TF Info Page for LHX3 (Homeodomain)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer 100 perc ID - in vitro

Description

Description: LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Entrez Summary This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Ensembl ID: ENSG00000107187
External Link: CisBP
Interpro IPR001356; IPR001781; IPR009057; IPR017970;
Protein Domain: ENSP00000360811
Protein Domain: ENSP00000360813
Protein Domain: ENSP00000483080
Domain:
Protein: ENSP00000360811DBD: HomeodomainOther: LIM
Protein: ENSP00000360813DBD: HomeodomainOther: LIM
Protein: ENSP00000483080DBD: HomeodomainOther: LIM

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15271874
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

Source Annotation Motif Evidence
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBerger08Inferred - Lhx3 (100% AA Identity, Mus musculus)
SELEXJASPARInferred - Lhx3 (100% AA Identity, Mus musculus)
MiscHOMERInferred - Lhx3 (100% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX4 (94% AA Identity, Homo sapiens)
PBMBerger08Inferred - Lhx4 (94% AA Identity, Mus musculus)
B1HJASPARInferred - Lim3 (92% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Lim3 (92% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Lim3 (92% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - LHX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX1 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Lhx1 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - LHX5 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX5 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX5 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Lhx5 (71% AA Identity, Mus musculus)
B1HJASPARInferred - Lim1 (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Lim1 (70% 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