RT1-CE2 (RT1 class I, locus CE2) - Rat Genome Database

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Gene: RT1-CE2 (RT1 class I, locus CE2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-CE2
Name: RT1 class I, locus CE2
RGD ID: 1598235
Description: Predicted to be involved in antigen processing and presentation of peptide antigen via MHC class I. Predicted to be located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be part of MHC class I protein complex. Human ortholog(s) of this gene implicated in several diseases, including arthritis (multiple); asthma (multiple); eye disease (multiple); inner ear disease (multiple); and vasculitis (multiple). Orthologous to several human genes including HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-F (major histocompatibility complex, class I, F); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 17alpha-ethynylestradiol; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MHC class I protein; RT1 class I, CE2; RT1-C/E2
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,542,984 - 3,546,753 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2203,538,452 - 3,541,841 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,537,809 - 3,541,790 (-)EnsemblmRatBN7.2
Rnor_6.0204,771,960 - 4,774,886 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,852,360 - 6,855,286 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4203,576,840 - 3,579,764 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera205,290,369 - 5,293,293 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse:




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

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


Genomics

Variants

.
Variants in RT1-CE2
369 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
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)20134066551Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013629303Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
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
Celera205,293,636 - 5,293,725UniSTS
Celera203,419,088 - 3,419,216UniSTS
RGSC_v3.1203,430,349 - 3,430,478RGD
RH 3.4 Map2051.4UniSTS
RH 3.4 Map2051.4RGD
RH 2.0 Map2039.4RGD
Cytogenetic Map20p12UniSTS
D20Mgh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera203,419,083 - 3,419,216UniSTS
Celera205,293,636 - 5,293,729UniSTS
RH 3.4 Map2052.52UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 7 32 53 95 61 2 40 27 32 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000049310   ⟹   ENSRNOP00000040885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,537,809 - 3,541,790 (-)Ensembl
RefSeq Acc Id: NM_001008840   ⟹   NP_001008840
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,543,374 - 3,546,517 (-)NCBI
mRatBN7.2203,538,698 - 3,541,841 (-)NCBI
Rnor_6.0204,771,960 - 4,774,886 (-)NCBI
Rnor_5.0206,852,360 - 6,855,286 (-)NCBI
RGSC_v3.4203,576,840 - 3,579,764 (-)RGD
Celera205,290,369 - 5,293,293 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098958   ⟹   XP_038954886
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,542,984 - 3,546,753 (-)NCBI
mRatBN7.2203,538,452 - 3,541,841 (-)NCBI
RefSeq Acc Id: XM_063279387   ⟹   XP_063135457
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,542,984 - 3,546,517 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001008840 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954886 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135457 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AVP72129 (Get FASTA)   NCBI Sequence Viewer  
  CAC85696 (Get FASTA)   NCBI Sequence Viewer  
  CAE84008 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001008840   ⟸   NM_001008840
- Peptide Label: precursor
- UniProtKB: Q861Q3 (UniProtKB/TrEMBL),   E9PTZ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038954886   ⟸   XM_039098958
- Peptide Label: isoform X2
- UniProtKB: A0A2P1NRX6 (UniProtKB/TrEMBL),   E9PTZ9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000040885   ⟸   ENSRNOT00000049310
RefSeq Acc Id: XP_063135457   ⟸   XM_063279387
- Peptide Label: isoform X1
- UniProtKB: E9PTZ9 (UniProtKB/TrEMBL)
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKH0-F1-model_v2 AlphaFold D3ZKH0 1-349 view protein structure
AF-E9PTZ9-F1-model_v2 AlphaFold E9PTZ9 1-375 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598235 AgrOrtholog
BioCyc Gene G2FUF-4671 BioCyc
Ensembl Genes ENSRNOG00000047706 Ensembl
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:414779 UniProtKB/TrEMBL
NCBI Gene 414779 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-CE2 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047706 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A2P1NRX6 ENTREZGENE, UniProtKB/TrEMBL
  E9PTZ9 ENTREZGENE
  Q861Q3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-CE2  RT1 class I, locus CE2  RT1-CE2  RT1 class I, CE2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 RT1-CE2  RT1 class I, CE2      Symbol and Name status set to provisional 70820 PROVISIONAL