RT1-CE12 (RT1 class I, locus CE12) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: RT1-CE12 (RT1 class I, locus CE12) Rattus norvegicus
Analyze
Symbol: RT1-CE12
Name: RT1 class I, locus CE12
RGD ID: 1359103
Description: Predicted to be located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane; PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC103694382; MHC class I antigen; MHC RT44 protein; RT1 class I histocompatibility antigen, AA alpha chain-like; RT1 class I, CE12; RT1.46; uncharacterized LOC103694382
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,290,831 - 3,347,349 (-)NCBIGRCr8
mRatBN7.2203,338,907 - 3,342,547 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx203,579,813 - 3,583,429 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,395,284 - 3,398,901 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0203,928,036 - 3,931,674 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,939,621 - 4,940,253 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,969,434 - 7,019,708 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2731966   PMID:21873635   PMID:29531166  


Genomics

Variants

.
Variants in RT1-CE12
500 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
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
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
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
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
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
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

Markers in Region
D20Mgh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,417,756 - 3,417,890 (+)MAPPERmRatBN7.2
mRatBN7.2203,516,801 - 3,516,931 (+)MAPPERmRatBN7.2
Rnor_6.0204,931,692 - 4,931,821NCBIRnor6.0
Rnor_6.0204,638,390 - 4,638,523NCBIRnor6.0
Rnor_5.0206,718,432 - 6,718,565UniSTSRnor5.0
Rnor_5.0207,007,836 - 7,007,965UniSTSRnor5.0
RGSC_v3.4203,551,934 - 3,552,063UniSTSRGSC3.4
RGSC_v3.4203,430,123 - 3,430,256UniSTSRGSC3.4
Celera203,419,083 - 3,419,216UniSTS
RH 3.4 Map2052.52RGD
RH 2.0 Map2045.1RGD
Cytogenetic Map20p12UniSTS
D20Wox4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,417,761 - 3,417,890 (+)MAPPERmRatBN7.2
mRatBN7.2203,516,806 - 3,516,931 (+)MAPPERmRatBN7.2
Rnor_6.0204,931,697 - 4,931,821NCBIRnor6.0
Rnor_6.0204,638,395 - 4,638,523NCBIRnor6.0
Rnor_5.0207,007,841 - 7,007,965UniSTSRnor5.0
Rnor_5.0206,718,437 - 6,718,565UniSTSRnor5.0
RGSC_v3.4203,551,939 - 3,552,063UniSTSRGSC3.4
RGSC_v3.4203,430,123 - 3,430,251UniSTSRGSC3.4
RGSC_v3.1203,430,349 - 3,430,478RGD
Celera205,293,636 - 5,293,725UniSTS
Celera203,419,088 - 3,419,216UniSTS
RH 3.4 Map2051.4UniSTS
RH 3.4 Map2051.4RGD
RH 2.0 Map2039.4RGD
Cytogenetic Map20p12UniSTS
RH143921  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,437,218 - 3,437,388 (+)MAPPERmRatBN7.2
mRatBN7.2203,504,546 - 3,504,716 (+)MAPPERmRatBN7.2
Rnor_6.0204,921,406 - 4,921,575NCBIRnor6.0
Rnor_6.0204,698,779 - 4,698,948NCBIRnor6.0
Rnor_5.0206,997,550 - 6,997,719UniSTSRnor5.0
Rnor_5.0206,779,353 - 6,779,522UniSTSRnor5.0
RGSC_v3.4203,539,679 - 3,539,848UniSTSRGSC3.4
Celera203,422,784 - 3,422,946UniSTS
Celera203,626,888 - 3,627,057UniSTS
Celera202,974,135 - 2,974,304UniSTS
RH 3.4 Map2054.73UniSTS
Cytogenetic Map20p12UniSTS
BQ194350  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,381,539 - 3,381,705 (+)MAPPERmRatBN7.2
mRatBN7.2203,481,255 - 3,481,421 (+)MAPPERmRatBN7.2
Rnor_6.0204,898,833 - 4,898,998NCBIRnor6.0
Rnor_6.020158,913 - 159,078NCBIRnor6.0
Rnor_5.0206,974,977 - 6,975,142UniSTSRnor5.0
Rnor_5.020160,095 - 160,260UniSTSRnor5.0
RGSC_v3.4203,467,198 - 3,467,363UniSTSRGSC3.4
RGSC_v3.4203,515,574 - 3,515,739UniSTSRGSC3.4
Celera204,695,194 - 4,695,359UniSTS
Celera203,383,388 - 3,383,553UniSTS
RH 3.4 Map2052.3UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279098 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF387339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M24026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  MG963106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: NM_001008835   ⟹   NP_001008835
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,225 (-)NCBI
mRatBN7.2203,338,907 - 3,342,547 (-)NCBI
Rnor_5.0206,969,434 - 7,019,708 (-)NCBI
RefSeq Acc Id: XM_063279094   ⟹   XP_063135164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,344 (-)NCBI
RefSeq Acc Id: XM_063279095   ⟹   XP_063135165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,290,831 - 3,347,349 (-)NCBI
RefSeq Acc Id: XM_063279096   ⟹   XP_063135166
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,336 (-)NCBI
RefSeq Acc Id: XM_063279097   ⟹   XP_063135167
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,337 (-)NCBI
RefSeq Acc Id: XM_063279098   ⟹   XP_063135168
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,289 (-)NCBI
RefSeq Acc Id: XM_063279099   ⟹   XP_063135169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,343,585 - 3,347,125 (-)NCBI
RefSeq Acc Id: XR_010060664
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,290,831 - 3,347,349 (-)NCBI
RefSeq Acc Id: XR_010060665
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,290,831 - 3,347,349 (-)NCBI
RefSeq Acc Id: XR_010060666
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,290,831 - 3,347,349 (-)NCBI
RefSeq Acc Id: XR_010060667
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,290,831 - 3,347,349 (-)NCBI
RefSeq Acc Id: NP_001008835   ⟸   NM_001008835
- Peptide Label: precursor
- UniProtKB: Q6MG32 (UniProtKB/TrEMBL),   A0A2P1NRX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135165   ⟸   XM_063279095
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K4S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135164   ⟸   XM_063279094
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K4S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135167   ⟸   XM_063279097
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K4S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135166   ⟸   XM_063279096
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K4S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135168   ⟸   XM_063279098
- Peptide Label: isoform X5
- UniProtKB: O62933 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135169   ⟸   XM_063279099
- Peptide Label: isoform X5
- UniProtKB: O62933 (UniProtKB/TrEMBL)
Protein Domains
Ig-like

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-4703 BioCyc
Ensembl Genes ENSRNOG00000030712 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082497.2 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_class-I_related 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:309600 UniProtKB/TrEMBL
NCBI Gene 309600 ENTREZGENE
PANTHER HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, C ALPHA CHAIN UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-CE12 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030712 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K4S5 ENTREZGENE, UniProtKB/TrEMBL
  A0A2P1NRX5 ENTREZGENE, UniProtKB/TrEMBL
  O62933 ENTREZGENE, UniProtKB/TrEMBL
  Q6MG32 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 RT1-CE12  RT1 class I, locus CE12  LOC103694382  uncharacterized LOC103694382  Data merged from RGD:9126709 737654 PROVISIONAL
2014-08-25 LOC103694382  uncharacterized LOC103694382      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-09-15 RT1-CE12  RT1 class I, locus CE12  RT1-CE12  RT1 class I, CE12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 RT1-CE12  RT1 class I, CE12      Symbol and Name status set to provisional 70820 PROVISIONAL