RT1-CE10 (RT1 class I, locus CE10) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: RT1-CE10 (RT1 class I, locus CE10) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-CE10
Name: RT1 class I, locus CE10
RGD ID: 1359292
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, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to localize to 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; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC114586; RT1 class I, CE10; similar to Class I histocompatibility antigen, Non-RT1.A alpha-1 chain precursor
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,377,284 - 3,380,301 (-)NCBI
Rnor_6.0 Ensembl20154,074 - 157,861 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.020129,192 - 157,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.020130,753 - 158,873 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,468,602 - 3,471,619 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,468,828 - 3,471,846 (+)NCBI
Celera206,447,218 - 6,451,978 (+)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

Additional References at PubMed
PMID:29531166  


Genomics

Position Markers
BI280335  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.020154,311 - 154,464NCBIRnor6.0
Rnor_5.020155,493 - 155,646UniSTSRnor5.0
RGSC_v3.4203,471,812 - 3,471,965UniSTSRGSC3.4
RH 3.4 Map2052.32UniSTS
Cytogenetic Map20p12UniSTS
BQ194350  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.020158,913 - 159,078NCBIRnor6.0
Rnor_6.0204,898,833 - 4,898,998NCBIRnor6.0
Rnor_5.020160,095 - 160,260UniSTSRnor5.0
Rnor_5.0206,974,977 - 6,975,142UniSTSRnor5.0
RGSC_v3.4203,515,574 - 3,515,739UniSTSRGSC3.4
RGSC_v3.4203,467,198 - 3,467,363UniSTSRGSC3.4
Celera204,695,194 - 4,695,359UniSTS
Celera203,383,388 - 3,383,553UniSTS
RH 3.4 Map2052.3UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:37
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000048858
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 3 10 33 17 19 17 1 13 14 11
Low 19 24 24 24 8 10 38 10 27 8
Below cutoff 12 36 12

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048858   ⟹   ENSRNOP00000039057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,658 - 157,665 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079494   ⟹   ENSRNOP00000070126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,074 - 157,677 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084461   ⟹   ENSRNOP00000069895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,664 - 157,861 (-)Ensembl
RefSeq Acc Id: NM_001008833   ⟹   NP_001008833
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,377,284 - 3,380,301 (-)NCBI
Rnor_6.020154,657 - 157,674 (-)NCBI
Rnor_5.020130,753 - 158,873 (-)NCBI
RGSC_v3.4203,468,602 - 3,471,619 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255847   ⟹   XP_006255909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020154,072 - 157,689 (-)NCBI
Rnor_5.020130,753 - 158,873 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601724   ⟹   XP_017457213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020129,192 - 157,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601725   ⟹   XP_017457214
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020154,183 - 157,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601726   ⟹   XP_017457215
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020154,183 - 157,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601727   ⟹   XP_017457216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020129,192 - 157,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601728   ⟹   XP_017457217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020154,183 - 157,689 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601729   ⟹   XP_017457218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.020129,192 - 157,689 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001008833 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98952 (Get FASTA)   NCBI Sequence Viewer  
  AVP72134 (Get FASTA)   NCBI Sequence Viewer  
  CAE84013 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001008833   ⟸   NM_001008833
- Peptide Label: precursor
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255909   ⟸   XM_006255847
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017457218   ⟸   XM_017601729
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017457216   ⟸   XM_017601727
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457213   ⟸   XM_017601724
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017457217   ⟸   XM_017601728
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017457214   ⟸   XM_017601725
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017457215   ⟸   XM_017601726
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000070126   ⟸   ENSRNOT00000079494
RefSeq Acc Id: ENSRNOP00000069895   ⟸   ENSRNOT00000084461
RefSeq Acc Id: ENSRNOP00000039057   ⟸   ENSRNOT00000048858
Protein Domains
Ig-like

Transcriptome

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

Promoters
RGD ID:13701261
Promoter ID:EPDNEW_R11785
Type:multiple initiation site
Name:RT1-CE10_1
Description:RT1 class I, locus CE10
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_6.020157,694 - 157,754EPDNEW

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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 156081 156082 G C snv HWY/Slc (KyushuU), F344/Stm (KyushuU)
20 156338 156339 G C snv GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW)
20 156760 156761 G C snv LEC/Tj (KyushuU), ZF (KyushuU), RCS/Kyo (KyushuU), LE/Stm (KyushuU)
20 156762 156763 T G snv RCS/Kyo (KyushuU), LEC/Tj (KyushuU), ZFDM (KyushuU), BDIX/NemOda (KyushuU), BUF/MNa (KyushuU), ZF (KyushuU), HTX/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU)
20 157882 157883 C A snv FHL/EurMcwi (MCW), SR/JrHsd (MCW)
20 157895 157896 C A snv IS-Tlk/Kyo (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), IS/Kyo (KyushuU), NIG-III/Hok (KyushuU)
20 157937 157938 C A snv IS-Tlk/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), NIG-III/Hok (KyushuU), IS/Kyo (KyushuU), ZFDM (KyushuU)
20 157975 157976 C G snv LE/Stm (KyushuU), NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), ZF (KyushuU), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU)
20 157980 157981 G C snv NIG-III/Hok (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU)
20 157980 157981 G T snv HWY/Slc (KyushuU)
20 157990 157991 G C snv HTX/Kyo (KyushuU)
20 157990 157991 G T snv F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/DuCrlCrlj (KyushuU), RCS/Kyo (KyushuU), F344/Jcl (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), BUF/MNa (KyushuU), LE/Stm (KyushuU)
20 158027 158028 G C snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW)
20 158112 158113 A T snv GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), ZF (KyushuU), RCS/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), HTX/Kyo (KyushuU)
20 158340 158341 A G snv NIG-III/Hok (KyushuU)
20 158341 158342 G C snv DOB/Oda (KyushuU), NIG-III/Hok (KyushuU)
20 158393 158394 G C snv BUF/MNa (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU)
20 158393 158394 G T snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
20 158395 158396 T G snv F344/NSlc (KyushuU), RCS/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), BUF/MNa (KyushuU)
20 158398 158399 G C snv DOB/Oda (KyushuU)
20 158548 158549 C T snv BDIX/NemOda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 154542 154543 T C snv CDS, ACI/EurMcwi (MCW), CDR, SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW)
20 155126 155127 C A snv SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW)
20 155139 155140 G A snv GH/OmrMcwi (MCW), SBH/Ygl (MCW), CDS, ACI/EurMcwi (MCW), CDR, SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), COP/CrCrl (MCW & UW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW)
20 155580 155581 T G snv CDR
20 156700 156701 C A snv FHH/EurMcwi (MCW)
20 156713 156714 C A snv CDR, CDS
20 156755 156756 C A snv CDR, GH/OmrMcwi (MCW), CDS
20 156793 156794 C G snv SBN/Ygl (MCW), SBH/Ygl (MCW)
20 156808 156809 G T snv SR/JrHsd (MCW), CDR, GH/OmrMcwi (MCW), CDS, SBN/Ygl (MCW), SBH/Ygl (MCW), SS/JrHsdMcwi (MCW)
20 156815 156816 G A snv COP/CrCrl (MCW & UW)
20 156845 156846 G C snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW)
20 156878 156879 T C snv CDS, CDR
20 156879 156880 C T snv CDS, CDR
20 156908 156909 C G snv GH/OmrMcwi (MCW)
20 156930 156931 A T snv FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW)
20 157185 157186 T C snv CDR, CDS
20 157211 157212 G C snv CDS, CDR
20 157213 157214 T G snv CDR, CDS
20 157318 157319 C T snv SS/JrHsdMcwi (MCW)
20 157366 157367 C T snv GH/OmrMcwi (MCW)
20 157647 157648 G A snv GH/OmrMcwi (MCW), SR/JrHsd (MCW), CDR, SBH/Ygl (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), CDS
20 157665 157666 T C snv SR/JrHsd (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), CDR, SBH/Ygl (MCW), SS/JrHsdMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3469063 3469064 A C snv SS/Jr (ICL), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), WKY/NCrl (ICL), WAG/Rij (ICL), SR/JrHsd (ICL), LEW/Crl (ICL), FHL/EurMcwi (ICL), FHH/EurMcwi (ICL)
20 3469065 3469066 C G snv SS/Jr (ICL), LCR/1Mco (UMich), WKY/NCrl (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), WAG/Rij (ICL), SHR/OlaIpcv (KNAW), LCR/2Mco (UMich), LEW/Crl (ICL), HCR/1Mco (UMich), SR/JrHsd (ICL), HCR/2Mco (UMich), FHL/EurMcwi (ICL)
20 3469431 3469432 C G snv LCR/1Mco (UMich), COP/CrCrl (MCW & UW), HCR/1Mco (UMich), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW)
20 3469483 3469484 G C snv SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)
20 3469521 3469522 G T snv BUF/N (KNAW), LE/Stm (KNAW), WN/N (KNAW)
20 3469576 3469577 G T snv F344/NRrrc (KNAW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW)
20 3470865 3470866 C T snv LCR/1Mco (UMich), HCR/2Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)
20 3470913 3470914 C T snv HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich)
20 3471120 3471121 C G snv HCR/1Mco (UMich), GH/OmrMcwi (MCW), HCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359292 AgrOrtholog
Ensembl Genes ENSRNOG00000050210 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039057 UniProtKB/TrEMBL
  ENSRNOP00000069895 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070126 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048858 UniProtKB/TrEMBL
  ENSRNOT00000079494 UniProtKB/TrEMBL
  ENSRNOT00000084461 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7129682 IMAGE-MGC_LOAD
  IMAGE:7366301 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:414792 UniProtKB/TrEMBL
MGC_CLONE MGC:114586 IMAGE-MGC_LOAD
  MGC:95149 IMAGE-MGC_LOAD
NCBI Gene 414792 ENTREZGENE
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-CE10 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 A0A2P1NRX9_RAT UniProtKB/TrEMBL
  F7EWE4_RAT UniProtKB/TrEMBL
  Q4FZX6_RAT UniProtKB/TrEMBL
  Q6MG34 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 RT1-CE10  RT1 class I, locus CE10  LOC684280  similar to Class I histocompatibility antigen, Non-RT1.A alpha-1 chain precursor  Data Merged 1643240 APPROVED
2009-09-15 RT1-CE10  RT1 class I, locus CE10  RT1-CE10  RT1 class I, CE10  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC684280  similar to Class I histocompatibility antigen, Non-RT1.A alpha-1 chain precursor      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-29 RT1-CE10  RT1 class I, CE10      Symbol and Name status set to provisional 70820 PROVISIONAL