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

No Alignment available for Unknown
Ensembl ID 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)
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.