Human Gene MSX1 (ENST00000382723.5) from GENCODE V44
  Description: Homo sapiens msh homeobox 1 (MSX1), mRNA. (from RefSeq NM_002448)
RefSeq Summary (NM_002448): 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].
Gencode Transcript: ENST00000382723.5
Gencode Gene: ENSG00000163132.8
Transcript (Including UTRs)
   Position: hg38 chr4:4,859,665-4,863,936 Size: 4,272 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr4:4,859,900-4,863,143 Size: 3,244 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:4,859,665-4,863,936)mRNA (may differ from genome)Protein (303 aa)
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GeneCardsHGNCHPRDLynxMalacardsMGI
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-  Comments and Description Text from UniProtKB
  ID: MSX1_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein MSX-1; AltName: Full=Homeobox protein Hox-7; AltName: Full=Msh homeobox 1-like protein;
FUNCTION: Acts as a transcriptional repressor. May play a role in limb-pattern formation. Acts in cranofacial development and specifically in odontogenesis. Expression in the developing nail bed mesenchyme is important for nail plate thickness and integrity.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in the developing nail bed mesenchyme.
PTM: Sumoylated by PIAS1, desumoylated by SENP1 (By similarity).
DISEASE: Defects in MSX1 are the cause of tooth agenesis selective type 1 (STHAG1) [MIM:106600]. A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). Tooth agenesis selective type 1 can be associated with orofacial cleft in some patients.
DISEASE: Note=MSX1 is deleted in some patients with Wolf- Hirschhorn syndrome (WHS). WHS results from sub-telomeric deletions in the short arm of chromosome 4.
DISEASE: Defects in MSX1 are the cause of Witkop syndrome (WITS) [MIM:189500]. WITS is a form of ectodermal dyslasia also called tooth-and-nail syndrome or dysplasia of nails with hypodontia. Ectodermal dysplasias (EDs) constitute a heterogeneous group of developmental disorders affecting tissues of ectodermal origin. EDs are characterized by abnormal development of two or more ectodermal structures such as hair, teeth, nails and sweat glands, with or without any additional clinical sign. Each combination of clinical features represents a different type of ectodermal dysplasia. Witkop syndrome is characterized by abnormalities largely limited largely to teeth (some of which are missing) and nails (which are poorly formed early in life, especially toenails). This condition is distinguished from anhidrotic ectodermal dysplasia by autosomal dominant inheritance and little involvement of hair and sweat glands. The teeth are not as severely affected.
DISEASE: Defects in MSX1 are the cause of non-syndromic orofacial cleft type 5 (OFC5) [MIM:608874]; also called non-syndromic cleft lip with or without cleft palate 5. Non-syndromic orofacial cleft is a common birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two- third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum.
SIMILARITY: Belongs to the Msh homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAH21285.4; Type=Erroneous initiation;

-  Primer design for this transcript
 

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-  MalaCards Disease Associations
  MalaCards Gene Search: MSX1
Diseases sorted by gene-association score: ectodermal dysplasia 3, witkop type* (1377), orofacial cleft 5* (1330), tooth agenesis, selective, 1, with or without orofacial cleft* (1300), tooth agenesis* (244), cleft lip (68), cleft lip/palate* (20), orofacial cleft (19), isolated cleft lip* (18), wolf-hirschhorn syndrome (16), cleft lip and alveolus* (14), cleft palate, isolated (13), anodontia (10), bamforth-lazarus syndrome (9), ellis-van creveld syndrome (7), physical disorder (5), hard palate cancer (4), ectodermal dysplasia 10b, hypohidrotic/hair/tooth type, autosomal recessive (4), agnathia-otocephaly complex (4), mouth disease (2), parkinson disease, late-onset (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 47.77 RPKM in Cervix - Endocervix
Total median expression: 247.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -138.30235-0.589 Picture PostScript Text
3' UTR -213.00793-0.269 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on P28360
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000982 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0002039 p53 binding
GO:0003677 DNA binding
GO:0035326 enhancer binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000902 cell morphogenesis
GO:0001701 in utero embryonic development
GO:0001837 epithelial to mesenchymal transition
GO:0003007 heart morphogenesis
GO:0003198 epithelial to mesenchymal transition involved in endocardial cushion formation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007507 heart development
GO:0007517 muscle organ development
GO:0008285 negative regulation of cell proliferation
GO:0009952 anterior/posterior pattern specification
GO:0010463 mesenchymal cell proliferation
GO:0021983 pituitary gland development
GO:0023019 signal transduction involved in regulation of gene expression
GO:0030308 negative regulation of cell growth
GO:0030326 embryonic limb morphogenesis
GO:0030509 BMP signaling pathway
GO:0030513 positive regulation of BMP signaling pathway
GO:0030900 forebrain development
GO:0030901 midbrain development
GO:0034504 protein localization to nucleus
GO:0035115 embryonic forelimb morphogenesis
GO:0035116 embryonic hindlimb morphogenesis
GO:0035880 embryonic nail plate morphogenesis
GO:0042474 middle ear morphogenesis
GO:0042475 odontogenesis of dentin-containing tooth
GO:0042476 odontogenesis
GO:0042481 regulation of odontogenesis
GO:0042733 embryonic digit morphogenesis
GO:0043066 negative regulation of apoptotic process
GO:0043392 negative regulation of DNA binding
GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048863 stem cell differentiation
GO:0050821 protein stabilization
GO:0051154 negative regulation of striated muscle cell differentiation
GO:0051216 cartilage development
GO:0060021 palate development
GO:0060325 face morphogenesis
GO:0060349 bone morphogenesis
GO:0060536 cartilage morphogenesis
GO:0061180 mammary gland epithelium development
GO:0061312 BMP signaling pathway involved in heart development
GO:0071316 cellular response to nicotine
GO:0090427 activation of meiosis
GO:1902255 positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
GO:2000678 negative regulation of transcription regulatory region DNA binding
GO:2001055 positive regulation of mesenchymal cell apoptotic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AK290636 - Homo sapiens cDNA FLJ75656 complete cds, highly similar to Homo sapiens msh homeo box homolog 1 (Drosophila) (MSX1), mRNA.
M97676 - Homo sapiens (region 7) homeobox protein (HOX7) mRNA, complete cds.
JD081503 - Sequence 62527 from Patent EP1572962.
BC021285 - Homo sapiens msh homeobox 1, mRNA (cDNA clone MGC:29576 IMAGE:5018103), complete cds.
JD382994 - Sequence 364018 from Patent EP1572962.
JD484934 - Sequence 465958 from Patent EP1572962.
JD216684 - Sequence 197708 from Patent EP1572962.
BC067353 - Homo sapiens msh homeobox 1, mRNA (cDNA clone MGC:78580 IMAGE:4893288), complete cds.
JD395225 - Sequence 376249 from Patent EP1572962.
JD272278 - Sequence 253302 from Patent EP1572962.
AB463898 - Synthetic construct DNA, clone: pF1KB8940, Homo sapiens MSX1 gene for msh homeobox 1, without stop codon, in Flexi system.
JD498471 - Sequence 479495 from Patent EP1572962.
JD109721 - Sequence 90745 from Patent EP1572962.
JD186089 - Sequence 167113 from Patent EP1572962.
JD528973 - Sequence 509997 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000382723.1, ENST00000382723.2, ENST00000382723.3, ENST00000382723.4, HOX7, MSX1_HUMAN, NM_002448, P28360, Q96NY4, uc003gif.1, uc003gif.2, uc003gif.3, uc003gif.4, uc003gif.5
UCSC ID: ENST00000382723.5
RefSeq Accession: NM_002448
Protein: P28360 (aka MSX1_HUMAN)
CCDS: CCDS3378.2

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.