The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Inferred motif	2 Obligate heteromer	In vivo/Misc source		Likely obligate heteromer (PMID: 9374395; PMID: 27782878).

Description

Description:	neuronal PAS domain protein 3 [Source:HGNC Symbol;Acc:HGNC:19311]
Entrez Summary	TBA
Ensembl ID:	ENSG00000151322
External Link:	T014216_1.02
Interpro	IPR000014; IPR011598; IPR013655; IPR013767;
Protein Domain:
Protein: ENSP00000319610	DBD: bHLH	Other: PAS, PAS_11, PAS_3, PAS_4, PAS_9
Protein: ENSP00000348460	DBD: bHLH	Other: PAS, PAS_11, PAS_3, PAS_4, PAS_9
Protein: ENSP00000350446	DBD: bHLH	Other: PAS, PAS_11, PAS_3, PAS_4, PAS_9
Protein: ENSP00000449542	DBD: bHLH	Other: PAS, PAS_3
Protein: ENSP00000448916	DBD: bHLH	Other: PAS, PAS_11, PAS_3, PAS_4, PAS_9
Protein: ENSP00000447213	DBD: bHLH	Other: PAS, PAS_3
Protein: ENSP00000446700	DBD: bHLH	Other: PAS

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific_Other_ PMIDS:16172381 9374395 16172381 10534623 16172381 16190882
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.	c
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 - HIF1A (69% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HIF1A (69% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HIF1A (69% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HIF1A (69% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - HIF1A (69% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - HIF1A (69% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - HIF1A (69% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EPAS1 (64% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EPAS1 (64% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - EPAS1 (64% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - EPAS1 (64% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Hif3a (61% AA Identity, Mus musculus)

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

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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": 23, "scoreName": "E-value", "accession": "PF00010.24", "start": 22, "score": 0.00032, "identifier": "Helix-loop-helix DNA-binding domain", "type": "DBD", "aliEnd": 72}}, {"startStyle": "straight", "end": 190, "endStyle": "jagged", "aliStart": 142, "text": "PAS_3", "colour": "#9999ff", "aliEnd": 180, "start": 141, "href": "http://pfam.xfam.org/family/PF08447.10", "type": "pfama", "display": "true", "metadata": {"end": 190, "description": "The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. 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The PAS fold appears in archaea, eubacteria and eukarya.", "database": "PfamA", "aliStart": 127, "scoreName": "E-value", "accession": "PF08448.8", "start": 125, "score": 0.00025, "identifier": "PAS fold", "type": "DBD", "aliEnd": 179}}, {"startStyle": "straight", "end": 379, "endStyle": "jagged", "aliStart": 304, "text": "PAS_4", "colour": "#9999ff", "aliEnd": 350, "start": 300, "href": "http://pfam.xfam.org/family/PF08448.8", "type": "pfama", "display": "true", "metadata": {"end": 379, "description": "The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.", "database": "PfamA", "aliStart": 304, "scoreName": "E-value", "accession": "PF08448.8", "start": 300, "score": 0.00025, "identifier": "PAS fold", "type": "DBD", "aliEnd": 350}}], "length": 904}

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TF Info Page for NPAS3 (bHLH)