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 5 [Source:HGNC Symbol;Acc:HGNC:8619]

Entrez Summary

This gene encodes a member of the paired box (PAX) family of transcription factors. The central feature of this gene family is a novel, highly conserved DNA-binding motif, known as the paired box. Paired box transcription factors are important regulators in early development, and alterations in the expression of their genes are thought to contribute to neoplastic transformation. This gene encodes the B-cell lineage specific activator protein that is expressed at early, but not late stages of B-cell differentiation. Its expression has also been detected in developing CNS and testis and so the encoded protein may also play a role in neural development and spermatogenesis. This gene is located at 9p13, which is involved in t(9;14)(p13;q32) translocations recurring in small lymphocytic lymphomas of the plasmacytoid subtype, and in derived large-cell lymphomas. This translocation brings the potent E-mu enhancer of the IgH gene into close proximity of the PAX5 promoter, suggesting that the deregulation of transcription of this gene contributes to the pathogenesis of these lymphomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

Ensembl ID:

ENSG00000196092

External Link:

CisBP

Interpro

IPR001523; IPR009057; IPR022130; ;

Protein Domain:

ENSP00000350844

Protein Domain:

ENSP00000367078

Protein Domain:

ENSP00000367083

Protein Domain:

ENSP00000367084

Protein Domain:

ENSP00000412188

Protein Domain:

ENSP00000404687

Protein Domain:

ENSP00000429291

Protein Domain:

ENSP00000430773

Protein Domain:

ENSP00000429359

Protein Domain:

ENSP00000428670

Protein Domain:

ENSP00000429197

Protein Domain:

ENSP00000429637

Protein Domain:

ENSP00000429404

Domain:

Protein: ENSP00000350844	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000367078	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000367083	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000367084	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000412188	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000404687	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000429291	DBD: Paired Box	Other:
Protein: ENSP00000430773	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000429359	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000428670	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000429197	DBD: Paired Box	Other: Pax2_C
Protein: ENSP00000429637	DBD: Paired Box	Other:
Protein: ENSP00000429404	DBD: Paired Box	Other: Pax2_C

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:8406007
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:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a 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
HT-SELEX	Jolma2013		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	JASPAR		Direct
ChIP-seq	modENCODE		Direct
ChIP-seq	modENCODE		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
Misc	HocoMoco		Direct
Misc	HocoMoco		Direct
Misc	HOMER		Direct
Misc	HOMER		Direct
PBM	TF_Evolution	Unpublished Data	Inferred - Pax5 (100% AA Identity, Gallus gallus)
PBM	Zoo_01		Inferred - pax2 (97% AA Identity, Xenopus tropicalis)
PBM	Zoo_01		Inferred - pax2b (96% AA Identity, Danio rerio)
HT-SELEX	Yin2017		Inferred - PAX8 (93% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PAX8 (93% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PAX8 (93% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - PAX8 (93% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - PAX8 (93% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Pax8 (93% AA Identity, Rattus norvegicus)
HT-SELEX	Nitta2015		Inferred - sv (86% AA Identity, Drosophila melanogaster)
PBM	TF_Evolution	Unpublished Data	Inferred - sv (86% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - egl-38 (71% AA Identity, Caenorhabditis elegans)
PBM	CEPD		Inferred - pax-2 (71% AA Identity, Caenorhabditis elegans)

Structure

Structure	PDB	1K78

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": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.8e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "straight", "end": 390, "endStyle": "straight", "aliStart": 285, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 390, "start": 279, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 390, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 285, "scoreName": "E-value", "accession": "PF12403.6", "start": 279, "score": 4.9e-51, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 390}}], "length": 392}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.1999999999999998e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "jagged", "end": 327, "endStyle": "straight", "aliStart": 302, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 327, "start": 297, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 327, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 302, "scoreName": "E-value", "accession": "PF12403.6", "start": 297, "score": 9.499999999999999e-05, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 327}}], "length": 329}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.3999999999999995e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "jagged", "end": 356, "endStyle": "straight", "aliStart": 292, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 356, "start": 278, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 356, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 292, "scoreName": "E-value", "accession": "PF12403.6", "start": 278, "score": 3.2000000000000003e-23, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 356}}], "length": 358}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.4999999999999996e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "straight", "end": 341, "endStyle": "jagged", "aliStart": 285, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 341, "start": 279, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 341, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 285, "scoreName": "E-value", "accession": "PF12403.6", "start": 279, "score": 9.9e-25, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 341}}, {"startStyle": "jagged", "end": 361, "endStyle": "straight", "aliStart": 339, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 361, "start": 338, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 361, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 339, "scoreName": "E-value", "accession": "PF12403.6", "start": 338, "score": 9.9e-25, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 361}}], "length": 363}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.6999999999999998e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "straight", "end": 347, "endStyle": "straight", "aliStart": 242, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 347, "start": 236, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 347, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 242, "scoreName": "E-value", "accession": "PF12403.6", "start": 236, "score": 2.0999999999999997e-51, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 347}}], "length": 349}

{"regions": [{"startStyle": "curved", "end": 115, "endStyle": "jagged", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 80, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 115, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 4.2e-32, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 80}}, {"startStyle": "jagged", "end": 290, "endStyle": "straight", "aliStart": 226, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 290, "start": 212, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 290, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 226, "scoreName": "E-value", "accession": "PF12403.6", "start": 212, "score": 2.2999999999999998e-23, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 290}}], "length": 292}

{"regions": [{"startStyle": "curved", "end": 140, "endStyle": "curved", "aliStart": 16, "text": "PAX", "colour": "#2cb42c", "aliEnd": 140, "start": 16, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 140, "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": 16, "scoreName": "E-value", "accession": "PF00292.16", "start": 16, "score": 1.3999999999999995e-74, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 140}}, {"startStyle": "straight", "end": 298, "endStyle": "jagged", "aliStart": 242, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 298, "start": 236, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 298, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 242, "scoreName": "E-value", "accession": "PF12403.6", "start": 236, "score": 9.399999999999999e-27, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 298}}, {"startStyle": "jagged", "end": 318, "endStyle": "straight", "aliStart": 296, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 318, "start": 295, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 318, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 296, "scoreName": "E-value", "accession": "PF12403.6", "start": 295, "score": 9.399999999999999e-27, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 318}}], "length": 320}

{"regions": [{"startStyle": "jagged", "end": 32, "endStyle": "curved", "aliStart": 1, "text": "PAX", "colour": "#2cb42c", "aliEnd": 32, "start": 1, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 32, "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": 4.1e-12, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 32}}, {"startStyle": "straight", "end": 282, "endStyle": "straight", "aliStart": 177, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 282, "start": 171, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 282, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 177, "scoreName": "E-value", "accession": "PF12403.6", "start": 171, "score": 2.5999999999999994e-51, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 282}}], "length": 284}

{"regions": [{"startStyle": "jagged", "end": 32, "endStyle": "curved", "aliStart": 1, "text": "PAX", "colour": "#2cb42c", "aliEnd": 32, "start": 1, "href": "http://pfam.xfam.org/family/PF00292.16", "type": "pfama", "display": "true", "metadata": {"end": 32, "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": 5.9e-12, "identifier": "'Paired box' domain", "type": "DBD", "aliEnd": 32}}, {"startStyle": "straight", "end": 197, "endStyle": "jagged", "aliStart": 177, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 196, "start": 171, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 197, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 177, "scoreName": "E-value", "accession": "PF12403.6", "start": 171, "score": 4.9e-05, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 196}}, {"startStyle": "jagged", "end": 219, "endStyle": "straight", "aliStart": 194, "text": "Pax2_C", "colour": "#9999ff", "aliEnd": 219, "start": 188, "href": "http://pfam.xfam.org/family/PF12403.6", "type": "pfama", "display": "true", "metadata": {"end": 219, "description": "This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with Pfam:PF00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis.", "database": "PfamA", "aliStart": 194, "scoreName": "E-value", "accession": "PF12403.6", "start": 188, "score": 4.9e-05, "identifier": "Paired-box protein 2 C terminal", "type": "DBD", "aliEnd": 219}}], "length": 221}

TF Info Page for PAX5 (Paired box)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution