Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
High-throughput in vitro
Description
Description:
orthodenticle homeobox 2 [Source:HGNC Symbol;Acc:HGNC:8522]
Entrez Summary
TBA
Ensembl ID:
ENSG00000165588
External Link:
T093356_1.02
Interpro
IPR001356 ; IPR003022 ; IPR003025 ; IPR009057 ; IPR013851 ; IPR017970 ;
Protein Domain:
Protein: ENSP00000343819DBD: HomeodomainOther: TF_OtxProtein: ENSP00000386185DBD: HomeodomainOther: TF_OtxProtein: ENSP00000474486DBD: HomeodomainOther: Protein: ENSP00000451357DBD: HomeodomainOther: TF_OtxProtein: ENSP00000452336DBD: HomeodomainOther: TF_Otx
Previous Annotations
Source
Annotation
TF-CAT classification
TF Gene Candidate_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:12559959 14625556
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:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IDA - PMID:12559959, PMID:20530484
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
Structure
Experimental History
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{"regions": [{"startStyle": "curved", "end": 95, "endStyle": "curved", "aliStart": 39, "text": "HD", "colour": "#228B22", "aliEnd": 95, "start": 39, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 95, "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": 39, "scoreName": "E-value", "accession": "PF00046.27", "start": 39, "score": 5.3e-22, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 95}}, {"startStyle": "straight", "end": 234, "endStyle": "straight", "aliStart": 153, "text": "TF_Otx", "colour": "#9999ff", "aliEnd": 234, "start": 153, "href": "http://pfam.xfam.org/family/PF03529.11", "type": "pfama", "display": "true", "metadata": {"end": 234, "description": NaN, "database": "PfamA", "aliStart": 153, "scoreName": "E-value", "accession": "PF03529.11", "start": 153, "score": 1.4e-32, "identifier": "Otx1 transcription factor", "type": "DBD", "aliEnd": 234}}], "length": 290}
{"regions": [{"startStyle": "curved", "end": 103, "endStyle": "curved", "aliStart": 47, "text": "HD", "colour": "#228B22", "aliEnd": 103, "start": 47, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 103, "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": 47, "scoreName": "E-value", "accession": "PF00046.27", "start": 47, "score": 3.9e-22, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 103}}, {"startStyle": "straight", "end": 239, "endStyle": "straight", "aliStart": 161, "text": "TF_Otx", "colour": "#9999ff", "aliEnd": 239, "start": 161, "href": "http://pfam.xfam.org/family/PF03529.11", "type": "pfama", "display": "true", "metadata": {"end": 239, "description": NaN, "database": "PfamA", "aliStart": 161, "scoreName": "E-value", "accession": "PF03529.11", "start": 161, "score": 2.1e-31, "identifier": "Otx1 transcription factor", "type": "DBD", "aliEnd": 239}}], "length": 239}
{"regions": [{"startStyle": "curved", "end": 95, "endStyle": "curved", "aliStart": 39, "text": "HD", "colour": "#228B22", "aliEnd": 95, "start": 39, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 95, "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": 39, "scoreName": "E-value", "accession": "PF00046.27", "start": 39, "score": 5.3e-22, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 95}}, {"startStyle": "straight", "end": 234, "endStyle": "straight", "aliStart": 153, "text": "TF_Otx", "colour": "#9999ff", "aliEnd": 234, "start": 153, "href": "http://pfam.xfam.org/family/PF03529.11", "type": "pfama", "display": "true", "metadata": {"end": 234, "description": NaN, "database": "PfamA", "aliStart": 153, "scoreName": "E-value", "accession": "PF03529.11", "start": 153, "score": 1.4e-32, "identifier": "Otx1 transcription factor", "type": "DBD", "aliEnd": 234}}], "length": 290}