The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro

Description

Description:	paired box 6 [Source:HGNC Symbol;Acc:HGNC:8620]
Entrez Summary	TBA
Ensembl ID:	ENSG00000007372
External Link:	T104402_1.02
Interpro	IPR001356; IPR001523; IPR009057; IPR017970;
Protein Domain:
Protein: ENSP00000241001	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000368406	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000368410	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000368418	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000404100	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000480026	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000368403	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000404356	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000388132	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000436365	DBD: Homeodomain,Paired box	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_Transactivation_ PMIDS:7753864 7841787 8132558 9710641 12756174
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 IDA - PMID:20592023 GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IEA - GO_REF:0000019 GO:0001227 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity TAS - PMID:10441571, PMID:10747901
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	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
PBM	Barrera2016		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Berger08		Inferred - Pax6 (100% AA Identity, Mus musculus)
HT-SELEX	Nitta2015		Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - ey (93% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - toy (90% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - toy (90% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - toy (90% AA Identity, Drosophila melanogaster)

Structure

Structure	PDB	6PAX

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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{"regions": [{"startStyle": "curved", "end": 61, "endStyle": "jagged", "aliStart": 4, "text": "PAX", "colour": "#2cb42c", "aliEnd": 52, "start": 4, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 61, "description": "Paired domain proteins can function as transcription repressors or activators. The paired domain contains three subdomains, which show functional differences in DNA-binding. The crystal structures of prd and Pax proteins show that the DNA-bound paired domain is bipartite, consisting of an N-terminal subdomain (PAI or NTD) and a C-terminal subdomain (RED or CTD), connected by a linker. PAI and RED each form a three-helical fold, with the most C-terminal helices comprising a helix-turn-helix (HTH) motif that binds the DNA major groove. In addition, the PAI subdomain encompasses an N-terminal beta-turn and beta-hairpin, also named 'wing', participating in DNA-binding. The linker can bind into the DNA minor groove. Different Pax proteins and their alternatively spliced isoforms use different (sub)domains for DNA-binding to mediate the specificity of sequence recognition [PUBMED:11103953, PUBMED:15148315].", "database": "PfamA", "aliStart": 4, "scoreName": "E-value", "accession": "PF00292.16", "start": 4, "score": 2.7e-22, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 52}}], "length": 62}

TF Info Page for PAX6 (Homeodomain; Paired box)