TF Info Page for LMX1B (Homeodomain)

Conclusion

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

Description

Description: LIM homeobox transcription factor 1 beta [Source:HGNC Symbol;Acc:HGNC:6654]
Entrez Summary NA
Ensembl ID: ENSG00000136944
External Link: CisBP
Interpro IPR001356; IPR001781; IPR009057; IPR017970;
Protein Domain: ENSP00000347684
Protein Domain: ENSP00000362573
Protein Domain: ENSP00000436930
Protein Domain: ENSP00000453580
Domain:
Protein: ENSP00000347684DBD: HomeodomainOther: LIM
Protein: ENSP00000362573DBD: HomeodomainOther: LIM
Protein: ENSP00000436930DBD: HomeodomainOther: LIM
Protein: ENSP00000453580DBD: HomeodomainOther: LIM

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_Transactivation_
PMIDS:10767331 11956245 1358758 15785774
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
IDA - PMID:10767331
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-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
HT-SELEXYin2017Inferred - LMX1A (100% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LMX1A (100% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - LMX1A (100% AA Identity, Homo sapiens)
PBMBerger08Inferred - Lmx1a (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Lmx1b (100% AA Identity, Mus musculus)
B1HJASPARInferred - CG32105 (84% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - CG32105 (84% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - CG4328 (82% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - SNAPOd2T00003340001 (74% AA Identity, Oikopleura dioica)

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