Msh2 (mutS homolog 2) - Rat Genome Database

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Gene: Msh2 (mutS homolog 2) Rattus norvegicus
Analyze
Symbol: Msh2
Name: mutS homolog 2
RGD ID: 620786
Description: Predicted to enable several functions, including ATP hydrolysis activity; DNA binding activity; and protein C-terminus binding activity. Predicted to contribute to several functions, including DNA binding activity; MutLalpha complex binding activity; and adenyl ribonucleotide binding activity. Involved in several processes, including response to amino acid; response to xenobiotic stimulus; and spermatogenesis. Located in nucleus. Biomarker of colitis and visual epilepsy. Human ortholog(s) of this gene implicated in several diseases, including Lynch syndrome (multiple); gastrointestinal system cancer (multiple); lung cancer (multiple); mismatch repair cancer syndrome; and transitional cell carcinoma. Orthologous to human MSH2 (mutS homolog 2); PARTICIPATES IN altered mismatch repair pathway; colorectal cancer pathway; mismatch repair pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA mismatch repair protein Msh2; mismatch repair protein; mutS homolog 2 (E. coli); mutS protein homolog 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.266,813,793 - 6,872,960 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl66,813,795 - 6,872,938 (-)Ensembl
Rnor_6.0611,215,951 - 11,274,916 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl611,215,963 - 11,274,932 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0621,198,374 - 21,256,838 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4611,199,906 - 11,258,350 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1611,199,905 - 11,258,350 (+)NCBI
Celera66,571,260 - 6,630,220 (-)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
ascending colon cancer  (ISO)
bile duct cancer  (ISO)
breast cancer  (ISO)
breast carcinoma  (ISO)
cervix uteri carcinoma in situ  (ISO)
colitis  (IEP)
colon cancer  (ISO)
colon carcinoma  (ISO)
Colon Diverticulum  (ISO)
Colonic Polyps  (ISO)
colorectal adenocarcinoma  (ISO)
colorectal cancer  (ISO)
Colorectal Neoplasms  (ISO)
endometrial carcinoma  (ISO)
Endometrial Neoplasms  (ISO)
esophagus squamous cell carcinoma  (ISO)
Germ Cell and Embryonal Neoplasms  (ISO)
glioblastoma  (ISO)
hepatoblastoma  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
Huntington's disease  (ISO)
Hydatidiform Mole  (ISO)
Hydatidiform Mole, Invasive  (ISO)
laryngeal squamous cell carcinoma  (ISO)
lung adenocarcinoma  (ISO)
lung cancer  (ISO)
lung non-small cell carcinoma  (ISO)
Lymphatic Metastasis  (ISO)
Lynch syndrome  (ISO)
Lynch syndrome 1  (ISO)
mismatch repair cancer syndrome  (ISO)
Mismatch Repair Cancer Syndrome 1  (ISO)
Mismatch Repair Cancer Syndrome 2  (ISO)
Muir-Torre syndrome  (ISO)
Neoplasm Metastasis  (ISO)
osteosarcoma  (ISO)
ovarian cancer  (ISO)
ovarian cyst  (ISO)
Ovarian Neoplasms  (ISO)
papillary renal cell carcinoma  (ISO)
Pitt-Hopkins-like syndrome 2  (ISO)
prostate cancer  (ISO)
renal cell carcinoma  (ISO)
rhabdomyosarcoma  (ISO)
sarcoma  (ISO)
sigmoid colon cancer  (ISO)
sigmoid neoplasm  (ISO)
transitional cell carcinoma  (ISO)
urinary bladder cancer  (ISO)
Urogenital Neoplasms  (ISO)
Uterine Cervical Neoplasms  (ISO)
visual epilepsy  (IEP)
Vulvar Neoplasms  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(-)-quinic acid  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arecoline  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP)
carbon nanotube  (ISO)
carboplatin  (EXP)
carmustine  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dichromium trioxide  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
Dimethyl phthalate  (EXP)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
floxuridine  (ISO)
folic acid  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
imiquimod  (ISO)
indirubin  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
Lasiocarpine  (ISO)
lead diacetate  (ISO)
lycopene  (ISO)
mechlorethamine  (ISO)
menadione  (ISO)
methoxychlor  (EXP)
methylarsonic acid  (EXP)
monocrotaline  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
olaparib  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
paracetamol  (ISO)
pergolide  (ISO)
phenobarbital  (ISO)
PhIP  (EXP,ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
pyrimidines  (ISO)
quercetin  (EXP,ISO)
resveratrol  (ISO)
riddelliine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
sterigmatocystin  (ISO)
succimer  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
tioguanine  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triptonide  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
B cell differentiation  (IEA,ISO)
B cell mediated immunity  (ISO)
cellular response to DNA damage stimulus  (ISO)
determination of adult lifespan  (IEA,ISO)
DNA repair  (ISO)
double-strand break repair  (IEA,ISO)
germ cell development  (IEA,ISO)
in utero embryonic development  (IEA,ISO)
intrinsic apoptotic signaling pathway in response to DNA damage  (ISO)
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (IEA,ISO)
isotype switching  (IEA,ISO)
maintenance of DNA repeat elements  (IEA,ISO)
male gonad development  (IEA,ISO)
mismatch repair  (IBA,IEA,ISO)
mitotic intra-S DNA damage checkpoint signaling  (IEA,ISO)
mitotic recombination  (IBA)
negative regulation of DNA recombination  (IEA,ISO)
negative regulation of neuron apoptotic process  (IEA,ISO)
oxidative phosphorylation  (IEA,ISO)
positive regulation of helicase activity  (IEA,ISO)
positive regulation of isotype switching to IgA isotypes  (IEA,ISO)
positive regulation of isotype switching to IgG isotypes  (IEA,ISO)
postreplication repair  (IEA,ISO,ISS)
protein localization to chromatin  (IEA,ISO)
regulation of cell cycle  (ISO)
response to amino acid  (IEP)
response to organic cyclic compound  (IEP)
response to UV-B  (IEA,ISO)
response to X-ray  (IEA,ISO)
response to xenobiotic stimulus  (IEP)
somatic hypermutation of immunoglobulin genes  (IEA,ISO)
somatic recombination of immunoglobulin gene segments  (ISO)
somatic recombination of immunoglobulin genes involved in immune response  (IBA,ISO)
spermatogenesis  (IEP)

Cellular Component
chromosome  (IEA)
MutSalpha complex  (IBA,IEA,ISO,ISS)
MutSbeta complex  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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22. Jentzsch T, etal., Anticancer Res. 2014 Dec;34(12):6961-72.
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38. MGD data from the GO Consortium
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Additional References at PubMed
PMID:7550317   PMID:7628020   PMID:7923193   PMID:8706033   PMID:8942985   PMID:9157971   PMID:9244348   PMID:9288110   PMID:9425892   PMID:9443401   PMID:9607915   PMID:9607916  
PMID:9697842   PMID:9697843   PMID:9788596   PMID:9927509   PMID:10097137   PMID:10430621   PMID:10545954   PMID:10581038   PMID:10720738   PMID:10856833   PMID:10874005   PMID:10992298  
PMID:11046134   PMID:11427529   PMID:11429706   PMID:11429708   PMID:11555625   PMID:11756455   PMID:11801590   PMID:11809883   PMID:11828012   PMID:11890935   PMID:12034830   PMID:12414623  
PMID:12477932   PMID:12531017   PMID:12687013   PMID:12743174   PMID:14563316   PMID:14568978   PMID:14657349   PMID:14676842   PMID:14706347   PMID:14744764   PMID:15105434   PMID:15166087  
PMID:15494304   PMID:15533840   PMID:15955838   PMID:16260499   PMID:16388310   PMID:16403449   PMID:16713580   PMID:16728433   PMID:16805809   PMID:17331550   PMID:17715146   PMID:17912366  
PMID:19135898   PMID:19946888   PMID:22082260   PMID:23071719   PMID:23603115   PMID:23622243   PMID:25249609   PMID:26300262  


Genomics

Comparative Map Data
Msh2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.266,813,793 - 6,872,960 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl66,813,795 - 6,872,938 (-)Ensembl
Rnor_6.0611,215,951 - 11,274,916 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl611,215,963 - 11,274,932 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0621,198,374 - 21,256,838 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4611,199,906 - 11,258,350 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1611,199,905 - 11,258,350 (+)NCBI
Celera66,571,260 - 6,630,220 (-)NCBICelera
Cytogenetic Map6q12NCBI
MSH2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38247,403,067 - 47,634,501 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl247,403,067 - 47,663,146 (+)EnsemblGRCh38hg38GRCh38
GRCh37247,630,206 - 47,710,367 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36247,483,767 - 47,563,864 (+)NCBINCBI36hg18NCBI36
Build 34247,541,913 - 47,622,011NCBI
Celera247,469,014 - 47,549,030 (+)NCBI
Cytogenetic Map2p21-p16.3NCBI
HuRef247,367,170 - 47,445,840 (+)NCBIHuRef
CHM1_1247,560,266 - 47,640,762 (+)NCBICHM1_1
T2T-CHM13v2.0247,408,101 - 47,488,281 (+)NCBI
Msh2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391787,979,960 - 88,031,141 (+)NCBIGRCm39mm39
GRCm39 Ensembl1787,979,758 - 88,031,141 (+)Ensembl
GRCm381787,672,532 - 87,723,713 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1787,672,330 - 87,723,713 (+)EnsemblGRCm38mm10GRCm38
MGSCv371788,071,897 - 88,123,053 (+)NCBIGRCm37mm9NCBIm37
MGSCv361787,580,883 - 87,632,039 (+)NCBImm8
Celera1792,079,522 - 92,130,140 (+)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1757.87NCBI
Msh2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544114,187,805 - 14,247,698 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544114,188,315 - 14,247,608 (+)NCBIChiLan1.0ChiLan1.0
MSH2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A48,447,207 - 48,525,638 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A48,447,207 - 48,554,461 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A47,524,468 - 47,602,376 (+)NCBIMhudiblu_PPA_v0panPan3
MSH2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11049,517,448 - 49,594,001 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1049,517,369 - 49,594,210 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1049,372,675 - 49,449,176 (+)NCBI
ROS_Cfam_1.01050,390,734 - 50,467,292 (+)NCBI
ROS_Cfam_1.0 Ensembl1050,390,727 - 50,467,285 (+)Ensembl
UMICH_Zoey_3.11050,098,560 - 50,174,750 (+)NCBI
UNSW_CanFamBas_1.01050,386,621 - 50,461,201 (+)NCBI
UU_Cfam_GSD_1.01050,572,222 - 50,649,102 (+)NCBI
Msh2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629233,515,476 - 33,584,710 (-)NCBI
SpeTri2.0NW_0049365084,943,987 - 5,013,356 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSH2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl393,081,219 - 93,163,628 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1393,082,958 - 93,163,556 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2399,052,166 - 99,101,600 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2399,274,469 - 99,306,160 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSH2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11459,730,101 - 59,802,857 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1459,729,789 - 59,802,819 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604552,045,654 - 52,118,250 (+)NCBIVero_WHO_p1.0
Msh2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473828,780,614 - 28,861,704 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473828,780,596 - 28,861,523 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:55
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000021538
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.


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 40 24 19 24 74 30 36 11
Low 1 17 17 17 17 8 11 5 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021538   ⟹   ENSRNOP00000021538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl66,813,795 - 6,872,938 (-)Ensembl
Rnor_6.0 Ensembl611,215,963 - 11,274,932 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100386   ⟹   ENSRNOP00000088140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl66,813,795 - 6,869,473 (-)Ensembl
RefSeq Acc Id: NM_031058   ⟹   NP_112320
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.266,813,802 - 6,872,864 (-)NCBI
Rnor_6.0611,215,951 - 11,274,916 (-)NCBI
Rnor_5.0621,198,374 - 21,256,838 (-)NCBI
RGSC_v3.4611,199,906 - 11,258,350 (+)RGD
Celera66,571,260 - 6,630,220 (-)RGD
Sequence:
RefSeq Acc Id: XM_039112994   ⟹   XP_038968922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.266,813,793 - 6,872,960 (-)NCBI
Protein Sequences
Protein RefSeqs NP_112320 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968922 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61846 (Get FASTA)   NCBI Sequence Viewer  
  CAA63789 (Get FASTA)   NCBI Sequence Viewer  
  EDM02635 (Get FASTA)   NCBI Sequence Viewer  
  P54275 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_112320   ⟸   NM_031058
- Sequence:
RefSeq Acc Id: ENSRNOP00000021538   ⟸   ENSRNOT00000021538
RefSeq Acc Id: XP_038968922   ⟸   XM_039112994
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000088140   ⟸   ENSRNOT00000100386
Protein Domains
DNA_MISMATCH_REPAIR_2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P54275-F1-model_v2 AlphaFold P54275 1-933 view protein structure

Transcriptome

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

Promoters
RGD ID:13694395
Promoter ID:EPDNEW_R4920
Type:multiple initiation site
Name:Msh2_1
Description:mutS homolog 2
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_6.0611,274,966 - 11,275,026EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 11218740 11218741 C T snv F344/NRrrc (MCW), Buf/N (MCW)
6 11218742 11218743 G A snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW)
6 11218785 11218786 T C snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
6 11218796 11218797 G A snv FHL/EurMcwi (MCW)
6 11218839 11218840 T C snv F344/Stm (2019), FHH/EurMcwi (2019), FXLE18/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF3/Stm (2020), LEXF10A/StmMcwi (2020), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), BUF/N (2020), FHH/EurMcwi (RGD), FHL/EurMcwi (MCW), CDS, FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620786 AgrOrtholog
BioCyc Gene G2FUF-38745 BioCyc
Ensembl Genes ENSRNOG00000015796 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021538 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021538 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.420.110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.1170.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9029023 IMAGE-MGC_LOAD
InterPro DNA_mismatch_repair_Msh2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS-lik_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_clamp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA_mmatch_repair_MutS_con_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Msh2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_con_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_family UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:81709 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187365 IMAGE-MGC_LOAD
NCBI Gene 81709 ENTREZGENE
PANTHER PTHR11361 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11361:SF35 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MutS_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_IV UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_V UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB MSH2 RGD
PhenoGen Msh2 PhenoGen
PIRSF MSH2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DNA_MISMATCH_REPAIR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART MUTSac UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MUTSd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48334 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B1WBQ7_RAT UniProtKB/TrEMBL
  MSH2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Msh2  mutS homolog 2  Msh2  mutS homolog 2 (E. coli)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Msh2  mutS homolog 2 (E. coli)    mismatch repair protein  Name updated 1299863 APPROVED
2002-08-07 Msh2  mismatch repair protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression greatest expression at 20 days of age in testes 729069
gene_protein 933 amino acids 729069