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 7 [Source:HGNC Symbol;Acc:HGNC:8621]
Entrez Summary	TBA
Ensembl ID:	ENSG00000009709
External Link:	T104403_1.02
Interpro	IPR001356; IPR001523; IPR009057; IPR017970; IPR022106; ;
Protein Domain:
Protein: ENSP00000364524	DBD: Homeodomain,Paired box	Other: Pax7
Protein: ENSP00000383502	DBD: Homeodomain,Paired box	Other: Pax7
Protein: ENSP00000403389	DBD: Homeodomain,Paired box	Other: Pax7

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific Transcription Regulatory Activity heterochromatin interaction/binding_DNA Binding Transactivation_ PMIDS:15688409
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:0000983 RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity TAS - PMID:9339373
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
SMiLE-seq	Isakova2017		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
PBM	Berger08		Inferred - Pax7 (92% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Pax7 (92% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Pax7 (92% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Pax7 (92% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PAX3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PAX3 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PAX3 (88% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - PAX3 (88% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - prd (79% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - prd (79% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - prd (79% AA Identity, Drosophila melanogaster)
Misc	iDMMPMM		Inferred - prd (79% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb-n (75% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb (73% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - gsb (73% AA Identity, Drosophila melanogaster)

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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{"regions": [{"startStyle": "curved", "end": 161, "endStyle": "curved", "aliStart": 34, "text": "PAX", "colour": "#2cb42c", "aliEnd": 161, "start": 34, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 161, "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": 34, "scoreName": "E-value", "accession": "PF00292.16", "start": 34, "score": 8.699999999999998e-72, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 161}}, {"startStyle": "curved", "end": 274, "endStyle": "curved", "aliStart": 218, "text": "HD", "colour": "#228B22", "aliEnd": 274, "start": 218, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 274, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 218, "scoreName": "E-value", "accession": "PF00046.27", "start": 218, "score": 1.1999999999999998e-23, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 274}}, {"startStyle": "straight", "end": 385, "endStyle": "straight", "aliStart": 346, "text": "Pax7", "colour": "#9999ff", "aliEnd": 385, "start": 345, "href": "http://pfam.xfam.org/family/PF12360.6", "type": "pfama", "display": "true", "metadata": {"end": 385, "description": "This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with Pfam:PF00046, Pfam:PF00292.  Pax7 belongs to a family of genes that encode paired-box-containing transcription factors involved in the control of developmental processes. Pax7 has a distinct role in the specification of myogenic satellite cells.", "database": "PfamA", "aliStart": 346, "scoreName": "E-value", "accession": "PF12360.6", "start": 345, "score": 4.3e-20, "identifier": "Paired box protein 7 ", "type": "DBD", "aliEnd": 385}}], "length": 506}

TF Info Page for PAX7 (Homeodomain; Paired box)