Atlas of Genetics and Cytogenetics in Oncology and Haematology


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MSX1 (msh homeobox 1)

Identity

Other namesECTD3
HOX7
HYD1
STHAG1
HGNC (Hugo) MSX1
LocusID (NCBI) 4487
Atlas_Id 51797
Location 4p16.2  [Link to chromosome band 4p16]
Location_base_pair Starts at 4861392 and ends at 4865660 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
MSX1 (4p16.2) / MSX1 (4p16.2)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)MSX1   7391
Cards
Entrez_Gene (NCBI)MSX1  4487  msh homeobox 1
AliasesECTD3; HOX7; HYD1; STHAG1
GeneCards (Weizmann)MSX1
Ensembl hg19 (Hinxton)ENSG00000163132 [Gene_View]  chr4:4861392-4865660 [Contig_View]  MSX1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000163132 [Gene_View]  chr4:4861392-4865660 [Contig_View]  MSX1 [Vega]
ICGC DataPortalENSG00000163132
TCGA cBioPortalMSX1
AceView (NCBI)MSX1
Genatlas (Paris)MSX1
WikiGenes4487
SOURCE (Princeton)MSX1
Genomic and cartography
GoldenPath hg19 (UCSC)MSX1  -     chr4:4861392-4865660 +  4p16.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)MSX1  -     4p16.2   [Description]    (hg38-Dec_2013)
EnsemblMSX1 - 4p16.2 [CytoView hg19]  MSX1 - 4p16.2 [CytoView hg38]
Mapping of homologs : NCBIMSX1 [Mapview hg19]  MSX1 [Mapview hg38]
OMIM106600   142983   189500   608874   
Gene and transcription
Genbank (Entrez)AK290636 AU117561 BC021285 BC067353 BU624994
RefSeq transcript (Entrez)NM_002448
RefSeq genomic (Entrez)NC_000004 NC_018915 NG_008121 NT_006051 NW_004929314
Consensus coding sequences : CCDS (NCBI)MSX1
Cluster EST : UnigeneHs.424414 [ NCBI ]
CGAP (NCI)Hs.424414
Alternative Splicing GalleryENSG00000163132
Gene ExpressionMSX1 [ NCBI-GEO ]   MSX1 [ EBI - ARRAY_EXPRESS ]   MSX1 [ SEEK ]   MSX1 [ MEM ]
Gene Expression Viewer (FireBrowse)MSX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4487
GTEX Portal (Tissue expression)MSX1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP28360 (Uniprot)
NextProtP28360  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP28360
Splice isoforms : SwissVarP28360 (Swissvar)
PhosPhoSitePlusP28360
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox_CS    Homeobox_dom    Homeobox_metazoa    Homeodomain-like   
Domain families : Pfam (Sanger)Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
DMDM Disease mutations4487
Blocks (Seattle)MSX1
SuperfamilyP28360
Human Protein AtlasENSG00000163132
Peptide AtlasP28360
HPRD00866
IPIIPI01021380   IPI00002939   
Protein Interaction databases
DIP (DOE-UCLA)P28360
IntAct (EBI)P28360
FunCoupENSG00000163132
BioGRIDMSX1
STRING (EMBL)MSX1
ZODIACMSX1
Ontologies - Pathways
QuickGOP28360
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  cell morphogenesis  RNA polymerase II regulatory region sequence-specific DNA binding  transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding  in utero embryonic development  p53 binding  epithelial to mesenchymal transition involved in endocardial cushion formation  nucleus  nucleoplasm  cytoplasm  transcription from RNA polymerase II promoter  muscle organ development  negative regulation of cell proliferation  anterior/posterior pattern specification  mesenchymal cell proliferation  signal transduction involved in regulation of gene expression  negative regulation of cell growth  positive regulation of BMP signaling pathway  forebrain development  midbrain development  protein localization to nucleus  embryonic forelimb morphogenesis  embryonic hindlimb morphogenesis  embryonic nail plate morphogenesis  middle ear morphogenesis  odontogenesis of dentin-containing tooth  regulation of odontogenesis  negative regulation of apoptotic process  positive regulation of DNA damage response, signal transduction by p53 class mediator  positive regulation of transcription from RNA polymerase II promoter  protein stabilization  negative regulation of striated muscle cell differentiation  palate development  face morphogenesis  bone morphogenesis  cartilage morphogenesis  mammary gland epithelium development  BMP signaling pathway involved in heart development  activation of meiosis  positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator  negative regulation of transcription regulatory region DNA binding  positive regulation of mesenchymal cell apoptotic process  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  cell morphogenesis  RNA polymerase II regulatory region sequence-specific DNA binding  transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding  in utero embryonic development  p53 binding  epithelial to mesenchymal transition involved in endocardial cushion formation  nucleus  nucleoplasm  cytoplasm  transcription from RNA polymerase II promoter  muscle organ development  negative regulation of cell proliferation  anterior/posterior pattern specification  mesenchymal cell proliferation  signal transduction involved in regulation of gene expression  negative regulation of cell growth  positive regulation of BMP signaling pathway  forebrain development  midbrain development  protein localization to nucleus  embryonic forelimb morphogenesis  embryonic hindlimb morphogenesis  embryonic nail plate morphogenesis  middle ear morphogenesis  odontogenesis of dentin-containing tooth  regulation of odontogenesis  negative regulation of apoptotic process  positive regulation of DNA damage response, signal transduction by p53 class mediator  positive regulation of transcription from RNA polymerase II promoter  protein stabilization  negative regulation of striated muscle cell differentiation  palate development  face morphogenesis  bone morphogenesis  cartilage morphogenesis  mammary gland epithelium development  BMP signaling pathway involved in heart development  activation of meiosis  positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator  negative regulation of transcription regulatory region DNA binding  positive regulation of mesenchymal cell apoptotic process  
Pathways : KEGGHTLV-I infection   
NDEx NetworkMSX1
Atlas of Cancer Signalling NetworkMSX1
Wikipedia pathwaysMSX1
Orthology - Evolution
OrthoDB4487
GeneTree (enSembl)ENSG00000163132
Phylogenetic Trees/Animal Genes : TreeFamMSX1
Homologs : HomoloGeneMSX1
Homology/Alignments : Family Browser (UCSC)MSX1
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerMSX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)MSX1
dbVarMSX1
ClinVarMSX1
1000_GenomesMSX1 
Exome Variant ServerMSX1
ExAC (Exome Aggregation Consortium)MSX1 (select the gene name)
Genetic variants : HAPMAP4487
Genomic Variants (DGV)MSX1 [DGVbeta]
Mutations
ICGC Data PortalMSX1 
TCGA Data PortalMSX1 
Broad Tumor PortalMSX1
OASIS PortalMSX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICMSX1 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch MSX1
DgiDB (Drug Gene Interaction Database)MSX1
DoCM (Curated mutations)MSX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)MSX1 (select a term)
intoGenMSX1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)4:4861392-4865660  ENSG00000163132
CONAN: Copy Number AnalysisMSX1 
Mutations and Diseases : HGMDMSX1
OMIM106600    142983    189500    608874   
MedgenMSX1
Genetic Testing Registry MSX1
NextProtP28360 [Medical]
TSGene4487
GENETestsMSX1
Huge Navigator MSX1 [HugePedia]
snp3D : Map Gene to Disease4487
BioCentury BCIQMSX1
ClinGenMSX1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4487
Chemical/Pharm GKB GenePA31196
Clinical trialMSX1
Miscellaneous
canSAR (ICR)MSX1 (select the gene name)
Probes
Litterature
PubMed113 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineMSX1
EVEXMSX1
GoPubMedMSX1
iHOPMSX1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 19 19:03:17 CEST 2016

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