confidence in Uniprot. The most similar gene, UBTLF1, is annotated as No evidence for or against specific DNA-binding by this class of HMG box containing proteins.

UFL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UHRF1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Structural evidence (PDB:2ZO0; PDB: 2ZO1; PMID: 18772888] and (PDB: 2ZKE) (PMID: 18772891) demonstrate direct DNA-binding. However, the extent to which it is sequence specific beyond hemimethylated DNA has not been extensively explored.

UHRF2

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds DNA in the crystal structure contacting the minor groove and backbone (PDB: 4PW5). Recognizes 5hmC-containing DNA (PDB: 4PW5)

UNG

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Involved in mismatch repair. Excises uracil bases from DNA. Binds DNA in the crystal structure (PDB: 1EMJ)

USP39

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

USP7

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

UTF1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

VAV1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Paper cited by GO annotation (PMID: 2477241) only presents evidence based on sequence similarity to a ZF motif, and other evidence (PMID: 11994417) only supports a role in coactivation of NFAT and NFKB without direct DNA-binding

VEGFA

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Extracellular signaling molecule. Included only because it regulates CREB.

VGLL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Likely transcriptional cofactor (PMID: 10518497)

VGLL2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Co-activator that binds TEF family TFs (PMID: 14762206)

VGLL3

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 23380592) describes this protein as a co-activator, and it doesnt seem to have a DBD (fig. 1)

VHLL

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Interacts with TFs as part of an E3 ubiquitin ligase complex (PMID: 12682018). No evidence for DNA binding.

VPS72

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

VPS72 (YL1) is a histone chaperone. YL1 binding to the H2A.Z-H2B dimer is mutually exclusive from the dimer binding DNA (PMID: 26974126)

WFS1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WNT1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WNT10B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a secreted signaling protein

WNT2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WNT3A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WNT5A

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

(PMID: 19847889) shows this protein as a part of a large EMSA shifting complex with RNA-Pol1, CHD1, and other DNA binding proteins. It does not, however, show evidence for it binding to DNA directly

WNT8B

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WNT family signaling molecule (PMID: 9536085)

WRN

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ATP dependent DNA helicase. Binds DNA in the crystal structure (PDB: 3AAF)

WWOX

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Co-factor of AP-2 (PMID: 15548692)

WWP2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

WWTR1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Transcriptional co-activator that binds to TEADs (PMID: 19324877) and TBX5 (PMID: 16332960)

XCL1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Protein is a secreted chemokine

XPA

Unknown

Yes

Known motif

1 Monomer or homomultimer

High-throughput in vitro

Functions in DNA repair (PMID: 19197159), but has a strong HT-SELEX-derived motif.

YEATS2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

YEATS4

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Lacks a DBD and the study cited by GO annotation (PMID: 9302258) doesnt have experimental evidence for DNA-binding

YOD1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ZBED6CL

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

No DBDs on UniProt or Ensembl

ZBP1

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

ZBP1 is structurally-specific for Z-DNA, but does not have any sequence specificity (PDB: 1J75; PMID: 11524677)

ZCCHC11

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Likely a ssDNA or RNA binding protein based on domain composition

ZCCHC6

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

(PMID: 23709223) shows that it binds single-stranded nucleid acids

ZDHHC11

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ZDHHC19

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

ER transmembrane protein

ZMAT2

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Possibly an RBP based on presence of a U1 ZF domain

ZNF137P

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Pseudogene

ZNF185

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Protein has a LIM-subtype ZF. This type of ZF is not likely to bind DNA (PMID: 17696879)

ZNF638

Unknown

No

Unlikely to be sequence specific TF

3 Low specificity DNA-binding protein

No motif

Binds C-rich dsDNA with low affinity (PMID: 8647861).

ZNF720

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contains a KRAB domain (associated with many C2H2 ZFs), but no annotated C2H2 on PDB or UniProt

ZNF738

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Contains a KRAB domain (associated with many C2H2 ZFs), but no annotated C2H2 on PDB or UniProt

ZNF862

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Has a putative AT-hook

Contains a KRAB domain (associated with many C2H2 ZFs), but no annotated C2H2 on PDB or UniProt

ZNFX1

Unknown

No

Unlikely to be sequence specific TF

4 Not a DNA binding protein

No motif

Probably an RBP (PMID: 22658674; PMID: 22681889)

ZRANB2

Unknown

No

ssDNA/RNA binding

4 Not a DNA binding protein

No motif

Its the wrong kind of zinc finger to bind DNA. Likely binds RNA. PMID cited by GO (PMID: 9931435) does not have evidence of sequence-specific DNA binding.

Collection of 69 putative Unknown human TFs out of 1023 considered proteins