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 enable ATP hydrolysis activity and single base insertion or deletion binding activity. Predicted to contribute to MutSalpha complex binding activity and single-stranded DNA binding activity. Involved in response to xenobiotic stimulus. Predicted to be located in several cellular components, including cytoplasmic ribonucleoprotein granule; cytosol; and nucleoplasm. Predicted to be part of MutLalpha complex. Human ortholog(s) of this gene implicated in Lynch syndrome; hereditary nonpolyposis colorectal cancer type 4; mismatch repair cancer syndrome; 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21210,676,819 - 10,701,161 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1210,676,764 - 10,701,066 (-)Ensembl
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


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
mRatBN7.21210,676,819 - 10,701,161 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1210,676,764 - 10,701,066 (-)Ensembl
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
GRCh3776,010,556 - 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_176,012,471 - 6,048,456 (-)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
GRCm39 Ensembl5143,846,782 - 143,870,786 (+)Ensembl
GRCm39 Ensembl5143,869,853 - 143,922,537 (+)Ensembl
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
CanFam3.1611,411,062 - 11,438,767 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl611,349,453 - 11,438,940 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha613,036,823 - 13,064,755 (-)NCBI
ROS_Cfam_1.0611,411,303 - 11,439,261 (-)NCBI
UMICH_Zoey_3.1611,287,969 - 11,315,948 (-)NCBI
UNSW_CanFamBas_1.0611,267,257 - 11,295,211 (-)NCBI
UU_Cfam_GSD_1.0611,493,877 - 11,521,829 (-)NCBI
Pms2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344139,477,659 - 139,505,890 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12815,174,359 - 15,209,962 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2815,172,100 - 15,209,852 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236661022,176 - 909,949 (+)NCBIVero_WHO_p1.0
Pms2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474031,315,121 - 31,345,137 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH141752  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21210,676,919 - 10,677,121 (+)MAPPERmRatBN7.2
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
RH 3.4 Map12124.1UniSTS
Cytogenetic Map12p11UniSTS


QTLs in Region (mRatBN7.2)
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)12119611090Rat
10755457Coatc14Coat color QTL 140.01759coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)12122591684Rat
6893681Bw109Body weight QTL 1092.30.004body mass (VT:0001259)body weight (CMO:0000012)12123297788Rat
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12129333307Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
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)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
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)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1600391Edcs2Endometrial carcinoma susceptibility QTL23.50.01uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)12683319017870186Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12844949028302290Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
1331739Hrtrt14Heart rate QTL 143.56232heart pumping trait (VT:2000009)heart rate (CMO:0000002)12931821612829686Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)12931821632103380Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat

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
mRatBN7.2 Ensembl1210,676,764 - 10,701,066 (-)Ensembl
Rnor_6.0 Ensembl1212,714,394 - 12,738,641 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078603   ⟹   ENSRNOP00000069740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1210,676,835 - 10,701,058 (-)Ensembl
Rnor_6.0 Ensembl1212,714,408 - 12,738,620 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094513   ⟹   ENSRNOP00000079389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1210,676,833 - 10,701,000 (-)Ensembl
RefSeq Acc Id: NM_001105908   ⟹   NP_001099378
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,676,819 - 10,701,066 (-)NCBI
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
mRatBN7.21210,676,829 - 10,701,161 (-)NCBI
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
mRatBN7.21210,676,829 - 10,701,161 (-)NCBI
Rnor_6.01212,714,404 - 12,738,617 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089178   ⟹   XP_038945106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,676,829 - 10,701,161 (-)NCBI
RefSeq Acc Id: XM_039089179   ⟹   XP_038945107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,682,224 - 10,701,161 (-)NCBI
RefSeq Acc Id: XM_039089180   ⟹   XP_038945108
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,682,245 - 10,701,161 (-)NCBI
RefSeq Acc Id: XR_005491606
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,681,556 - 10,701,161 (-)NCBI
RefSeq Acc Id: XR_005491607
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21210,681,556 - 10,701,161 (-)NCBI
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
RefSeq Acc Id: XP_038945106   ⟸   XM_039089178
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038945107   ⟸   XM_039089179
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038945108   ⟸   XM_039089180
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000079389   ⟸   ENSRNOT00000094513
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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)
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Sequenced By: MCW
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
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
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)
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Sequenced By: MCW
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)
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Sequenced By: MCW