TF Info Page for MSX1 (Homeodomain)

Conclusion

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

Description

Description: msh homeobox 1 [Source:HGNC Symbol;Acc:HGNC:7391]
Entrez Summary This gene encodes a member of the muscle segment homeobox gene family. The encoded protein functions as a transcriptional repressor during embryogenesis through interactions with components of the core transcription complex and other homeoproteins. It may also have roles in limb-pattern formation, craniofacial development, particularly odontogenesis, and tumor growth inhibition. Mutations in this gene, which was once known as homeobox 7, have been associated with nonsyndromic cleft lip with or without cleft palate 5, Witkop syndrome, Wolf-Hirschom syndrome, and autosomoal dominant hypodontia. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000163132
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000372170
Domain:
Protein: ENSP00000372170DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15192231 17030628
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 GO:0000982
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IEA - GO_REF:0000019
GO:0001227
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor
IEA - GO_REF:0000019
GO:0001228
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor
IEA - GO_REF:0000019
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-SELEXJolma2013Direct
HT-SELEXYin2017Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
PBMBerger08Inferred - Msx1 (100% AA Identity, Mus musculus)
PBMBerger08Inferred - Msx3 (98% AA Identity, Mus musculus)
PBMBarrera2016Inferred - MSX2 (96% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - MSX2 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - MSX2 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - MSX2 (96% AA Identity, Homo sapiens)
PBMBerger08Inferred - Msx2 (96% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - MSX2 (96% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - MSX2 (96% AA Identity, Homo sapiens)
MiscHocoMocoInferred - MSX2 (96% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - MSX2 (94% AA Identity, Homo sapiens)
PBMBusserDevelopment2012Inferred - Dr (91% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Dr (91% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 1IG7

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