Msh6 (mutS homolog 6) - Rat Genome Database

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Gene: Msh6 (mutS homolog 6) Rattus norvegicus
Analyze
Symbol: Msh6
Name: mutS homolog 6
RGD ID: 2322311
Description: Predicted to enable several functions, including DNA binding activity; chromatin binding activity; and methylated histone binding activity. Predicted to contribute to several functions, including DNA binding activity; MutLalpha complex binding activity; and adenyl ribonucleotide binding activity. Involved in mismatch repair and spermatogenesis. Predicted to be located in Golgi apparatus; cytosol; and nucleoplasm. Predicted to be part of MutSalpha complex and chromatin. Predicted to be active in nucleus. Used to study hereditary nonpolyposis colorectal cancer type 5. Human ortholog(s) of this gene implicated in Lynch syndrome; colorectal carcinoma; endometrial cancer; hereditary nonpolyposis colorectal cancer type 5; and mismatch repair cancer syndrome. Orthologous to human MSH6 (mutS homolog 6); PARTICIPATES IN altered mismatch repair pathway; colorectal cancer pathway; endometrial cancer pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; gentamycin.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: DNA mismatch repair protein Msh6; LOC100360342; mutS homolog 6 (E. coli); rCG61559-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Msh6m1Hubr  
Genetic Models: WI- Msh6m1Hubr
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.266,562,631 - 6,579,995 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl66,562,632 - 6,579,956 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx66,844,774 - 6,862,085 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.067,154,179 - 7,171,490 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.066,681,324 - 6,698,635 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0611,644,565 - 11,662,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl611,644,578 - 11,662,499 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0621,616,672 - 21,634,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4611,525,292 - 11,542,592 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera66,326,162 - 6,343,370 (-)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adrenocortical carcinoma  (ISO)
autosomal recessive limb-girdle muscular dystrophy type 2B  (ISO)
autosomal recessive progressive external ophthalmoplegia 1  (ISO)
B-lymphoblastic leukemia/lymphoma with BCR-ABL1  (ISO)
bilateral breast cancer  (ISO)
breast cancer  (ISO)
Breast Cancer, Familial  (ISO)
breast carcinoma  (ISO)
CEREBELLAR ATAXIA INFANTILE WITH PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA  (ISO)
cerebellar medulloblastoma  (ISO)
colon adenocarcinoma  (ISO)
colon carcinoma  (ISO)
colorectal cancer  (ISO)
colorectal carcinoma  (ISO)
Colorectal Neoplasms  (ISO)
Digestive System Neoplasms  (ISO)
endometrial cancer  (ISO)
endometrial carcinoma  (ISO)
Endometrial Neoplasms  (ISO)
Familial Prostate Cancer  (ISO)
Gaucher's disease  (ISO)
Gaucher's disease type I  (ISO)
genetic disease  (ISO)
Genetic Predisposition to Disease  (ISO)
hepatoblastoma  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
Hereditary Neoplastic Syndromes  (ISO)
hereditary nonpolyposis colorectal cancer type 5  (IMP,ISO)
INTELLECTUAL DEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES AND BEHAVIORAL ABNORMALITIES  (ISO)
lung adenocarcinoma  (ISO)
lung sarcomatoid carcinoma  (ISO)
Lynch syndrome  (ISO)
Lynch syndrome 1  (ISO)
Microsatellite Instability  (IMP,ISO)
mismatch repair cancer syndrome  (ISO)
Mismatch Repair Cancer Syndrome 1  (ISO)
Mismatch Repair Cancer Syndrome 3  (ISO)
multiple acyl-CoA dehydrogenase deficiency  (ISO)
Neurodevelopmental Disorders  (ISO)
osteosarcoma  (ISO)
ovarian cancer  (ISO)
ovarian carcinoma  (ISO)
Ovarian Neoplasms  (ISO)
Pitt-Hopkins-like syndrome 2  (ISO)
progressive myoclonus epilepsy 5  (ISO)
prostate cancer  (ISO)
rhabdomyosarcoma  (ISO)
sensory ataxic neuropathy, dysarthria, and ophthalmoparesis  (ISO)
sigmoid colon cancer  (ISO)
sigmoid neoplasm  (ISO)
stomach cancer  (ISO)
Thyroid Neoplasms  (ISO)
urinary bladder cancer  (ISO)
Urogenital Neoplasms  (ISO)
uterine corpus cancer  (ISO)
xeroderma pigmentosum group D  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-colchicine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
adenine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid A  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (ISO)
bortezomib  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
cannabidiol  (ISO)
celastrol  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gedunin  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
ivermectin  (ISO)
Lasiocarpine  (ISO)
leflunomide  (ISO)
lycopene  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
menadione  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methidathion  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
mitomycin C  (ISO)
monocrotaline  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (EXP)
N-methyl-N-nitrosourea  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
riddelliine  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
tamibarotene  (ISO)
tebufenpyrad  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
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. DNA mismatch repair defects: role in colorectal carcinogenesis. Jacob S and Praz F, Biochimie. 2002 Jan;84(1):27-47.
4. Expression of MSH2 and MSH6 on a tissue microarray in patients with osteosarcoma. Jentzsch T, etal., Anticancer Res. 2014 Dec;34(12):6961-72.
5. Mechanisms and functions of DNA mismatch repair. Li GM Cell Res. 2008 Jan;18(1):85-98.
6. Frameshift mutational target gene analysis identifies similarities and differences in constitutional mismatch repair-deficiency and Lynch syndrome. Maletzki C, etal., Mol Carcinog. 2017 Jul;56(7):1753-1764. doi: 10.1002/mc.22632. Epub 2017 Mar 30.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation 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. Lack of DNA mismatch repair protein MSH6 in the rat results in hereditary non-polyposis colorectal cancer-like tumorigenesis. van Boxtel R, etal., Carcinogenesis. 2008 Apr 15;.
Additional References at PubMed
PMID:8782829   PMID:8942985   PMID:9390556   PMID:10545954   PMID:10662804   PMID:10871409   PMID:11691815   PMID:11756455   PMID:11801590   PMID:11809883   PMID:12034830   PMID:12370835  
PMID:14632208   PMID:15105434   PMID:15238604   PMID:15324697   PMID:16388310   PMID:16403449   PMID:16618598   PMID:16713580   PMID:16728433   PMID:17015724   PMID:17715146   PMID:22871113  
PMID:23071719   PMID:23603115   PMID:23622243   PMID:26300262  


Genomics

Comparative Map Data
Msh6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.266,562,631 - 6,579,995 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl66,562,632 - 6,579,956 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx66,844,774 - 6,862,085 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.067,154,179 - 7,171,490 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.066,681,324 - 6,698,635 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0611,644,565 - 11,662,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl611,644,578 - 11,662,499 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0621,616,672 - 21,634,338 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4611,525,292 - 11,542,592 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera66,326,162 - 6,343,370 (-)NCBICelera
Cytogenetic Map6q12NCBI
MSH6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38247,783,145 - 47,810,101 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl247,695,530 - 47,810,063 (+)EnsemblGRCh38hg38GRCh38
GRCh37248,010,284 - 48,034,092 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36247,863,725 - 47,887,596 (+)NCBINCBI36Build 36hg18NCBI36
Build 34247,921,936 - 47,945,743NCBI
Celera247,849,755 - 47,873,614 (+)NCBICelera
Cytogenetic Map2p16.3NCBI
HuRef247,746,516 - 47,770,575 (+)NCBIHuRef
CHM1_1247,940,665 - 47,964,487 (+)NCBICHM1_1
T2T-CHM13v2.0247,789,083 - 47,816,050 (+)NCBIT2T-CHM13v2.0
Msh6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391788,282,478 - 88,298,320 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1788,282,490 - 88,298,320 (+)EnsemblGRCm39 Ensembl
GRCm381787,975,050 - 87,990,892 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1787,975,062 - 87,990,892 (+)EnsemblGRCm38mm10GRCm38
MGSCv371788,374,390 - 88,390,232 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361787,883,410 - 87,899,389 (+)NCBIMGSCv36mm8
Celera1792,385,348 - 92,401,193 (+)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1757.87NCBI
Msh6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544114,451,307 - 14,471,227 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544114,451,207 - 14,471,316 (+)NCBIChiLan1.0ChiLan1.0
MSH6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan12A78,582,203 - 78,607,350 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A47,901,591 - 47,926,662 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A48,824,469 - 48,849,779 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A48,824,350 - 48,849,779 (+)Ensemblpanpan1.1panPan2
MSH6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11049,825,330 - 49,838,036 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1049,803,898 - 49,838,028 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1049,669,446 - 49,693,588 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01050,687,723 - 50,711,873 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1050,687,741 - 50,711,873 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11050,394,939 - 50,419,090 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01050,681,795 - 50,705,920 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01050,869,560 - 50,893,685 (+)NCBIUU_Cfam_GSD_1.0
Msh6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629233,280,052 - 33,300,065 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365084,708,661 - 4,728,787 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365084,708,661 - 4,728,671 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSH6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl392,785,664 - 92,814,238 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1392,792,590 - 92,814,154 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2398,710,956 - 98,732,503 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSH6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11459,375,602 - 59,400,252 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1459,375,691 - 59,400,174 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604552,443,508 - 52,468,664 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msh6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473829,083,692 - 29,108,792 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473829,083,696 - 29,108,792 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Msh6
62 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:72
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000021923
Prediction methods:Microtar, Miranda, Rnahybrid
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
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

Markers in Region
RH126790  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.266,562,426 - 6,562,642 (-)MAPPERmRatBN7.2
Rnor_6.0611,662,378 - 11,662,593NCBIRnor6.0
Rnor_5.0621,634,327 - 21,634,542UniSTSRnor5.0
RGSC_v3.4611,542,581 - 11,542,796UniSTSRGSC3.4
Celera66,325,958 - 6,326,173UniSTS
Cytogenetic Map6q12UniSTS
RH127753  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.266,563,204 - 6,563,911 (-)MAPPERmRatBN7.2
Rnor_6.0611,661,110 - 11,661,816NCBIRnor6.0
Rnor_5.0621,633,059 - 21,633,765UniSTSRnor5.0
RGSC_v3.4611,541,312 - 11,542,018UniSTSRGSC3.4
Celera66,326,736 - 6,327,442UniSTS
AW550279  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.266,563,211 - 6,563,325 (-)MAPPERmRatBN7.2
Rnor_6.0611,661,696 - 11,661,809NCBIRnor6.0
Rnor_5.0621,633,645 - 21,633,758UniSTSRnor5.0
RGSC_v3.4611,541,898 - 11,542,011UniSTSRGSC3.4
Celera66,326,743 - 6,326,856UniSTS
RH140511  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.266,562,226 - 6,562,406 (-)MAPPERmRatBN7.2
Rnor_6.0611,662,614 - 11,662,793NCBIRnor6.0
Rnor_5.0621,634,563 - 21,634,742UniSTSRnor5.0
RGSC_v3.4611,542,817 - 11,542,996UniSTSRGSC3.4
Celera66,325,758 - 6,325,937UniSTS
Cytogenetic Map6q12UniSTS


Genetic Models
This gene Msh6 is modified in the following models/strains:


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 3 27 39 23 19 23 2 2 74 29 38 11 2
Low 16 18 18 18 6 9 6 3 6
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000021923   ⟹   ENSRNOP00000021923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl66,562,640 - 6,574,783 (-)Ensembl
Rnor_6.0 Ensembl611,644,578 - 11,662,499 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093464
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl611,661,927 - 11,662,392 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl611,661,455 - 11,662,042 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093689   ⟹   ENSRNOP00000076177
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl66,562,632 - 6,579,956 (-)Ensembl
Rnor_6.0 Ensembl611,644,628 - 11,662,389 (+)Ensembl
RefSeq Acc Id: NM_001398548   ⟹   NP_001385477
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.266,562,631 - 6,579,948 (-)NCBI
RefSeq Acc Id: XM_039113054   ⟹   XP_038968982
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.266,562,631 - 6,579,995 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001385477 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968982 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021923.7
  ENSRNOP00000076177
  ENSRNOP00000076177.2
RefSeq Acc Id: ENSRNOP00000021923   ⟸   ENSRNOT00000021923
RefSeq Acc Id: ENSRNOP00000076177   ⟸   ENSRNOT00000093689
RefSeq Acc Id: XP_038968982   ⟸   XM_039113054
- Peptide Label: isoform X1
- UniProtKB: A0A1W2Q695 (UniProtKB/TrEMBL),   A6H9C6 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001385477   ⟸   NM_001398548
- UniProtKB: A0A1W2Q695 (UniProtKB/TrEMBL),   A6H9C6 (UniProtKB/TrEMBL)
Protein Domains
PWWP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A0U9-F1-model_v2 AlphaFold D4A0U9 1-1362 view protein structure

Transcriptome

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

Promoters
RGD ID:13694404
Promoter ID:EPDNEW_R4923
Type:multiple initiation site
Name:Msh6_1
Description:mutS homolog 6
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_6.0611,644,596 - 11,644,656EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2322311 AgrOrtholog
BioCyc Gene G2FUF-38749 BioCyc
Ensembl Genes ENSRNOG00000016134 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021923.8 UniProtKB/TrEMBL
  ENSRNOT00000093689 ENTREZGENE
  ENSRNOT00000093689.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1420.10 UniProtKB/TrEMBL
  2.30.30.140 UniProtKB/TrEMBL
  3.30.420.110 UniProtKB/TrEMBL
  3.40.1170.10 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
InterPro DNA_mismatch_repair_MutS-lik_N UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS/MSH UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_C UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_clamp UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_connt UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_core UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_N UniProtKB/TrEMBL
  DNA_mismatch_repair_MutS_sf UniProtKB/TrEMBL
  MutS_con_dom_sf UniProtKB/TrEMBL
  MutS_family UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
NCBI Gene 100360342 ENTREZGENE
PANTHER DNA MISMATCH REPAIR PROTEIN MSH6 UniProtKB/TrEMBL
  PTHR11361 UniProtKB/TrEMBL
Pfam MutS_I UniProtKB/TrEMBL
  MutS_II UniProtKB/TrEMBL
  MutS_III UniProtKB/TrEMBL
  MutS_IV UniProtKB/TrEMBL
  MutS_V UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
PhenoGen Msh6 PhenoGen
PIRSF DNA_mis_repair_Msh6 UniProtKB/TrEMBL
PROSITE DNA_MISMATCH_REPAIR_2 UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016134 RatGTEx
SMART MUTSac UniProtKB/TrEMBL
  MUTSd UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
Superfamily-SCOP DNA_mismatch_repair_MutS_N UniProtKB/TrEMBL
  DNA_repair_MutS_domIII UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
  SSF53150 UniProtKB/TrEMBL
  Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt A0A1W2Q695 ENTREZGENE, UniProtKB/TrEMBL
  A6H9C6 ENTREZGENE, UniProtKB/TrEMBL
  D4A0U9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Msh6  mutS homolog 6  Msh6  mutS homolog 6 (E. coli)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-06 Msh6  mutS homolog 6 (E. coli)  LOC100360342  rCG61559-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100360342  rCG61559-like      Symbol and Name status set to provisional 70820 PROVISIONAL