RT1-A2 (RT1 class Ia, locus A2) - Rat Genome Database

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Gene: RT1-A2 (RT1 class Ia, locus A2) Rattus norvegicus
Analyze
Symbol: RT1-A2
Name: RT1 class Ia, locus A2
RGD ID: 1595923
Description: Predicted to have peptide antigen binding activity and signaling receptor binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to colocalize with membrane raft. Human ortholog(s) of this gene implicated in several diseases, including asthma (multiple); autoimmune disease (multiple); eye disease (multiple); human immunodeficiency virus infectious disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-E (major histocompatibility complex, class I, E); HLA-F (major histocompatibility complex, class I, F); and HLA-G (major histocompatibility complex, class I, G); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,6-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: MGC95123; RT1 class I gene (A-2); RT1 class Ia, A2n; RT1 class Ia, locus A2 (mapped); RT1-A2_mapped; RT1-A2n; RT1.A2(N); RT1A-2
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,870,939 - 4,910,183 (+)NCBI
Rnor_6.0 Ensembl205,374,985 - 5,378,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,374,990 - 5,378,536 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,433,437 - 7,436,984 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,021,816 - 5,025,341 (+)NCBIRGSC3.4rn4RGSC3.4
Celera206,470,599 - 6,474,124 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

References

Additional References at PubMed
PMID:1538753   PMID:9443915   PMID:11685465   PMID:12477932   PMID:12763482   PMID:12902470   PMID:14735325   PMID:19666135   PMID:20018625   PMID:22562814   PMID:23100519   PMID:29531166  


Genomics

Comparative Map Data
RT1-A2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,870,939 - 4,910,183 (+)NCBI
Rnor_6.0 Ensembl205,374,985 - 5,378,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,374,990 - 5,378,536 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,433,437 - 7,436,984 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,021,816 - 5,025,341 (+)NCBIRGSC3.4rn4RGSC3.4
Celera206,470,599 - 6,474,124 (+)NCBICelera
Cytogenetic Map20p12NCBI
H2-D1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,482,070 - 35,486,473 (+)NCBIGRCm39mm39
GRCm39 Ensembl1735,481,706 - 35,486,475 (+)Ensembl
GRCm381735,263,094 - 35,267,497 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,262,730 - 35,267,499 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,400,039 - 35,404,442 (+)NCBIGRCm37mm9NCBIm37
MGSCv361734,376,195 - 34,380,445 (+)NCBImm8
MGSCv361734,871,167 - 34,875,408 (+)NCBImm8
Cytogenetic Map17B1NCBI
cM Map1718.61NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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:168
Count of miRNA genes:75
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000038660, ENSRNOT00000052270
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.


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 7 26 17 15 17 1 3 9 17 9
Low 30 31 24 4 24 8 10 66 26 23 2 8
Below cutoff 6 5 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,375,650 - 5,377,440 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000052270   ⟹   ENSRNOP00000050701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,374,985 - 5,378,539 (+)Ensembl
RefSeq Acc Id: NM_001008829   ⟹   NP_001008829
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,871,012 - 4,874,537 (+)NCBI
Rnor_6.0205,375,011 - 5,378,536 (+)NCBI
Rnor_5.0207,433,437 - 7,436,984 (+)NCBI
RGSC_v3.4205,021,816 - 5,025,341 (+)RGD
Celera206,470,599 - 6,474,124 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601545   ⟹   XP_017457034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,870,945 - 4,874,540 (+)NCBI
Rnor_6.0205,374,990 - 5,378,535 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098426   ⟹   XP_038954354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,870,939 - 4,874,540 (+)NCBI
RefSeq Acc Id: XM_039098427   ⟹   XP_038954355
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,870,939 - 4,910,183 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001008829   ⟸   NM_001008829
- Peptide Label: precursor
- UniProtKB: Q6MGB8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457034   ⟸   XM_017601545
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000050701   ⟸   ENSRNOT00000052270
RefSeq Acc Id: XP_038954355   ⟸   XM_039098427
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954354   ⟸   XM_039098426
- Peptide Label: isoform X2
Protein Domains
Ig-like

Transcriptome

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

Promoters
RGD ID:13701406
Promoter ID:EPDNEW_R11930
Type:single initiation site
Name:RT1-A2_1
Description:RT1 class Ia, locus A2
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_6.0205,374,985 - 5,375,045EPDNEW

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)
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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/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
WKY/NHsd (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
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
20 7433489 7433490 C G snv FHL/EurMcwi (MCW)
20 7433744 7433745 G T snv LE/OrlBarth (UDEL)
20 7433758 7433759 G A snv SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)
20 7433771 7433772 C A snv ZFDM (KyushuU)
20 7433786 7433787 C T snv IS/Kyo (KyushuU), ZFDM (KyushuU), DOB/Oda (KyushuU), F344/Jcl (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU)
20 7433791 7433792 T C snv F344/Stm (KyushuU), DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Jcl (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), ZFDM (KyushuU), HWY/Slc (KyushuU), F344/DuCrlCrlj (KyushuU), IS/Kyo (KyushuU), F344/NSlc (KyushuU)
20 7433888 7433889 G A snv HTX/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), ZFDM (KyushuU), RCS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU)
20 7433897 7433898 C T snv SBH/Ygl (MCW)
20 7433911 7433912 A G snv BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), HWY/Slc (KyushuU)
20 7433942 7433943 A G snv SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW)
20 7433948 7433949 A C snv RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), ZF (KyushuU), ZFDM (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), LEC/Tj (KyushuU)
20 7433962 7433963 A G snv SDLEF7/Barth (UDEL)
20 7433974 7433975 C T snv SDLEF7/Barth (UDEL)
20 7433991 7433992 C A snv SDLEF7/Barth (UDEL)
20 7434224 7434225 G A snv SBN/Ygl (MCW), SS/JrHsdMcwi (MCW)
20 7434227 7434228 G C snv HTX/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), RCS/Kyo (KyushuU), DOB/Oda (KyushuU)
20 7434270 7434271 G T snv Crl:SD (UDEL)
20 7434308 7434309 A G snv RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), LEC/Tj (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU), SDLEF7/Barth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), IS-Tlk/Kyo (KyushuU)
20 7434320 7434321 T A snv DOB/Oda (KyushuU), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)
20 7434321 7434322 T C snv RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), LEC/Tj (KyushuU)
20 7434322 7434323 T G snv RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), IS/Kyo (KyushuU), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), LEC/Tj (KyushuU)
20 7434324 7434325 C T snv RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), HTX/Kyo (KyushuU), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), BUF/MNa (KyushuU), ZF (KyushuU)
20 7434333 7434334 T A snv F344/NSlc (KyushuU), F344/Stm (KyushuU), DOB/Oda (KyushuU), ACI/EurMcwi (MCW), F344/DuCrlCrlj (KyushuU), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW)
20 7434334 7434335 C G snv IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), DOB/Oda (KyushuU), ZFDM (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), IS/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU)
20 7434339 7434340 G A snv RCS/Kyo (KyushuU), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), ZFDM (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
20 7434359 7434360 G C snv BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), HWY/Slc (KyushuU), SBH/Ygl (MCW)
20 7434365 7434366 G A snv SDLEF7/Barth (UDEL)
20 7434380 7434381 G T snv ACI/EurMcwi (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW)
20 7434383 7434384 T G snv F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU)
20 7434390 7434391 A T snv SDLEF7/Barth (UDEL)
20 7434392 7434393 G A snv Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
20 7434404 7434405 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SDLEF7/Barth (UDEL), SS/JrHsdMcwi (MCW), Crl:SD (UDEL), LE/OrlBarth (UDEL), SR/JrHsd (MCW)
20 7434409 7434410 G C snv SDLEF7/Barth (UDEL)
20 7434417 7434418 G A snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), Crl:SD (UDEL)
20 7434420 7434421 A T snv SDLEF7/Barth (UDEL)
20 7435449 7435450 G A snv SS/JrHsdMcwi (MCW), F344/Stm (KyushuU), F344/NSlc (KyushuU), F344/DuCrlCrlj (KyushuU), SR/JrHsd (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW)
20 7435450 7435451 C T snv FHH/EurMcwi (MCW), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), F344/DuCrlCrlj (KyushuU), SS/JrHsdMcwi (MCW), F344/Jcl (KyushuU), Crl:SD (UDEL)
20 7435472 7435473 A C snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), SBN/Ygl (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW)
20 7435485 7435486 G A snv SR/JrHsd (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW)
20 7435533 7435534 C A snv FHH/EurMcwi (MCW)
20 7435537 7435538 C T snv FHH/EurMcwi (MCW)
20 7435544 7435545 G T snv SDLEF7/Barth (UDEL)
20 7435572 7435573 A G snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBN/Ygl (MCW)
20 7435602 7435603 G T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 7435642 7435643 T C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SDLEF7/Barth (UDEL), Crl:SD (UDEL)
20 7435645 7435646 G C snv SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)
20 7435657 7435658 A G snv SR/JrHsd (MCW), Crl:SD (UDEL), FHL/EurMcwi (MCW), LE/OrlBarth (UDEL), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), SDLEF7/Barth (UDEL), SBH/Ygl (MCW), FHH/EurMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW)
20 7435669 7435670 G A snv SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), BDIX/NemOda (KyushuU), BN/SsNSlc (KyushuU), NIG-III/Hok (KyushuU)
20 7435676 7435677 G T snv FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), LEC/Tj (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (MCW), KFRS3B/Kyo (KyushuU), LE/OrlBarth (UDEL), ACI/EurMcwi (MCW), BUF/MNa (KyushuU), Crl:SD (UDEL), RCS/Kyo (KyushuU)
20 7435686 7435687 C A snv Crl:SD (UDEL)
20 7435696 7435697 C T snv GH/OmrMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), F344/NSlc (KyushuU), F344/Jcl (KyushuU)
20 7435698 7435699 C A snv BUF/MNa (KyushuU), LE/OrlBarth (UDEL), LEC/Tj (KyushuU), HTX/Kyo (KyushuU), SDLEF7/Barth (UDEL), Crl:SD (UDEL)
20 7435810 7435811 C T snv LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), Crl:SD (UDEL)
20 7435822 7435823 A C snv SDLEF7/Barth (UDEL)
20 7435828 7435829 T A snv SDLEF7/Barth (UDEL), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW)
20 7435858 7435859 G T snv ZF (KyushuU)
20 7435861 7435862 C A snv IS/Kyo (KyushuU), NIG-III/Hok (KyushuU), IS-Tlk/Kyo (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU)
20 7436118 7436119 A G snv FHL/EurMcwi (MCW), SBN/Ygl (MCW), BUF/MNa (KyushuU), ZF (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU)
20 7436140 7436141 C G snv BN/SsNSlc (KyushuU)
20 7436352 7436353 C G snv BUF/MNa (KyushuU), KFRS3B/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), SBN/Ygl (MCW), HTX/Kyo (KyushuU), ZF (KyushuU), FHL/EurMcwi (MCW), LEC/Tj (KyushuU), LE/OrlBarth (UDEL), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), FHH/EurMcwi (MCW), F344/NSlc (KyushuU), SR/JrHsd (MCW)
20 7436363 7436364 G A snv F344/Stm (KyushuU), F344/NSlc (KyushuU), SR/JrHsd (MCW), F344/DuCrlCrlj (KyushuU)
20 7436375 7436376 C G snv ZF (KyushuU), KFRS3B/Kyo (KyushuU), DOB/Oda (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5375041 5375042 C G snv SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW)
20 5375071 5375072 C T snv MR/N (MCW), FHL/EurMcwi (MCW)
20 5375310 5375311 G A snv MR/N (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW)
20 5375311 5375312 C G snv CDS, CDR, FHL/EurMcwi (MCW)
20 5375323 5375324 C A snv GH/OmrMcwi (MCW), CDS, CDR
20 5375338 5375339 C T snv SBH/Ygl (MCW), GH/OmrMcwi (MCW), CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), ACI/EurMcwi (MCW), CDS, COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW)
20 5375343 5375344 T C snv CDS, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), GH/OmrMcwi (MCW), CDR, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHH/EurMcwi (MCW)
20 5375359 5375360 A T snv SBN/Ygl (MCW)
20 5375440 5375441 G A snv COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), MR/N (MCW), SBN/Ygl (MCW)
20 5375463 5375464 A G snv CDS, CDR
20 5375500 5375501 A C snv CDR, CDS
20 5375505 5375506 G A snv CDR, CDS
20 5375514 5375515 A G snv SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), CDS, ACI/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), CDR, FHH/EurMcwi (MCW)
20 5375520 5375521 G C snv CDR, CDS
20 5375526 5375527 C T snv SBN/Ygl (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)
20 5375540 5375541 G C snv SBN/Ygl (MCW)
20 5375547 5375548 G A snv SBN/Ygl (MCW)
20 5375744 5375745 T C snv GH/OmrMcwi (MCW)
20 5375750 5375751 G T snv CDR, CDS
20 5375765 5375766 A T snv CDR, CDS, WN/N (MCW)
20 5375776 5375777 G A snv COP/CrCrl (MCW & UW), SBN/Ygl (MCW)
20 5375779 5375780 G C snv SR/JrHsd (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SBN/Ygl (MCW)
20 5375783 5375784 G T snv CDS
20 5375791 5375792 C T snv GH/OmrMcwi (MCW)
20 5375794 5375795 G A snv COP/CrCrl (MCW & UW)
20 5375822 5375823 G T snv SBN/Ygl (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW)
20 5375855 5375856 C T snv M520/N (MCW)
20 5375860 5375861 A G snv GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW)
20 5375861 5375862 C T snv CDS, ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), CDR
20 5375872 5375873 T A snv CDR, GH/OmrMcwi (MCW)
20 5375873 5375874 T C snv GH/OmrMcwi (MCW), CDR
20 5375876 5375877 C T snv GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), ACI/N (MCW), CDS, CDR, SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 5375885 5375886 T A snv SR/JrHsd (MCW), ACI/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW)
20 5375886 5375887 C G snv GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), GK/Ox (RGD), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 5375891 5375892 G A snv CDR, SBN/Ygl (MCW), WKY/N (MCW), ACI/EurMcwi (MCW), SBH/Ygl (MCW), WN/N (MCW), FHH/EurMcwi (MCW), CDS, ACI/N (MCW), WN/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), WKY/N (MCW), COP/CrCrl (MCW & UW), M520/N (MCW), MR/N (MCW), MR/N (MCW), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW)
20 5375891 5375892 G T snv WKY/N (MCW), WKY/N (MCW)
20 5375911 5375912 G C snv SBH/Ygl (MCW)
20 5375917 5375918 G A snv SBH/Ygl (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW)
20 5375918 5375919 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)
20 5375935 5375936 T G snv F344/NRrrc (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)
20 5375944 5375945 G A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW)
20 5375956 5375957 G A snv ACI/EurMcwi (MCW), CDS, CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)
20 5375961 5375962 G T snv COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)
20 5375965 5375966 C T snv CDR, CDS
20 5375966 5375967 G A snv COP/CrCrl (MCW & UW)
20 5375969 5375970 G A snv SBH/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 5375971 5375972 T C snv M520/N (MCW)
20 5377001 5377002 G A snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW)
20 5377002 5377003 C T snv FHH/EurMcwi (MCW)
20 5377024 5377025 A C snv SBH/Ygl (MCW), SBN/Ygl (MCW), CDS, CDR, FHL/EurMcwi (MCW)
20 5377028 5377029 G C snv GH/OmrMcwi (MCW), CDR
20 5377037 5377038 G A snv COP/CrCrl (MCW & UW), CDR, FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW), ACI/EurMcwi (MCW)
20 5377062 5377063 G A snv CDR
20 5377078 5377079 C A snv CDR, SR/JrHsd (MCW), SBH/Ygl (MCW)
20 5377085 5377086 C A snv FHH/EurMcwi (MCW)
20 5377085 5377086 C G snv CDR, CDS
20 5377089 5377090 C T snv FHH/EurMcwi (MCW)
20 5377096 5377097 G T snv CDR, CDS
20 5377106 5377107 G C snv CDR, CDS
20 5377124 5377125 A G snv ACI/EurMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 5377133 5377134 G A snv FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 5377154 5377155 G T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW)
20 5377161 5377162 C A snv SBN/Ygl (MCW)
20 5377190 5377191 C G snv SBH/Ygl (MCW)
20 5377194 5377195 T C snv COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 5377197 5377198 G C snv SS/JrHsdMcwi (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW)
20 5377209 5377210 A G snv FHL/EurMcwi (MCW), SBN/Ygl (MCW), FHH/EurMcwi (MCW), CDS, COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), GH/OmrMcwi (MCW), CDR, SBH/Ygl (MCW), SR/JrHsd (MCW)
20 5377210 5377211 T G snv SS/JrHsdMcwi (MCW)
20 5377221 5377222 G A snv FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SR/JrHsd (MCW)
20 5377228 5377229 G T snv SBN/Ygl (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW)
20 5377248 5377249 C T snv CDS, F344/NRrrc (MCW), CDR, GH/OmrMcwi (MCW), SR/JrHsd (MCW), ACI/N (MCW), SS/JrHsdMcwi (MCW)
20 5377361 5377362 G C snv WN/N (MCW), WKY/N (MCW)
20 5377362 5377363 C T snv GH/OmrMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SBH/Ygl (MCW)
20 5377380 5377381 T A snv GH/OmrMcwi (MCW)
20 5377408 5377409 T C snv CDS, CDR
20 5377413 5377414 C A snv CDS, GH/OmrMcwi (MCW), CDR
20 5377485 5377486 A G snv CDS, CDR
20 5377670 5377671 A G snv SBN/Ygl (MCW)
20 5377904 5377905 C G snv FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), CDR, SS/JrHsdMcwi (MCW)
20 5377911 5377912 C G snv CDR
20 5377915 5377916 G A snv SR/JrHsd (MCW)
20 5377927 5377928 C G snv SBH/Ygl (MCW), CDR
20 5377931 5377932 A T snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5021826 5021827 C A snv HCR/2Mco (UMich), LCR/2Mco (UMich), LCR/1Mco (UMich)
20 5021831 5021832 A T snv LCR/1Mco (UMich), LCR/2Mco (UMich), HCR/2Mco (UMich)
20 5021846 5021847 C G snv FHL/EurMcwi (MCW)
20 5021876 5021877 C T snv MR/N (KNAW)
20 5021877 5021878 G T snv HCR/2Mco (UMich), LCR/1Mco (UMich)
20 5022115 5022116 G A snv MHS/Gib (ICL), MR/N (KNAW), FHL/EurMcwi (MCW), LE/Stm (ICL), FHL/EurMcwi (ICL), LH/MavRrrc (ICL), LCR/2Mco (UMich), SBH/Ygl (ICL), SBN/Ygl (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich)
20 5022179 5022180 A C snv SHRSP/Gcrc (MDC)
20 5022245 5022246 G A snv MR/N (KNAW)
20 5022268 5022269 A G snv HCR/2Mco (UMich), LCR/2Mco (UMich)
20 5022299 5022300 A G snv GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)
20 5022325 5022326 G C snv HCR/1Mco (UMich), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich)
20 5022570 5022571 A T snv WN/N (KNAW)
20 5022581 5022582 G A snv COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), FHH/EurMcwi (MDC), ACI/EurMcwi (MCW)
20 5022653 5022654 C A snv HCR/2Mco (UMich)
20 5022660 5022661 C T snv M520/N (KNAW)
20 5022665 5022666 A G snv HCR/2Mco (UMich), FHL/EurMcwi (MCW), LCR/2Mco (UMich)
20 5022677 5022678 T A snv COP/CrCrl (MCW & UW)
20 5022679 5022680 T G snv COP/CrCrl (MCW & UW)
20 5022681 5022682 C T snv ACI/N (KNAW)
20 5022690 5022691 T A snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW)
20 5022691 5022692 C G snv COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), FHL/EurMcwi (MCW)
20 5022696 5022697 G A snv LCR/2Mco (UMich), M520/N (KNAW), ACI/N (KNAW), MR/N (KNAW), LE/Stm (KNAW), F344/NRrrc (KNAW), LCR/1Mco (UMich), BUF/N (KNAW), WN/N (KNAW), WKY/N (KNAW)
20 5022696 5022697 G T snv WKY/N (KNAW)
20 5022716 5022717 G C snv LCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich)
20 5022737 5022738 G T snv FHL/EurMcwi (MCW), HCR/2Mco (UMich), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), HCR/1Mco (UMich)
20 5022740 5022741 T G snv F344/NRrrc (KNAW)
20 5022761 5022762 G A snv COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), SHR/OlaIpcv (ICL), SS/JrHsdMcwi (MDC), HCR/2Mco (UMich), LCR/1Mco (UMich)
20 5022766 5022767 G T snv LCR/1Mco (UMich)
20 5022771 5022772 G A snv COP/CrCrl (MCW & UW)
20 5022776 5022777 T C snv LE/Stm (KNAW), M520/N (KNAW)
20 5022784 5022785 A T snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)
20 5023807 5023808 C T snv SS/JrHsdMcwi (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), SHR/NHsd (ICL), SR/JrHsd (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich)
20 5023842 5023843 G A snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), LCR/1Mco (UMich), HCR/1Mco (UMich), HCR/2Mco (UMich), SR/JrHsd (MCW)
20 5023879 5023880 C G snv FHH/EurMcwi (MCW)
20 5023890 5023891 C A snv FHH/EurMcwi (MCW)
20 5023894 5023895 C T snv FHH/EurMcwi (MCW)
20 5023921 5023922 C T snv FHH/EurMcwi (MCW)
20 5023929 5023930 A G snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 5023995 5023996 C G snv FHH/EurMcwi (MDC)
20 5023999 5024000 T C snv FHL/EurMcwi (MCW), SR/JrHsd (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 5024002 5024003 G C snv SR/JrHsd (MCW), FHL/EurMcwi (MCW)
20 5024014 5024015 A G snv ACI/EurMcwi (MCW), LCR/2Mco (UMich), FHH/EurMcwi (MDC), SHRSP/Gcrc (MDC), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), WKY/NCrl (ICL), WKY/NHsd (ICL), WKY/Gcrc (ICL), SS/JrHsdMcwi (ICL), SS/Jr (ICL), SR/JrHsd (ICL), SHRSP/Gcrc (ICL), SHR/OlaIpcv (ICL), SBN/Ygl (ICL), SBH/Ygl (ICL), MNS/Gib (ICL), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL)
20 5024026 5024027 G A snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW)
20 5024033 5024034 G T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW)
20 5024053 5024054 C T snv F344/NRrrc (KNAW), LCR/1Mco (UMich), GH/OmrMcwi (MCW), ACI/N (KNAW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), HCR/2Mco (UMich), HCR/1Mco (UMich)
20 5024185 5024186 T A snv GH/OmrMcwi (MCW)
20 5024218 5024219 C A snv FHL/EurMcwi (MCW)
20 5024234 5024235 G C snv GH/OmrMcwi (MCW)
20 5024475 5024476 A G snv FHL/EurMcwi (MCW)
20 5024497 5024498 C T snv FHH/EurMcwi (MCW)
20 5024709 5024710 C G snv SR/JrHsd (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW)
20 5024720 5024721 G A snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 5024732 5024733 C G snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW)
20 5024741 5024742 A G snv HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595923 AgrOrtholog
Ensembl Genes ENSRNOG00000030712 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050701 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000052270 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127909 IMAGE-MGC_LOAD
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/TrEMBL
  Ig_C1-set UniProtKB/TrEMBL
  MHC_I-like_Ag-recog UniProtKB/TrEMBL
  MHC_I-like_Ag-recog_sf UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  MHC_I_a_a1/a2 UniProtKB/TrEMBL
  MHC_I_a_C UniProtKB/TrEMBL
KEGG Report rno:24974 UniProtKB/TrEMBL
MGC_CLONE MGC:95123 IMAGE-MGC_LOAD
NCBI Gene 24974 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-A2 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt Q6MGB8 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F7ERG5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-12 RT1-A2  RT1 class Ia, locus A2  RT1-A2_mapped  RT1 class Ia, locus A2 (mapped)  Data Merged 737654 APPROVED
2006-11-20 RT1-A2_mapped  RT1 class Ia, locus A2(mapped)  RT1-A2  RT1 class Ia, locus A2  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-A2  RT1 class Ia, locus A2      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-13 RT1-A2  RT1 class Ia, locus A2  RT1A-2  RT1 class I gene (A-2)  Data Merged 737654 APPROVED
2002-06-10 RT1-A2  RT1 class Ia, locus A2      Symbol and Name status set to approved 70586 APPROVED