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

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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: Enables beta-2-microglobulin binding activity and peptide binding activity. Involved in T cell tolerance induction; negative regulation of natural killer cell mediated cytotoxicity; and positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. 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; 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: MGC114586; RT1 class I, CE10; similar to Class I histocompatibility antigen, Non-RT1.A alpha-1 chain precursor
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,381,377 - 3,385,052 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2203,377,284 - 3,380,301 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.020129,192 - 157,689 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl20154,074 - 157,861 (-)Ensemblrn6Rnor6.0
Rnor_5.020130,753 - 158,873 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4203,468,602 - 3,471,619 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera206,447,218 - 6,451,978 (+)NCBICelera
RGSC_v3.1203,468,828 - 3,471,846 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




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
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8597563   PMID:10837412   PMID:10856297   PMID:11773898   PMID:12817008   PMID:16000395   PMID:29531166  


Genomics

Variants

.
Variants in RT1-CE10
437 total Variants
miRNA Target Status (No longer updated)

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.


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
BI280335  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8203,381,615 - 3,381,769 (+)Marker Load Pipeline
mRatBN7.2203,376,937 - 3,377,091 (+)MAPPERmRatBN7.2
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
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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 62 153 91 90 59 71 59 6 310 165 10 132 62 92 31 10 10

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001443515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279417 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC083874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098952 (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

Ensembl Acc Id: ENSRNOT00000048858   ⟹   ENSRNOP00000039057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,658 - 157,665 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000079494   ⟹   ENSRNOP00000070126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,074 - 157,677 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000084461   ⟹   ENSRNOP00000069895
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,664 - 157,861 (-)Ensembl
RefSeq Acc Id: NM_001008833   ⟹   NP_001008833
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,381,962 - 3,384,979 (-)NCBI
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_063279417   ⟹   XP_063135487
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,381,377 - 3,385,052 (-)NCBI
RefSeq Acc Id: XM_063279418   ⟹   XP_063135488
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,381,377 - 3,385,052 (-)NCBI
RefSeq Acc Id: XM_063279419   ⟹   XP_063135489
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,381,377 - 3,385,052 (-)NCBI
RefSeq Acc Id: NP_001008833   ⟸   NM_001008833
- Peptide Label: precursor
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL),   A0A0G2K1E1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070126   ⟸   ENSRNOT00000079494
Ensembl Acc Id: ENSRNOP00000069895   ⟸   ENSRNOT00000084461
Ensembl Acc Id: ENSRNOP00000039057   ⟸   ENSRNOT00000048858
RefSeq Acc Id: XP_063135487   ⟸   XM_063279417
- Peptide Label: isoform X1
- UniProtKB: Q4FZX6 (UniProtKB/TrEMBL),   A0A0G2K1E1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135488   ⟸   XM_063279418
- Peptide Label: isoform X2
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL),   A0A0G2K1E1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135489   ⟸   XM_063279419
- Peptide Label: isoform X2
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL),   A0A0G2K1E1 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F7EWE4-F1-model_v2 AlphaFold F7EWE4 1-367 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359292 AgrOrtholog
BioCyc Gene G2FUF-4693 BioCyc
Ensembl Genes ENSRNOG00000050210 Ensembl
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_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
KEGG Report rno:414792 UniProtKB/TrEMBL
MGC_CLONE MGC:114586 IMAGE-MGC_LOAD
  MGC:95149 IMAGE-MGC_LOAD
NCBI Gene 414792 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
PhenoGen RT1-CE10 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000050210 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K1E1 ENTREZGENE
  Q4FZX6 ENTREZGENE, 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 from RGD:1592667 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