MSH4 (mutS homolog 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: MSH4 (mutS homolog 4) Chlorocebus sabaeus
Analyze
Symbol: MSH4
Name: mutS homolog 4
RGD ID: 18785188
Description: ENCODES a protein that exhibits ATP binding (inferred); ATP-dependent DNA damage sensor activity (inferred); DNA binding (inferred); INVOLVED IN female gamete generation (ortholog); homologous chromosome pairing at meiosis (ortholog); meiotic cell cycle (ortholog); ASSOCIATED WITH genetic disease (ortholog); hereditary breast ovarian cancer syndrome (ortholog); medium chain acyl-CoA dehydrogenase deficiency (ortholog); FOUND IN chromosome (inferred); condensed chromosome (inferred); condensed nuclear chromosome (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: mutS protein homolog 4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12057,283,723 - 57,397,871 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2057,284,575 - 57,396,797 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603360,112,696 - 60,228,261 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
MSH4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12057,283,723 - 57,397,871 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2057,284,575 - 57,396,797 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603360,112,696 - 60,228,261 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
MSH4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38175,796,882 - 75,913,242 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl175,796,882 - 75,913,242 (+)EnsemblGRCh38hg38GRCh38
GRCh37176,262,567 - 76,378,927 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36176,035,218 - 76,151,511 (+)NCBINCBI36Build 36hg18NCBI36
Build 34175,974,650 - 76,090,944NCBI
Celera174,502,536 - 74,619,128 (+)NCBICelera
Cytogenetic Map1p31.1NCBI
HuRef174,392,386 - 74,509,072 (+)NCBIHuRef
CHM1_1176,377,843 - 76,494,293 (+)NCBICHM1_1
T2T-CHM13v2.0175,633,544 - 75,751,219 (+)NCBIT2T-CHM13v2.0
Msh4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393153,562,783 - 153,611,495 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3153,562,786 - 153,611,775 (-)EnsemblGRCm39 Ensembl
GRCm383153,857,141 - 153,906,138 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3153,857,149 - 153,906,138 (-)EnsemblGRCm38mm10GRCm38
MGSCv373153,520,111 - 153,569,102 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363153,794,533 - 153,843,524 (-)NCBIMGSCv36mm8
Celera3160,320,812 - 160,369,813 (-)NCBICelera
Cytogenetic Map3H3NCBI
cM Map378.7NCBI
Msh4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82245,445,118 - 245,504,493 (-)NCBIGRCr8
mRatBN7.22242,785,392 - 242,844,609 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2242,792,661 - 242,843,487 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2250,616,144 - 250,666,160 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02248,509,973 - 248,559,983 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02243,408,533 - 243,458,548 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02260,057,708 - 260,108,897 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2260,057,855 - 260,108,897 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02278,716,760 - 278,773,060 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42251,801,090 - 251,851,133 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12251,815,109 - 251,866,523 (-)NCBI
Celera2234,728,057 - 234,775,779 (-)NCBICelera
Cytogenetic Map2q45NCBI
Msh4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542317,093,573 - 17,154,910 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542317,093,573 - 17,154,910 (-)NCBIChiLan1.0ChiLan1.0
MSH4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21150,974,838 - 151,096,427 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11150,135,382 - 150,256,962 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0175,011,947 - 75,130,036 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1176,983,852 - 77,099,896 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl176,983,852 - 77,099,896 (+)Ensemblpanpan1.1panPan2
MSH4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1670,745,777 - 70,822,507 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl670,746,634 - 70,823,004 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha673,406,292 - 73,487,796 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0671,334,444 - 71,416,137 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1670,834,791 - 70,912,065 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0670,780,166 - 70,856,995 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0671,269,093 - 71,350,596 (-)NCBIUU_Cfam_GSD_1.0
Msh4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505887,311,249 - 87,388,210 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365712,822,058 - 2,898,562 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365712,827,283 - 2,898,562 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
Msh4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474221,098,101 - 21,167,398 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474221,098,102 - 21,167,472 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system hemolymphoid system nervous system
High
Medium
Low 2 13 18
Below cutoff 33 7 42

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_007978253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACDXN010000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCSAT00000017141   ⟹   ENSCSAP00000016626
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2057,284,575 - 57,396,797 (-)Ensembl
RefSeq Acc Id: XM_007978253   ⟹   XP_007976444
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.12057,283,723 - 57,397,871 (-)NCBI
Vero_WHO_p1.0NW_02366603360,112,696 - 60,228,261 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_007976444 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000016626.1
Reference Protein Sequences
RefSeq Acc Id: XP_007976444   ⟸   XM_007978253
RefSeq Acc Id: ENSCSAP00000016626   ⟸   ENSCSAT00000017141


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000001392 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000017141.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1420.10 UniProtKB/TrEMBL
  3.30.420.110 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro DNA_mismatch_repair_MutS_C UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_clamp UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_core UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_sf UniProtKB/TrEMBL
  DNA_mmatch_repair_MutS_con_dom UniProtKB/TrEMBL
  MutS_con_dom_sf UniProtKB/TrEMBL
  MutS_family UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
KEGG Report csab:103224588 UniProtKB/TrEMBL
NCBI Gene MSH4 ENTREZGENE
PANTHER MUTS PROTEIN HOMOLOG 4 UniProtKB/TrEMBL
  PTHR11361 UniProtKB/TrEMBL
Pfam MutS_II UniProtKB/TrEMBL
  MutS_III UniProtKB/TrEMBL
  MutS_IV UniProtKB/TrEMBL
  MutS_V UniProtKB/TrEMBL
PROSITE DNA_MISMATCH_REPAIR_2 UniProtKB/TrEMBL
SMART MUTSac UniProtKB/TrEMBL
  MUTSd UniProtKB/TrEMBL
Superfamily-SCOP SSF48334 UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A0D9S6Y7_CHLSB UniProtKB/TrEMBL