Msh3 (mutS homolog 3) - Rat Genome Database

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Gene: Msh3 (mutS homolog 3) Rattus norvegicus
Analyze
Symbol: Msh3
Name: mutS homolog 3
RGD ID: 1563954
Description: Predicted to enable centromeric DNA binding activity; damaged DNA binding activity; and enzyme binding activity. Predicted to contribute to dinucleotide repeat insertion binding activity; single guanine insertion binding activity; and single-stranded DNA binding activity. Involved in spermatogenesis. Predicted to be part of MutSbeta complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in colorectal carcinoma; endometrial cancer; endometrial carcinoma; familial adenomatous polyposis 4; and lung non-small cell carcinoma. Orthologous to human MSH3 (mutS homolog 3); PARTICIPATES IN mismatch repair pathway; colorectal cancer pathway; INTERACTS WITH (+)-schisandrin B; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA mismatch repair protein Msh3; mutS homolog 3 (E. coli)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8225,179,400 - 25,320,857 (-)NCBIGRCr8
mRatBN7.2223,444,326 - 23,585,777 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx230,479,042 - 30,620,224 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0228,579,397 - 28,720,585 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0223,406,403 - 23,548,408 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0221,790,048 - 21,931,791 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl221,790,044 - 21,931,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0240,996,035 - 41,137,686 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4222,462,934 - 22,606,874 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera219,534,848 - 19,675,746 (-)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Cloning of rat MLH1 and expression analysis of MSH2, MSH3, MSH6, and MLH1 during spermatogenesis. Geeta Vani R, etal., Genomics 1999 Dec 15;62(3):460-7.
3. Mechanisms and functions of DNA mismatch repair. Li GM Cell Res. 2008 Jan;18(1):85-98.
4. Association between DNA mismatch repair gene polymorphisms and platinum-based chemotherapy toxicity in non-small cell lung cancer patients. Liu JY, etal., Chin J Cancer. 2017 Jan 16;36(1):12. doi: 10.1186/s40880-016-0175-2.
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Mutation of MSH3 in endometrial cancer and evidence for its functional role in heteroduplex repair. Risinger JI, etal., Nat Genet. 1996 Sep;14(1):102-5.
12. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
13. Mutation of hMSH3 and hMSH6 mismatch repair genes in genetically unstable human colorectal and gastric carcinomas. Yin J, etal., Hum Mutat. 1997;10(6):474-8.
Additional References at PubMed
PMID:8942985   PMID:10545954   PMID:10662804   PMID:10706084   PMID:11427529   PMID:11691815   PMID:11756455   PMID:11809883   PMID:15238604   PMID:16260499   PMID:16388310   PMID:16728433  
PMID:17715146   PMID:19946888   PMID:26300262  


Genomics

Comparative Map Data
Msh3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8225,179,400 - 25,320,857 (-)NCBIGRCr8
mRatBN7.2223,444,326 - 23,585,777 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx230,479,042 - 30,620,224 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0228,579,397 - 28,720,585 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0223,406,403 - 23,548,408 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0221,790,048 - 21,931,791 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl221,790,044 - 21,931,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0240,996,035 - 41,137,686 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4222,462,934 - 22,606,874 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera219,534,848 - 19,675,746 (-)NCBICelera
Cytogenetic Map2q12NCBI
MSH3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38580,654,652 - 80,876,815 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl580,654,652 - 80,876,815 (+)EnsemblGRCh38hg38GRCh38
GRCh37579,950,471 - 80,172,634 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36579,986,050 - 80,208,390 (+)NCBINCBI36Build 36hg18NCBI36
Build 34579,986,294 - 80,208,389NCBI
Celera575,854,379 - 76,076,910 (+)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef575,159,370 - 75,381,401 (+)NCBIHuRef
CHM1_1579,383,713 - 79,605,325 (+)NCBICHM1_1
T2T-CHM13v2.0581,139,552 - 81,361,456 (+)NCBIT2T-CHM13v2.0
Msh3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391392,348,387 - 92,491,515 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1392,348,380 - 92,491,511 (-)EnsemblGRCm39 Ensembl
GRCm381392,211,878 - 92,355,004 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1392,211,872 - 92,355,003 (-)EnsemblGRCm38mm10GRCm38
MGSCv371392,981,836 - 93,124,958 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361393,312,634 - 93,455,756 (-)NCBIMGSCv36mm8
Celera1395,828,509 - 95,961,232 (-)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1347.63NCBI
Msh3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541829,150,085 - 29,274,437 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541829,149,595 - 29,274,067 (-)NCBIChiLan1.0ChiLan1.0
MSH3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2434,432,400 - 34,653,426 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1532,582,453 - 32,806,981 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0534,408,469 - 34,663,483 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1534,719,261 - 34,938,521 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl534,719,322 - 34,938,469 (-)Ensemblpanpan1.1panPan2
MSH3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1326,335,788 - 26,520,633 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl326,336,403 - 26,518,521 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha327,571,200 - 27,762,336 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0326,250,075 - 26,441,642 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl326,250,084 - 26,441,647 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1326,190,404 - 26,381,864 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0326,171,404 - 26,356,535 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0326,451,047 - 26,636,178 (-)NCBIUU_Cfam_GSD_1.0
Msh3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213182,351,062 - 182,542,651 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646983,285 - 273,561 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493646982,967 - 275,772 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSH3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl289,250,003 - 89,453,936 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1289,255,647 - 89,456,102 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2291,102,138 - 91,281,732 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MSH3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1474,811,181 - 75,032,067 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl474,811,198 - 75,032,005 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604923,674,149 - 23,899,258 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msh3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247431,461,077 - 1,581,180 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247431,461,952 - 1,581,524 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Msh3
1263 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:56
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000018449
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22238462767384627Rat
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)218960362228801039Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat

Markers in Region
UniSTS:498245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2223,582,236 - 23,582,422 (+)MAPPERmRatBN7.2
Rnor_6.0221,928,127 - 21,928,312NCBIRnor6.0
Rnor_5.0241,134,024 - 41,134,209UniSTSRnor5.0
RGSC_v3.4222,603,334 - 22,603,519UniSTSRGSC3.4
Celera219,672,206 - 19,672,391UniSTS
Cytogenetic Map2q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000018449   ⟹   ENSRNOP00000018449
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl221,790,044 - 21,931,720 (-)Ensembl
RefSeq Acc Id: NM_001191957   ⟹   NP_001178886
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,857 (-)NCBI
mRatBN7.2223,444,326 - 23,585,777 (-)NCBI
Rnor_6.0221,790,048 - 21,931,667 (-)NCBI
Rnor_5.0240,996,035 - 41,137,686 (-)NCBI
Celera219,534,848 - 19,675,746 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063282325   ⟹   XP_063138395
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282326   ⟹   XP_063138396
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282327   ⟹   XP_063138397
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282328   ⟹   XP_063138398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282329   ⟹   XP_063138399
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,320,647 (-)NCBI
RefSeq Acc Id: XM_063282330   ⟹   XP_063138400
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,207,780 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282331   ⟹   XP_063138401
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,224,231 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282332   ⟹   XP_063138402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,224,129 - 25,320,857 (-)NCBI
RefSeq Acc Id: XM_063282333   ⟹   XP_063138403
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,304,603 (-)NCBI
RefSeq Acc Id: XM_063282335   ⟹   XP_063138405
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8225,179,400 - 25,308,066 (-)NCBI
RefSeq Acc Id: NP_001178886   ⟸   NM_001191957
- Sequence:
Ensembl Acc Id: ENSRNOP00000018449   ⟸   ENSRNOT00000018449
RefSeq Acc Id: XP_063138398   ⟸   XM_063282328
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063138397   ⟸   XM_063282327
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063138396   ⟸   XM_063282326
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063138395   ⟸   XM_063282325
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063138399   ⟸   XM_063282329
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063138405   ⟸   XM_063282335
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063138403   ⟸   XM_063282333
- Peptide Label: isoform X9
RefSeq Acc Id: XP_063138400   ⟸   XM_063282330
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063138402   ⟸   XM_063282332
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063138401   ⟸   XM_063282331
- Peptide Label: isoform X7
Protein Domains
DNA mismatch repair proteins mutS family

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LQM8-F1-model_v2 AlphaFold F1LQM8 1-1104 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691056
Promoter ID:EPDNEW_R1581
Type:single initiation site
Name:Msh3_1
Description:mutS homolog 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0221,931,715 - 21,931,775EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563954 AgrOrtholog
BioCyc Gene G2FUF-54869 BioCyc
Ensembl Genes ENSRNOG00000013673 Ensembl
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7302809 IMAGE-MGC_LOAD
InterPro DNA_mismatch_repair_MutS_C UniProtKB/TrEMBL
  MutS_family UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
MGC_CLONE MGC:109173 IMAGE-MGC_LOAD
NCBI Gene 499505 ENTREZGENE
PANTHER DNA MISMATCH REPAIR PROTEIN MSH3 UniProtKB/TrEMBL
  PTHR11361 UniProtKB/TrEMBL
Pfam MutS_V UniProtKB/TrEMBL
PhenoGen Msh3 PhenoGen
PROSITE DNA_MISMATCH_REPAIR_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013673 RatGTEx
SMART MUTSac UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt Q5BJY1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Msh3  mutS homolog 3  Msh3  mutS homolog 3 (E. coli)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Msh3  mutS homolog 3 (E. coli)      Symbol and Name status set to provisional 70820 PROVISIONAL