RT1-T24-1 (RT1 class I, locus T24, gene 1) - Rat Genome Database

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Gene: RT1-T24-1 (RT1 class I, locus T24, gene 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-T24-1
Name: RT1 class I, locus T24, gene 1
RGD ID: 1359499
Description: Predicted to enable 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, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to be integral component of membrane. Predicted to be active in external side of plasma membrane and extracellular space; PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H2-T24; histocompatibility 2, T region locus 24; RT1 class I, T24, gene 1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2202,761,541 - 2,774,749 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl202,718,279 - 2,776,154 (+)Ensembl
Rnor_6.0203,269,315 - 3,282,523 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,242,492 - 3,282,523 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,367,427 - 5,388,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,907,237 - 2,922,971 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1202,907,463 - 2,923,198 (+)NCBI
Celera20188,032 - 200,983 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Comparison of exon 5 sequences from 35 class I genes of the BALB/c mouse. Brorson KA, etal., J Exp Med 1989 Dec 1;170(6):1837-58.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15060004  


Genomics

Position Markers
D20Yum33  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,766,460 - 2,766,623 (+)MAPPERmRatBN7.2
Rnor_6.0203,274,235 - 3,274,397NCBIRnor6.0
Rnor_5.0205,372,401 - 5,372,563UniSTSRnor5.0
RGSC_v3.4202,912,157 - 2,912,319UniSTSRGSC3.4
Celera20192,943 - 193,105UniSTS
Cytogenetic Map20p12UniSTS
BI298734  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,685,051 - 2,685,205 (+)MAPPERmRatBN7.2
mRatBN7.2202,761,943 - 2,762,097 (+)MAPPERmRatBN7.2
Rnor_6.0203,269,718 - 3,269,871NCBIRnor6.0
Rnor_6.0203,189,994 - 3,190,147NCBIRnor6.0
Rnor_5.0205,367,884 - 5,368,037UniSTSRnor5.0
Rnor_5.0205,288,160 - 5,288,313UniSTSRnor5.0
RGSC_v3.4202,830,285 - 2,830,438UniSTSRGSC3.4
RGSC_v3.4202,907,640 - 2,907,793UniSTSRGSC3.4
Celera20188,435 - 188,588UniSTS
Celera20115,465 - 115,618UniSTS
RH 3.4 Map2015.8UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000041502
Prediction methods: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 1 1 1 1 2 1 5 2
Low 2 40 56 40 17 40 6 9 58 30 36 9 6
Below cutoff 2 2 2 16 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041502   ⟹   ENSRNOP00000050015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,741,359 (+)Ensembl
Rnor_6.0 Ensembl203,242,492 - 3,282,523 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000061299   ⟹   ENSRNOP00000058011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,375 - 2,741,958 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000070903   ⟹   ENSRNOP00000064880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078110   ⟹   ENSRNOP00000075284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,482 - 2,774,583 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078454   ⟹   ENSRNOP00000074530
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082449   ⟹   ENSRNOP00000072021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,369 - 2,776,124 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089044   ⟹   ENSRNOP00000075312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,356 - 2,741,958 (+)Ensembl
Rnor_6.0 Ensembl203,269,284 - 3,282,248 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116904   ⟹   ENSRNOP00000079819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,510 - 2,776,154 (+)Ensembl
RefSeq Acc Id: NM_001008858   ⟹   NP_001008858
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2202,761,541 - 2,774,749 (+)NCBI
Rnor_6.0203,269,315 - 3,282,523 (+)NCBI
Rnor_5.0205,367,427 - 5,388,777 (+)NCBI
RGSC_v3.4202,907,237 - 2,922,971 (+)RGD
Celera20188,032 - 200,983 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008858 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84042 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008858   ⟸   NM_001008858
- UniProtKB: Q6MG05 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075312   ⟸   ENSRNOT00000089044
RefSeq Acc Id: ENSRNOP00000050015   ⟸   ENSRNOT00000041502
RefSeq Acc Id: ENSRNOP00000079819   ⟸   ENSRNOT00000116904
RefSeq Acc Id: ENSRNOP00000072021   ⟸   ENSRNOT00000082449
RefSeq Acc Id: ENSRNOP00000075284   ⟸   ENSRNOT00000078110
RefSeq Acc Id: ENSRNOP00000064880   ⟸   ENSRNOT00000070903
RefSeq Acc Id: ENSRNOP00000058011   ⟸   ENSRNOT00000061299
RefSeq Acc Id: ENSRNOP00000074530   ⟸   ENSRNOT00000078454
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG05-F1-model_v2 AlphaFold Q6MG05 1-330 view protein structure

Transcriptome

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

Promoters
RGD ID:13701289
Promoter ID:EPDNEW_R11812
Type:multiple initiation site
Name:RT1-T24-1_1
Description:RT1 class I, locus T24, gene 1
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_6.0203,269,284 - 3,269,344EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
BUF/N (2020)
Visual CSV TAB Printer
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
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)
Visual CSV TAB Printer
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
F344/NCrl (2019)
Visual CSV TAB Printer
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/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
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
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
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
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
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
LE/Stm (2019)
Visual CSV TAB Printer
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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
WKY/N (2020)
Visual CSV TAB Printer
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
WKY/NCrl (2019)
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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
WN/N (2020)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3281316 3281317 C G snv CDR, WN/N (2020), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), Buf/N (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), BUF/N (2020), BXH2/CubMcwi (2020), FXLE16/Stm (2020), GK/FarMcwi (2019), HXB2/IpcvMcwi (2019), HXB31/IpcvMcwi (2019), LEW/Crl (2019), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LN/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), M520/N (2020), MWF/Hsd (2019), PVG/Seac (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), WKY/N (2020), CDS
20 3281812 3281813 C T snv BUF/N (2020), LH/MavRrrcAek (2020), M520/NRrrcMcwi (2019)
20 3281867 3281868 C A snv M520/NRrrcMcwi (2019), BUF/N (2020)
20 3281965 3281966 T G snv LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), SS/JrHsdMcwi (2019), SR/JrHsd (2020), MR/N (2020), LL/MavRrrcAek (2020), LEXF3/Stm (2020), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), F344/NRrrc (MCW), ACI/EurMcwi (2019), ACI/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), LEXF2B/Stm (2019), LEXF1C/Stm (2019)
20 3282014 3282015 A T snv SR/JrHsd (MCW), SBN/Ygl (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), CDR, CDS
20 3282027 3282028 G T snv BUF/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LN/MavRrrcAek (2020), LH/MavRrrcAek (2020), LE/Stm (2019), M520/N (2020), FHL/EurMcwi (MCW), FXLE16/Stm (2020), LEXF4/Stm (2020)
20 3282216 3282217 G A snv FHH/EurMcwi (MCW)
20 3282237 3282238 T C snv M520/N (MCW), LE/Stm (2019), LH/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), M520/N (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 5379482 5379483 C G snv ZFDM (KyushuU), FHL/EurMcwi (MCW), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SBN/Ygl (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), ZF (KyushuU)
20 5380131 5380132 T G snv SS/JrHsdMcwi (MCW), Crl:SD (UDEL), SR/JrHsd (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)
20 5380180 5380181 A T snv DOB/Oda (KyushuU), BDIX/NemOda (KyushuU), ZFDM (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SBN/Ygl (MCW), SBH/Ygl (MCW), BDIX.Cg-Tal/NemOda (KyushuU)
20 5380193 5380194 G T snv LE/Stm (KyushuU), FHL/EurMcwi (MCW)
20 5380403 5380404 T C snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 2921764 2921765 C G snv LCR/2Mco (UMich), WKY/Gcrc (ICL), LCR/1Mco (UMich), WKY/NHsd (ICL), FHL/EurMcwi (MCW), SHRSP/Gcrc (MDC), BUF/N (KNAW), LE/Stm (KNAW), M520/N (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), SHR/OlaIpcv (KNAW), GH/OmrMcwi (MCW), FHL/EurMcwi (ICL), GK/Ox (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LN/MavRrrc (ICL), MHS/Gib (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WAG/Rij (ICL), WKY/NCrl (ICL), HCR/2Mco (UMich)
20 2922413 2922414 T G snv LCR/1Mco (UMich), LCR/2Mco (UMich), HCR/1Mco (UMich), SS/JrHsdMcwi (ICL), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), FHH/EurMcwi (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), F344/NRrrc (KNAW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), LL/MavRrrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL)
20 2922475 2922476 G T snv FHL/EurMcwi (MCW), HCR/2Mco (UMich), LCR/2Mco (UMich)
20 2922685 2922686 T C snv M520/N (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 2773542 2773543 C G snv SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), MWF/Hsd (2019), M520/N (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LN/MavRrrcAek (2020), LH/MavRrrcAek (2020), LE/Stm (2019), LEXF4/Stm (2020), LEW/Crl (2019), HXB31/IpcvMcwi (2019), HXB2/IpcvMcwi (2019), GK/FarMcwi (2019), FXLE16/Stm (2020), BXH2/CubMcwi (2020), BUF/N (2020), WN/N (2020), WKY/N (2020), WKY/NCrl (2019), WAG/RijCrl (2020), PVG/Seac (2019)
20 2774191 2774192 T G snv SS/JrHsdMcwi (2019), SR/JrHsd (2020), MR/N (2020), LL/MavRrrcAek (2020), LEXF3/Stm (2020), LEXF2B/Stm (2019), LEXF1C/Stm (2019), LEXF1A/Stm (2019), LEXF11/Stm (2020), FXLE18/Stm (2020), FHH/EurMcwi (2019), F344/Stm (2019), F344/N (2020), F344/NCrl (2019), F344/DuCrl (2019), DA/OlaHsd (2019), ACI/EurMcwi (2019), ACI/N (2020)
20 2774253 2774254 G T snv LEXF4/Stm (2020), M520/NRrrcMcwi (2019), LEXF10A/StmMcwi (2020), LN/MavRrrcAek (2020), M520/N (2020), BUF/N (2020), FXLE16/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020)
20 2774463 2774464 T C snv M520/N (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LEXF10A/StmMcwi (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359499 AgrOrtholog
BioCyc Gene G2FUF-4798 BioCyc
Ensembl Genes ENSRNOG00000032596 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050015.2 UniProtKB/TrEMBL
  ENSRNOP00000058011.4 UniProtKB/TrEMBL
  ENSRNOP00000064880.2 UniProtKB/TrEMBL
  ENSRNOP00000072021.2 UniProtKB/TrEMBL
  ENSRNOP00000074530.2 UniProtKB/TrEMBL
  ENSRNOP00000075284.2 UniProtKB/TrEMBL
  ENSRNOP00000075312.2 UniProtKB/TrEMBL
  ENSRNOP00000079819 ENTREZGENE
  ENSRNOP00000079819.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041502.3 UniProtKB/TrEMBL
  ENSRNOT00000061299.4 UniProtKB/TrEMBL
  ENSRNOT00000070903.3 UniProtKB/TrEMBL
  ENSRNOT00000078110.2 UniProtKB/TrEMBL
  ENSRNOT00000078454.2 UniProtKB/TrEMBL
  ENSRNOT00000082449.2 UniProtKB/TrEMBL
  ENSRNOT00000089044.2 UniProtKB/TrEMBL
  ENSRNOT00000116904 ENTREZGENE
  ENSRNOT00000116904.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
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
KEGG Report rno:361787 UniProtKB/TrEMBL
NCBI Gene 361787 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-T24-1 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 A0A0G2K1X5_RAT UniProtKB/TrEMBL
  A0A0G2K8A4_RAT UniProtKB/TrEMBL
  A0A0G2KA70_RAT UniProtKB/TrEMBL
  A0A0G2KA93_RAT UniProtKB/TrEMBL
  F1LXB3_RAT UniProtKB/TrEMBL
  F7EZJ6_RAT UniProtKB/TrEMBL
  M0R642_RAT UniProtKB/TrEMBL
  Q6MG05 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-T24-1  RT1 class I, locus T24, gene 1  RT1-T24-1  RT1 class I, T24, gene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-09-14 RT1-T24-1  RT1 class I, T24, gene 1  RT1-T24-1  histocompatibility 2, T region locus 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RT1-T24-1  histocompatibility 2, T region locus 24      Symbol and Name updated 1559027 APPROVED
2005-07-29 RT1-T24-1  histocompatibility 2, T region locus 24      Symbol and Name status set to provisional 70820 PROVISIONAL