Msh5 (mutS homolog 5) - Rat Genome Database

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Gene: Msh5 (mutS homolog 5) Rattus norvegicus
Analyze
Symbol: Msh5
Name: mutS homolog 5
RGD ID: 1303008
Description: Predicted to have DNA-dependent ATPase activity. Predicted to be involved in female gamete generation and meiosis I cell cycle process. Predicted to localize to synaptonemal complex. Human ortholog(s) of this gene implicated in primary ovarian insufficiency. Orthologous to human MSH5 (mutS homolog 5); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 4-amino-2,6-dinitrotoluene; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: mutS homolog 5 (E. coli); mutS protein homolog 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,773,867 - 3,793,337 (+)NCBI
Rnor_6.0 Ensembl205,020,667 - 5,037,088 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,020,690 - 5,037,125 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,093,706 - 7,110,044 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,845,731 - 3,862,011 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,846,041 - 3,862,242 (+)NCBI
Celera204,233,160 - 4,249,400 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10809667   PMID:12477932   PMID:15060004   PMID:15467367   PMID:15489334   PMID:15640358   PMID:16260499  


Genomics

Comparative Map Data
Msh5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,773,867 - 3,793,337 (+)NCBI
Rnor_6.0 Ensembl205,020,667 - 5,037,088 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,020,690 - 5,037,125 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,093,706 - 7,110,044 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,845,731 - 3,862,011 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,846,041 - 3,862,242 (+)NCBI
Celera204,233,160 - 4,249,400 (-)NCBICelera
Cytogenetic Map20p12NCBI
MSH5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl631,739,677 - 31,762,678 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl631,739,677 - 31,762,676 (+)EnsemblGRCh38hg38GRCh38
GRCh38631,740,005 - 31,762,676 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37631,707,782 - 31,730,453 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,815,753 - 31,838,432 (+)NCBINCBI36hg18NCBI36
Build 34631,815,755 - 31,840,601NCBI
Celera633,305,954 - 33,328,700 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef631,493,957 - 31,516,883 (+)NCBIHuRef
CHM1_1631,709,839 - 31,732,578 (+)NCBICHM1_1
Msh5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,247,581 - 35,267,842 (-)NCBIGRCm39mm39
GRCm39 Ensembl1735,247,581 - 35,265,721 (-)Ensembl
GRCm381735,028,605 - 35,046,997 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,028,605 - 35,046,745 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,165,550 - 35,183,668 (-)NCBIGRCm37mm9NCBIm37
MGSCv361734,636,661 - 34,654,678 (-)NCBImm8
Celera1738,124,846 - 38,143,436 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.57NCBI
Msh5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955437275,976 - 297,268 (+)NCBIChiLan1.0ChiLan1.0
MSH5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1632,289,318 - 32,313,411 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0631,401,343 - 31,424,665 (+)NCBIMhudiblu_PPA_v0panPan3
MSH5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,221,278 - 1,243,042 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,357,836 - 1,379,567 (+)NCBI
ROS_Cfam_1.0121,364,526 - 1,386,294 (+)NCBI
UMICH_Zoey_3.1121,223,762 - 1,245,520 (+)NCBI
UNSW_CanFamBas_1.0121,290,998 - 1,312,682 (+)NCBI
UU_Cfam_GSD_1.0121,358,882 - 1,380,614 (+)NCBI
Msh5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,767,176 - 35,785,306 (+)NCBI
SpeTri2.0NW_0049367271,776,038 - 1,794,152 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSH5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1723,852,864 - 23,872,760 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
MSH5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11740,260,979 - 40,283,872 (-)NCBI
Vero_WHO_p1.0NW_02366604431,652,919 - 31,675,016 (+)NCBI
Msh5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,453,750 - 24,477,574 (-)NCBI

Position Markers
D20Got4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,775,830 - 3,776,003 (-)MAPPER
Rnor_6.0205,038,027 - 5,038,199NCBIRnor6.0
Rnor_5.0207,110,957 - 7,111,129UniSTSRnor5.0
RGSC_v3.4203,844,619 - 3,844,792RGDRGSC3.4
RGSC_v3.4203,844,620 - 3,844,792UniSTSRGSC3.4
RGSC_v3.1203,844,846 - 3,845,019RGD
Celera204,250,339 - 4,250,511UniSTS
RH 3.4 Map2052.12UniSTS
RH 3.4 Map2052.12RGD
RH 2.0 Map2064.2RGD
Cytogenetic Map20p12UniSTS
BG372572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,792,642 - 3,793,155 (-)MAPPER
Rnor_6.0205,020,876 - 5,021,388NCBIRnor6.0
Rnor_5.0207,093,892 - 7,094,404UniSTSRnor5.0
RGSC_v3.4203,861,317 - 3,861,829UniSTSRGSC3.4
Celera204,233,342 - 4,233,854UniSTS
RH 3.4 Map213.3UniSTS
Cytogenetic Map20p12UniSTS
AI408685  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map2052.52UniSTS
Cytogenetic Map20p12UniSTS
RH142514  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,781,318 - 3,781,418 (-)MAPPER
Rnor_6.0205,032,613 - 5,032,712NCBIRnor6.0
Rnor_5.0207,105,543 - 7,105,642UniSTSRnor5.0
RGSC_v3.4203,850,107 - 3,850,206UniSTSRGSC3.4
Celera204,244,925 - 4,245,024UniSTS
RH 3.4 Map2049.9UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2039105555533640Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2040391135875448Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:41
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000060762
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 23
Low 3 28 38 22 18 22 1 1 59 35 18 3 1
Below cutoff 12 11 11 1 11 5 8 15 8 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060762   ⟹   ENSRNOP00000057489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,020,690 - 5,037,088 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091022   ⟹   ENSRNOP00000074342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,020,667 - 5,037,022 (-)Ensembl
RefSeq Acc Id: NM_212536   ⟹   NP_997701
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,776,942 - 3,793,337 (+)NCBI
Rnor_6.0205,020,694 - 5,037,088 (-)NCBI
Rnor_5.0207,093,706 - 7,110,044 (-)NCBI
RGSC_v3.4203,845,731 - 3,862,011 (+)RGD
Celera204,233,160 - 4,249,400 (-)RGD
Sequence:
RefSeq Acc Id: XM_017601574   ⟹   XP_017457063
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,020,690 - 5,037,125 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601575   ⟹   XP_017457064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,020,690 - 5,037,124 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601576   ⟹   XP_017457065
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,020,690 - 5,037,104 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098491   ⟹   XP_038954419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,773,867 - 3,790,525 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_997701   ⟸   NM_212536
- UniProtKB: Q6MG62 (UniProtKB/Swiss-Prot),   A0A0H2UI03 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457063   ⟸   XM_017601574
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457064   ⟸   XM_017601575
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457065   ⟸   XM_017601576
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000057489   ⟸   ENSRNOT00000060762
RefSeq Acc Id: ENSRNOP00000074342   ⟸   ENSRNOT00000091022
RefSeq Acc Id: XP_038954419   ⟸   XM_039098491
- Peptide Label: isoform X1
Protein Domains
DNA_MISMATCH_REPAIR_2

Transcriptome

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

Promoters
RGD ID:13701383
Promoter ID:EPDNEW_R11907
Type:single initiation site
Name:Msh5_1
Description:mutS homolog 5
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_6.0205,037,108 - 5,037,168EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 7094971 7094972 G A snv HTX/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5022245 5022246 C T snv F344/NRrrc (MCW), M520/N (MCW), ACI/N (MCW)
20 5023343 5023344 C T snv SS/Jr (RGD), F344/NCrl (RGD), LL/MavRrrc (RGD), SS/JrHsdMcwi (RGD), SR/JrHsd (RGD)
20 5023516 5023517 C T snv LE/Stm (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), SBH/Ygl (RGD)
20 5023842 5023843 T C snv M520/N (MCW), F344/NRrrc (MCW), Buf/N (MCW), ACI/N (MCW)
20 5024401 5024402 T C snv F344/NRrrc (MCW), Buf/N (MCW), ACI/N (MCW), M520/N (MCW)
20 5035563 5035564 G A snv F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303008 AgrOrtholog
Ensembl Genes ENSRNOG00000000857 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057489 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074342 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000060762 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091022 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133915 IMAGE-MGC_LOAD
InterPro DNA_mismatch_repair_Msh2 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_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294252 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:95266 IMAGE-MGC_LOAD
NCBI Gene 294252 ENTREZGENE
Pfam MutS_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_IV UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MutS_V UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Msh5 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 A0A0H2UI03 ENTREZGENE, UniProtKB/TrEMBL
  MSH5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5XHZ5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Msh5  mutS homolog 5  Msh5  mutS homolog 5 (E. coli)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Msh5  mutS homolog 5 (E. coli)    mutS homolog 5  Name updated 1299863 APPROVED
2005-02-14 Msh5  mutS homolog 5      Symbol and Name status set to provisional 70820 PROVISIONAL