Pms2 (PMS1 homolog 2, mismatch repair system component) - Rat Genome Database
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Gene: Pms2 (PMS1 homolog 2, mismatch repair system component) Rattus norvegicus
Analyze
Symbol: Pms2
Name: PMS1 homolog 2, mismatch repair system component
RGD ID: 1305483
Description: Predicted to contribute to MutSalpha complex binding activity and single-stranded DNA binding activity. Involved in response to drug. Predicted to localize to several cellular components, including cytoplasmic ribonucleoprotein granule; cytosol; and nucleus. Human ortholog(s) of this gene implicated in Lynch syndrome; hereditary nonpolyposis colorectal cancer type 4; ovarian cancer; and urinary bladder cancer. Orthologous to human PMS2 (PMS1 homolog 2, mismatch repair system component); PARTICIPATES IN altered mismatch repair pathway; colorectal cancer pathway; mismatch repair pathway; INTERACTS WITH 2,6-dinitrotoluene; 4-hydroperoxycyclophosphamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC288479; mismatch repair endonuclease PMS2; PMS2 postmeiotic segregation increased 2; postmeiotic segregation increased 2; postmeiotic segregation increased 2 (S. cerevisiae)
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
Rnor_6.01212,714,394 - 12,738,654 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1212,714,394 - 12,738,641 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01214,757,747 - 14,781,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41211,004,507 - 11,028,754 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11211,034,447 - 11,058,818 (-)NCBI
Celera1212,474,260 - 12,498,506 (-)NCBICelera
Cytogenetic Map12p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9500552   PMID:9618520   PMID:10359802   PMID:10429667   PMID:10430621   PMID:10871409   PMID:11313994   PMID:11809883   PMID:11828012   PMID:12477932   PMID:15480418   PMID:16204034  
PMID:16403449   PMID:16713580   PMID:16728433   PMID:23071719   PMID:23709753  


Genomics

Comparative Map Data
Pms2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01212,714,394 - 12,738,654 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1212,714,394 - 12,738,641 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01214,757,747 - 14,781,994 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41211,004,507 - 11,028,754 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11211,034,447 - 11,058,818 (-)NCBI
Celera1212,474,260 - 12,498,506 (-)NCBICelera
Cytogenetic Map12p11NCBI
PMS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl75,970,925 - 6,009,106 (-)EnsemblGRCh38hg38GRCh38
GRCh3875,970,925 - 6,009,106 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3776,012,870 - 6,048,737 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3675,979,396 - 6,015,263 (-)NCBINCBI36hg18NCBI36
Build 3475,786,113 - 5,821,915NCBI
Celera760,142,236 - 60,149,112 (-)NCBI
Celera75,957,552 - 5,958,444 (-)NCBI
Cytogenetic Map7p22.1NCBI
HuRef75,894,376 - 5,920,472 (-)NCBIHuRef
CHM1_176,774,489 - 6,793,088 (+)NCBICHM1_1
CRA_TCAGchr7v276,059,215 - 6,095,082 (-)NCBI
Pms2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395143,846,379 - 143,922,538 (+)NCBIGRCm39mm39
GRCm385143,909,901 - 143,972,745 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5143,909,964 - 143,933,968 (+)EnsemblGRCm38mm10GRCm38
MGSCv375144,670,870 - 144,692,625 (+)NCBIGRCm37mm9NCBIm37
MGSCv365144,163,492 - 144,184,971 (+)NCBImm8
Celera5140,892,468 - 140,914,240 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map582.82NCBI
Pms2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495546013,762,854 - 13,791,462 (+)NCBIChiLan1.0ChiLan1.0
LOC100976787
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.176,175,913 - 6,203,094 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl76,167,403 - 6,202,984 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v077,433,031 - 7,459,560 (+)NCBIMhudiblu_PPA_v0panPan3
PMS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl611,349,453 - 11,438,940 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1611,411,062 - 11,438,767 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pms2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936750439,396 - 468,747 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PMS2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl35,113,230 - 5,145,634 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.135,118,002 - 5,145,634 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.235,179,132 - 5,206,754 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103246803
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2815,172,100 - 15,209,852 (-)Ensembl
ChlSab1.12815,174,359 - 15,209,962 (-)NCBI
Pms2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474031,315,121 - 31,345,137 (+)NCBI

Position Markers
RH141752  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01212,714,495 - 12,714,696NCBIRnor6.0
Rnor_5.01214,757,848 - 14,758,049UniSTSRnor5.0
RGSC_v3.41211,004,608 - 11,004,809UniSTSRGSC3.4
Celera1212,474,361 - 12,474,562UniSTS
Cytogenetic Map12p11UniSTS
RH 3.4 Map12124.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312418Kidm41Kidney mass QTL 413.70.0001kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)12122650917Rat
10450854Stl34Serum triglyceride level QTL 343.50.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)12122853017Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12123035872Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123758197Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12824960820590080Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)121176499514489679Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:208
Count of miRNA genes:157
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000067021
Prediction methods:Microtar, 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 27 16 18 16 1 1 74 27 38 11 1
Low 1 17 30 25 1 25 7 10 8 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067021   ⟹   ENSRNOP00000061927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1212,714,394 - 12,738,641 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078603   ⟹   ENSRNOP00000069740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1212,714,408 - 12,738,620 (-)Ensembl
RefSeq Acc Id: NM_001105908   ⟹   NP_001099378
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01212,714,394 - 12,738,641 (-)NCBI
Rnor_5.01214,757,747 - 14,781,994 (-)NCBI
RGSC_v3.41211,004,507 - 11,028,754 (-)RGD
Celera1212,474,260 - 12,498,506 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248862   ⟹   XP_006248924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01212,714,404 - 12,738,654 (-)NCBI
Rnor_5.01214,757,747 - 14,781,994 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598288   ⟹   XP_017453777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01212,714,404 - 12,738,617 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001099378   ⟸   NM_001105908
- UniProtKB: D4A360 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248924   ⟸   XM_006248862
- Peptide Label: isoform X1
- UniProtKB: B1H246 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453777   ⟸   XM_017598288
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000061927   ⟸   ENSRNOT00000067021
RefSeq Acc Id: ENSRNOP00000069740   ⟸   ENSRNOT00000078603
Protein Domains
DNA_mis_repair   MutL_C

Transcriptome

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

Promoters
RGD ID:13698434
Promoter ID:EPDNEW_R8957
Type:multiple initiation site
Name:Pms2_1
Description:PMS1 homolog 2, mismatch repair system component
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_6.01212,738,606 - 12,738,666EPDNEW

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)
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
MHS/Gib (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
MNS/Gib (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
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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 14763347 14763348 C A snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305483 AgrOrtholog
Ensembl Genes ENSRNOG00000001040 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061927 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069740 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067021 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078603 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.20 UniProtKB/TrEMBL
  3.30.1370.100 UniProtKB/TrEMBL
  3.30.230.10 UniProtKB/TrEMBL
  3.30.565.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8365723 IMAGE-MGC_LOAD
InterPro DNA_mismatch_repair UniProtKB/TrEMBL
  DNA_mismatch_repair_C UniProtKB/TrEMBL
  DNA_mismatch_repair_CS UniProtKB/TrEMBL
  HATPase_C_sf UniProtKB/TrEMBL
  MutL/Mlh/Pms UniProtKB/TrEMBL
  MutL_C UniProtKB/TrEMBL
  MutL_C_dimsub UniProtKB/TrEMBL
  MutL_C_regsub UniProtKB/TrEMBL
  MutL_C_sf UniProtKB/TrEMBL
  Ribosomal_S5_D2-typ_fold UniProtKB/TrEMBL
  Ribosomal_S5_D2-typ_fold_subgr UniProtKB/TrEMBL
KEGG Report rno:288479 UniProtKB/TrEMBL
MGC_CLONE MGC:187611 IMAGE-MGC_LOAD
NCBI Gene 288479 ENTREZGENE
PANTHER PTHR10073 UniProtKB/TrEMBL
Pfam DNA_mis_repair UniProtKB/TrEMBL
  MutL_C UniProtKB/TrEMBL
PharmGKB PMS2 RGD
PhenoGen Pms2 PhenoGen
PROSITE DNA_MISMATCH_REPAIR_1 UniProtKB/TrEMBL
SMART DNA_mis_repair UniProtKB/TrEMBL
  MutL_C UniProtKB/TrEMBL
Superfamily-SCOP Ribosomal_S5_D2-typ_fold UniProtKB/TrEMBL
  SSF118116 UniProtKB/TrEMBL
  SSF55874 UniProtKB/TrEMBL
TIGRFAMs mutl UniProtKB/TrEMBL
UniGene Rn.102072 ENTREZGENE
UniProt B1H246 ENTREZGENE, UniProtKB/TrEMBL
  D4A360 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-04 Pms2  PMS1 homolog 2, mismatch repair system component  Pms2  postmeiotic segregation increased 2 (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-26 Pms2  postmeiotic segregation increased 2 (S. cerevisiae)  Pms2  PMS2 postmeiotic segregation increased 2 (S. cerevisiae)  Name changed 629549 APPROVED
2008-09-09 Pms2  PMS2 postmeiotic segregation increased 2 (S. cerevisiae)  Pms2  postmeiotic segregation increased 2 (S. cerevisiae)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pms2  postmeiotic segregation increased 2 (S. cerevisiae)   Pms2_predicted  postmeiotic segregation increased 2 (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pms2_predicted  postmeiotic segregation increased 2 (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED