Gene: Msx1

Basic information

Tag Content
Uniprot ID P13297; Q91W75; Q9ERF6;
Entrez ID 17701
Genbank protein ID CAA32626.1; AAA37823.1; CAA41944.1; AAG32466.1; EDL37531.1; AAH16426.1; CAA32871.1;
Genbank nucleotide ID NM_010835.2
Ensembl protein ID ENSMUSP00000058354
Ensembl nucleotide ID ENSMUSG00000048450
Gene name Homeobox protein MSX-1
Gene symbol Msx1
Organism Mus musculus
NCBI taxa ID 10090
Cleft type CPO,CLP
Developmental stage E11.5, E13.0, E12.5, E14.0, E13.5, E14.5, E15.0, E15.5, E16.0
Data sources Manually collected
Reference 17654563; 9256350; 7914451; 16330189; 19934017; 20123092; 10512191;
Functional description Acts as a transcriptional repressor. May play a role in limb-pattern formation. Acts in cranofacial development and specifically in odontogenesis.
Sequence
MAPAAAMTSL PLGVKVEDSA FAKPAGGGVG QAPGAAAATA TAMGTDEEGA KPKVPASLLP 60
FSVEALMADH RKPGAKESVL VASEGAQAAG GSVQHLGTRP GSLGAPDAPS SPRPLGHFSV 120
GGLLKLPEDA LVKAESPEKL DRTPWMQSPR FSPPPARRLS PPACTLRKHK TNRKPRTPFT 180
TAQLLALERK FRQKQYLSIA ERAEFSSSLS LTETQVKIWF QNRRAKAKRL QEAELEKLKM 240
AAKPMLPPAA FGLSFPLGGP AAVAAAAGAS LYSASGPFQR AALPVAPVGL YTAHVGYSMY 300
HLT 303

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

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Protein structural annotations

3D structure in PDB database


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Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologMSX1102190677A0A452EK01Capra hircusPredictionMore>>
1:1 orthologMSX14487P28360CPO,CL/PHomo sapiensPublicationMore>>
1:1 orthologMsx117701P13297CPO,CLPE11.5, E13.0, E12.5, E14.0, E13.5, E14.5, E15.0, E15.5, E16.0Mus musculusPublicationMore>>
1:1 orthologMSX1461092Q2VL88Pan troglodytesPredictionMore>>
1:1 orthologMSX1F1S5G6Sus scrofaPredictionMore>>
1:1 orthologMsx1G3V6U7Rattus norvegicusPredictionMore>>
1:1 orthologmsx1aB3DG59Danio rerioPredictionMore>>

Identified variants/mutations related to cleft phenotype

Gene symbol Significant Variants/SNPS Methods PubMed ID
MSX1rs12532-AASequence analysis24603642
MSX1rs11726039PCR25953455
MSX1169 bp allelePCR; TDT23903689
MSX1rs3821949TDT; conditional logistic regression models23580168
MSX1c.799G>TPCR; restriction enzyme digestion21972896
MSX1p.P147QPCR-RFLP21689018
MSX1c.68C>G; p.A34GGWAS; direct sequencing21740177
MSX1rs12532-ATDT20635363
MSX1c.1170G>AGenotyping; sequencing; TDT17326252
MSX1c.101C>G; p.A34GGenotyping16868654
MSX1c.799G>T;p.G267CGenotyping16868654
MSX1c.832C>T; p.P278SGenotyping16868654
MSX1c.440C>A; p.P147QDirect sequencing; TDT15354328
MSX1p.G98EDirect sequencing; TDT15354328
MSX1c.101C>G; p.A34GGenotyping; direct sequencing21866112
MSX1c.330C>T; p.G110GGenotyping; direct sequencing21866112
MSX1c.440C>A; p.P147QGenotyping; direct sequencing21866112
MSX1c.109A>C; p.M37LGenotyping; direct sequencing21866112
MSX1c.800G>C; p.G267AGenotyping; direct sequencing21866112
MSX1c.768C>T; p.Gly110Gly (X1.3 )Genotyping; sequencing; TDT9683588
MSX1rs34246903A>CGWAS28232668
MSX1rs1907989G>AGWAS28232668
MSX1rs6446693C>TGenotyping21462296
MSX1rs868257C>GGenotyping21462296
MSX1rs2034461G>AGenotyping21462296
MSX1rs11726039T>CGenotyping20572854
MSX1rs868257C>GGenotyping20572854
MSX1rs6446693C>TGenotyping20572854
MSX1rs1907998A>GGenotyping20572854
MSX1rs6832405G>TGenotyping20572854
MSX1rs34165410; c.348C>T; p.G111GSequencing; SSCP; PCR-RFLP29738289
MSX1rs3775261*AGenotyping26602496

Other genetic variants/mutations

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA bindingIDA
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA bindingIBA
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA bindingIMP
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificIDA
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificIBA
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specificIDA
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specificIMP
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specificIDA
GO:0002039 p53 bindingISO
GO:0005515 protein bindingIPI
GO:0035326 cis-regulatory region bindingIDA
GO:0043565 sequence-specific DNA bindingIDA

GO:Biological Process

GO ID GO Term Evidence
GO:0000122 negative regulation of transcription by RNA polymerase IIIDA
GO:0000122 negative regulation of transcription by RNA polymerase IIIGI
GO:0000902 cell morphogenesisISO
GO:0001701 in utero embryonic developmentIMP
GO:0001837 epithelial to mesenchymal transitionIMP
GO:0003007 heart morphogenesisIGI
GO:0003198 epithelial to mesenchymal transition involved in endocardial cushion formationIGI
GO:0007507 heart developmentIGI
GO:0007517 muscle organ developmentIPI
GO:0008285 negative regulation of cell population proliferationIGI
GO:0009952 anterior/posterior pattern specificationIGI
GO:0010463 mesenchymal cell proliferationIMP
GO:0021983 pituitary gland developmentIEA
GO:0023019 signal transduction involved in regulation of gene expressionIGI
GO:0030308 negative regulation of cell growthISO
GO:0030326 embryonic limb morphogenesisIGI
GO:0030509 BMP signaling pathwayIGI
GO:0030509 BMP signaling pathwayIDA
GO:0030509 BMP signaling pathwayISO
GO:0030513 positive regulation of BMP signaling pathwayIGI
GO:0030900 forebrain developmentIMP
GO:0030901 midbrain developmentIMP
GO:0034504 protein localization to nucleusISO
GO:0035115 embryonic forelimb morphogenesisIGI
GO:0035116 embryonic hindlimb morphogenesisIGI
GO:0035880 embryonic nail plate morphogenesisISO
GO:0035880 embryonic nail plate morphogenesisIMP
GO:0035880 embryonic nail plate morphogenesisIGI
GO:0042474 middle ear morphogenesisIMP
GO:0042475 odontogenesis of dentin-containing toothISO
GO:0042475 odontogenesis of dentin-containing toothIMP
GO:0042476 odontogenesisIMP
GO:0042476 odontogenesisIGI
GO:0042481 regulation of odontogenesisIGI
GO:0042733 embryonic digit morphogenesisIGI
GO:0043066 negative regulation of apoptotic processIGI
GO:0043392 negative regulation of DNA bindingIDA
GO:0045892 negative regulation of transcription, DNA-templatedIDA
GO:0045944 positive regulation of transcription by RNA polymerase IIIGI
GO:0045944 positive regulation of transcription by RNA polymerase IIIMP
GO:0048598 embryonic morphogenesisIBA
GO:0048863 stem cell differentiationIGI
GO:0050821 protein stabilizationISO
GO:0051154 negative regulation of striated muscle cell differentiationIDA
GO:0051154 negative regulation of striated muscle cell differentiationIGI
GO:0051216 cartilage developmentISO
GO:0060021 roof of mouth developmentIMP
GO:0060325 face morphogenesisISO
GO:0060325 face morphogenesisIMP
GO:0060325 face morphogenesisIGI
GO:0060349 bone morphogenesisIMP
GO:0060349 bone morphogenesisIGI
GO:0060536 cartilage morphogenesisIMP
GO:0061180 mammary gland epithelium developmentIGI
GO:0061312 BMP signaling pathway involved in heart developmentIGI
GO:0071316 cellular response to nicotineIEA
GO:0090427 activation of meiosisIGI
GO:1902255 positive regulation of intrinsic apoptotic signaling pathway by p53 class mediatorISO
GO:2000678 negative regulation of transcription regulatory region DNA bindingIGI
GO:2001055 positive regulation of mesenchymal cell apoptotic processIGI

GO:Cellular Component

GO ID GO Term Evidence
GO:0005634 nucleusISO
GO:0005634 nucleusIGI
GO:0005634 nucleusIBA
GO:0005654 nucleoplasmISO

Reactome Pathway

Reactome ID Reactome Term Evidence

Functional annotations

Keywords

Keyword ID Keyword Term
KW-0002 3D-structure
KW-0217 Developmental protein
KW-0238 DNA-binding
KW-0371 Homeobox
KW-1017 Isopeptide bond
KW-0539 Nucleus
KW-1185 Reference proteome
KW-0678 Repressor
KW-0804 Transcription
KW-0805 Transcription regulation
KW-0832 Ubl conjugation

Interpro

InterPro ID InterPro Term
IPR009057 Homeobox-like_sf
IPR017970 Homeobox_CS
IPR001356 Homeobox_dom
IPR020479 Homeobox_metazoa

PROSITE

PROSITE ID PROSITE Term
PS00027 HOMEOBOX_1
PS50071 HOMEOBOX_2

Pfam

Pfam ID Pfam Term
PF00046 Homeodomain

Protein-protein interaction

Protein-miRNA interaction