TF Info Page for LHX6 (Homeodomain)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro

Description

Description: LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Entrez Summary This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]
Ensembl ID: ENSG00000106852
External Link: CisBP
Interpro IPR001356; IPR001781; IPR009057; IPR017970;
Protein Domain: ENSP00000340137
Protein Domain: ENSP00000362859
Protein Domain: ENSP00000362860
Protein Domain: ENSP00000377854
Protein Domain: ENSP00000452811
Protein Domain: ENSP00000453798
Protein Domain: ENSP00000441464
Protein Domain: ENSP00000475927
Domain:
Protein: ENSP00000340137DBD: HomeodomainOther: LIM
Protein: ENSP00000362859DBD: HomeodomainOther: LIM
Protein: ENSP00000362860DBD: HomeodomainOther: LIM
Protein: ENSP00000377854DBD: HomeodomainOther: LIM
Protein: ENSP00000452811DBD: HomeodomainOther:
Protein: ENSP00000453798DBD: HomeodomainOther:
Protein: ENSP00000441464DBD: HomeodomainOther: LIM
Protein: ENSP00000475927DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification Indeterminate - There is no evidence for or against this genes role as a TF___
PMIDS:0
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:0003700
sequence-specific DNA binding transcription factor activity
NAS - PMID:10393337
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
SMiLE-seqIsakova2017Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMZoo_01Direct
PBMBerger08Inferred - Lhx6 (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Lhx6_CONSTRUCT (100% AA Identity, PBM CONSTRUCTS)
HT-SELEXYin2017Inferred - LHX8 (94% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - LHX8 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX8 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX8 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LHX8 (94% AA Identity, Homo sapiens)
PBMBerger08Inferred - Lhx8 (94% AA Identity, Mus musculus)
B1HJASPARInferred - Awh (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Awh (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Awh (66% 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