Human Gene MSH4 (ENST00000263187.4) from GENCODE V44
  Description: Homo sapiens mutS homolog 4 (MSH4), mRNA. (from RefSeq NM_002440)
RefSeq Summary (NM_002440): This gene encodes a member of the DNA mismatch repair mutS family. This member is a meiosis-specific protein that is not involved in DNA mismatch correction, but is required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis I. This protein and MSH5 form a heterodimer which binds uniquely to a Holliday Junction and its developmental progenitor, thus provoking ADP-ATP exchange, and stabilizing the interaction between parental chromosomes during meiosis double-stranded break repair. [provided by RefSeq, Aug 2011].
Gencode Transcript: ENST00000263187.4
Gencode Gene: ENSG00000057468.7
Transcript (Including UTRs)
   Position: hg38 chr1:75,796,882-75,913,242 Size: 116,361 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg38 chr1:75,796,986-75,912,887 Size: 115,902 Coding Exon Count: 20 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:75,796,882-75,913,242)mRNA (may differ from genome)Protein (936 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MSH4_HUMAN
DESCRIPTION: RecName: Full=MutS protein homolog 4; Short=hMSH4;
FUNCTION: Involved in meiotic recombination. Required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis.
SUBUNIT: Heterooligomer of MSH4 and MSH5.
TISSUE SPECIFICITY: Testis and ovary specific.
SIMILARITY: Belongs to the DNA mismatch repair MutS family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/msh4/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: MSH4
Diseases sorted by gene-association score: schwannomatosis (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.91 RPKM in Testis
Total median expression: 13.27 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.40104-0.379 Picture PostScript Text
3' UTR -45.10355-0.127 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
IPR000432 - DNA_mismatch_repair_MutS_C
IPR007861 - DNA_mismatch_repair_MutS_clamp
IPR007860 - DNA_mismatch_repair_MutS_connt
IPR007696 - DNA_mismatch_repair_MutS_core

Pfam Domains:
PF05188 - MutS domain II
PF05192 - MutS domain III
PF05190 - MutS family domain IV
PF00488 - MutS domain V

ModBase Predicted Comparative 3D Structure on O15457
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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 BrowserNo orthologGenome BrowserGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsembl WormBaseSGD
Protein SequenceProtein SequenceProtein Sequence Protein SequenceProtein Sequence
AlignmentAlignmentAlignment AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 DNA-dependent ATPase activity
GO:0030983 mismatched DNA binding
GO:0003684 damaged DNA binding

Biological Process:
GO:0001541 ovarian follicle development
GO:0006298 mismatch repair
GO:0007129 synapsis
GO:0007131 reciprocal meiotic recombination
GO:0007283 spermatogenesis
GO:0007292 female gamete generation
GO:0051026 chiasma assembly
GO:0051321 meiotic cell cycle

Cellular Component:
GO:0000793 condensed chromosome
GO:0000794 condensed nuclear chromosome
GO:0000795 synaptonemal complex
GO:0005634 nucleus
GO:0005713 recombination nodule
GO:0032300 mismatch repair complex


-  Descriptions from all associated GenBank mRNAs
  BC033030 - Homo sapiens mutS homolog 4 (E. coli), mRNA (cDNA clone MGC:33143 IMAGE:5266997), complete cds.
U89293 - Homo sapiens MSH4 (HMSH4) mRNA, complete cds.
AF104243 - Homo sapiens meiosis-specific MutS homolog (MSH4) mRNA, complete cds.
KJ897201 - Synthetic construct Homo sapiens clone ccsbBroadEn_06595 MSH4 gene, encodes complete protein.
AB528458 - Synthetic construct DNA, clone: pF1KB8501, Homo sapiens MSH4 gene for mutS homolog 4, without stop codon, in Flexi system.
DQ894445 - Synthetic construct Homo sapiens clone IMAGE:100008905; FLH170499.01L; RZPDo839G0197D mutS homolog 4 (E. coli) (MSH4) gene, encodes complete protein.
DQ891259 - Synthetic construct clone IMAGE:100003889; FLH170503.01X; RZPDo839G0198D mutS homolog 4 (E. coli) (MSH4) gene, encodes complete protein.
AB209023 - Homo sapiens mRNA for Rab geranylgeranyltransferase, beta subunit variant protein.
JD102295 - Sequence 83319 from Patent EP1572962.
JD487196 - Sequence 468220 from Patent EP1572962.
JD344910 - Sequence 325934 from Patent EP1572962.
CU689598 - Synthetic construct Homo sapiens gateway clone IMAGE:100017853 5' read MSH4 mRNA.
AJ844635 - Homo sapiens partial mRNA for mutS homolog 4 (MSH4 gene).
JD436039 - Sequence 417063 from Patent EP1572962.
JD113165 - Sequence 94189 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O15457 (Reactome details) participates in the following event(s):

R-HSA-912446 Meiotic recombination
R-HSA-1500620 Meiosis
R-HSA-1474165 Reproduction
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000263187.1, ENST00000263187.2, ENST00000263187.3, MSH4_HUMAN, NM_002440, O15457, Q5T4U6, Q8NEB3, Q9UNP8, uc001dhd.1, uc001dhd.2, uc001dhd.3, uc001dhd.4
UCSC ID: ENST00000263187.4
RefSeq Accession: NM_002440
Protein: O15457 (aka MSH4_HUMAN)
CCDS: CCDS670.1

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