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 4 [Source:HGNC Symbol;Acc:HGNC:8618]
Entrez Summary	TBA
Ensembl ID:	ENSG00000106331
External Link:	T104405_1.02
Interpro	IPR001356; IPR001523; IPR009057; IPR017970;
Protein Domain:
Protein: ENSP00000339906	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000368014	DBD: Homeodomain,Paired box	Other:
Protein: ENSP00000451923	DBD: Homeodomain,Paired box	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:10567553
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"	No
GO-Info	GO:0001206 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involv IEA - GO_REF:0000019
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
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Nitta2015		Direct
HT-SELEX	Nitta2015		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
SELEX	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
PBM	Berger08		Inferred - Pax4 (90% 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

{"regions": [{"startStyle": "curved", "end": 121, "endStyle": "curved", "aliStart": 1, "text": "PAX", "colour": "#2cb42c", "aliEnd": 121, "start": 1, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 121, "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": 1, "scoreName": "E-value", "accession": "PF00292.16", "start": 1, "score": 7.7e-55, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 121}}, {"startStyle": "curved", "end": 219, "endStyle": "curved", "aliStart": 164, "text": "HD", "colour": "#228B22", "aliEnd": 219, "start": 163, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 164, "scoreName": "E-value", "accession": "PF00046.27", "start": 163, "score": 3.2000000000000003e-20, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 219}}], "length": 344}

{"regions": [{"startStyle": "curved", "end": 121, "endStyle": "curved", "aliStart": 1, "text": "PAX", "colour": "#2cb42c", "aliEnd": 121, "start": 1, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 121, "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": 1, "scoreName": "E-value", "accession": "PF00292.16", "start": 1, "score": 7.1e-55, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 121}}, {"startStyle": "curved", "end": 219, "endStyle": "curved", "aliStart": 164, "text": "HD", "colour": "#228B22", "aliEnd": 219, "start": 163, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 219, "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": 164, "scoreName": "E-value", "accession": "PF00046.27", "start": 163, "score": 3.1e-20, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 219}}], "length": 341}

{"regions": [{"startStyle": "jagged", "end": 119, "endStyle": "curved", "aliStart": 28, "text": "PAX", "colour": "#2cb42c", "aliEnd": 119, "start": 18, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 119, "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": 28, "scoreName": "E-value", "accession": "PF00292.16", "start": 18, "score": 3.5000000000000003e-34, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 119}}, {"startStyle": "curved", "end": 217, "endStyle": "curved", "aliStart": 162, "text": "HD", "colour": "#228B22", "aliEnd": 217, "start": 161, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 217, "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": 162, "scoreName": "E-value", "accession": "PF00046.27", "start": 161, "score": 3.9e-20, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 217}}], "length": 342}

TF Info Page for PAX4 (Homeodomain; Paired box)