The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Inferred motif	2 Obligate heteromer	In vivo/Misc source		TAL1, TAL2 and LYL are very similar and have a basic region with a bulky tryptophan inserting into the cluster of the basic residues. Binds DNA as a heterodimer with TCF3 (PDB:2YPB and PDB:2YPA).

Description

Description:	lymphoblastic leukemia associated hematopoiesis regulator 1 [Source:HGNC Symbol;Acc:HGNC:6734]
Entrez Summary	TBA
Ensembl ID:	ENSG00000104903
External Link:	T014175_1.02
Interpro	IPR011598; ;
Protein Domain:
Protein: ENSP00000264824	DBD: bHLH	Other:
Protein: ENSP00000468122	DBD: bHLH	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	a
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0000981 sequence-specific DNA binding RNA polymerase II transcription factor activity IBA - GO_REF:0000033
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a2, Orthologous HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
Transfac	Transfac	License required	Inferred - TAL1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TAL1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - TAL1 (88% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - TAL1 (88% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - TAL1 (88% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Tal1 (88% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Tal1 (88% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - NHLH2 (60% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NHLH2 (60% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Nhlh2 (60% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - NHLH1 (60% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - NHLH1 (60% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Nhlh2 (60% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - NHLH1 (60% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - HLH4C (56% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - HLH4C (56% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - HLH4C (56% AA Identity, Drosophila melanogaster)
HT-SELEX	Yin2017		Inferred - HAND2 (52% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - HAND2 (52% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - NEUROG1 (50% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - NEUROG1 (50% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NEUROG1 (50% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NEUROG1 (50% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Neurog1 (50% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - NEUROG2 (50% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - NEUROG2 (50% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NEUROG2 (50% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - NEUROG2 (50% AA Identity, Homo sapiens)

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 203, "endStyle": "curved", "aliStart": 151, "text": "HLH", "colour": "#2cb42c", "aliEnd": 202, "start": 151, "href": "http://pfam.xfam.org/family/PF00010.24", "type": "pfama", "display": "true", "metadata": {"end": 203, "description": "A number of eukaryotic proteins, which probably are sequence specific DNA-binding proteins that act as transcription factors, share a conserved domain of 40 to 50 amino acid residues. It has been proposed [PUBMED:2493990] that this domain is formed of two amphipathic helices joined by a variable length linker region that could form a loop. This 'helix-loop-helix' (HLH) domain mediates protein dimerization and has been found in the proteins listed below [PUBMED:1521738]. Most of these proteins have an extra basic region of about 15 amino acid residues that is adjacent to the HLH domain and specifically binds to DNA. They are refered as basic helix-loop-helix proteins (bHLH), and are classified in two groups: class A (ubiquitous) and class B (tissue-specific). Members of the bHLH family bind variations on the core sequence 'CANNTG', also refered to as the E-box motif. The homo- or heterodimerization mediated by the HLH domain is independent of, but necessary for DNA binding, as two basic regions are required for DNA binding activity. The HLH proteins lacking the basic domain (Emc, Id) function as negative regulators, since they form heterodimers, but fail to bind DNA. The hairy-related proteins (hairy, E(spl), deadpan) also repress transcription although they can bind DNA. The proteins of this subfamily act together with co-repressor proteins, like groucho, through their C-terminal motif WRPW.", "database": "PfamA", "aliStart": 151, "scoreName": "E-value", "accession": "PF00010.24", "start": 151, "score": 5.3e-15, "identifier": "Helix-loop-helix DNA-binding domain", "type": "DBD", "aliEnd": 202}}], "length": 281}

TF Info Page for LYL1 (bHLH)