Conclusion
Assessment
Binding Mode
Motif Status
Notes
Comments
Known motif
1 Monomer or homomultimer
High-throughput in vitro
Has a putative AT-hook
Description
Description:
LIM homeobox 2 [Source:HGNC Symbol;Acc:HGNC:6594]
Entrez Summary
TBA
Ensembl ID:
ENSG00000106689
External Link:
T093256_1.02
Interpro
IPR001356 ; IPR001781 ; IPR009057 ; IPR017970 ;
Protein Domain:
Protein: ENSP00000362717DBD: HomeodomainOther: LIMProtein: ENSP00000394978DBD: HomeodomainOther: LIMProtein: ENSP00000476200DBD: HomeodomainOther: Protein: ENSP00000453448DBD: HomeodomainOther: LIM
Previous Annotations
Source
Annotation
TF-CAT classification
TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:7513049 10593900
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
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": 329, "endStyle": "curved", "aliStart": 273, "text": "HD", "colour": "#228B22", "aliEnd": 329, "start": 273, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 329, "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": 273, "scoreName": "E-value", "accession": "PF00046.27", "start": 273, "score": 3.8e-19, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 329}}, {"startStyle": "straight", "end": 108, "endStyle": "straight", "aliStart": 51, "text": "LIM", "colour": "#9999ff", "aliEnd": 106, "start": 51, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 108, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 51, "scoreName": "E-value", "accession": "PF00412.20", "start": 51, "score": 3.8999999999999997e-31, "identifier": "LIM domain", "type": "DBD", "aliEnd": 106}}, {"startStyle": "straight", "end": 178, "endStyle": "straight", "aliStart": 121, "text": "LIM", "colour": "#9999ff", "aliEnd": 176, "start": 121, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 178, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 121, "scoreName": "E-value", "accession": "PF00412.20", "start": 121, "score": 3.8999999999999997e-31, "identifier": "LIM domain", "type": "DBD", "aliEnd": 176}}], "length": 413}
{"regions": [{"startStyle": "curved", "end": 113, "endStyle": "jagged", "aliStart": 68, "text": "HD", "colour": "#228B22", "aliEnd": 112, "start": 68, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 113, "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": 68, "scoreName": "E-value", "accession": "PF00046.27", "start": 68, "score": 1.4e-11, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 112}}], "length": 116}
{"regions": [{"startStyle": "straight", "end": 69, "endStyle": "straight", "aliStart": 12, "text": "LIM", "colour": "#9999ff", "aliEnd": 69, "start": 12, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 69, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 12, "scoreName": "E-value", "accession": "PF00412.20", "start": 12, "score": 5.2e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 69}}, {"startStyle": "straight", "end": 131, "endStyle": "straight", "aliStart": 74, "text": "LIM", "colour": "#9999ff", "aliEnd": 129, "start": 74, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 131, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 74, "scoreName": "E-value", "accession": "PF00412.20", "start": 74, "score": 5.2e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 129}}], "length": 147}