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

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Pathways
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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: 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 active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (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-E (major histocompatibility complex, class I, E); 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: PROVISIONAL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,381,377 - 3,385,052 (-)NCBIGRCr8
mRatBN7.2203,377,284 - 3,380,301 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.020129,192 - 157,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl20154,074 - 157,861 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.020130,753 - 158,873 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,468,602 - 3,471,619 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

Cellular Component

Molecular Function

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:29531166  


Genomics

Variants

.
Variants in RT1-CE10
555 total Variants
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.


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
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat

Markers in Region
BI280335  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,658 - 157,665 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079494   ⟹   ENSRNOP00000070126
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl20154,074 - 157,677 (-)Ensembl
RefSeq 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: PROVISIONAL
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
Protein Sequences
Protein RefSeqs NP_001008833 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135487 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135488 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135489 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98952 (Get FASTA)   NCBI Sequence Viewer  
  CAE84013 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000071804.2
Reference Protein Sequences
RefSeq Acc Id: NP_001008833   ⟸   NM_001008833
- Peptide Label: precursor
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL),   A0A0G2K1E1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070126   ⟸   ENSRNOT00000079494
RefSeq Acc Id: ENSRNOP00000069895   ⟸   ENSRNOT00000084461
RefSeq Acc Id: ENSRNOP00000039057   ⟸   ENSRNOT00000048858
RefSeq Acc Id: XP_063135487   ⟸   XM_063279417
- Peptide Label: isoform X1
- UniProtKB: Q4FZX6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135488   ⟸   XM_063279418
- Peptide Label: isoform X2
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135489   ⟸   XM_063279419
- Peptide Label: isoform X2
- UniProtKB: Q6MG34 (UniProtKB/TrEMBL)
Protein Domains
Ig-like

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 ENSRNOG00000038999 UniProtKB/TrEMBL
  ENSRNOG00000050210 Ensembl
Ensembl Transcript ENSRNOT00000080900.2 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
KEGG Report rno:414792 UniProtKB/TrEMBL
MGC_CLONE MGC:114586 IMAGE-MGC_LOAD
  MGC:95149 IMAGE-MGC_LOAD
NCBI Gene 414792 ENTREZGENE
PANTHER CLASS IB MHC ANTIGEN QA-2-RELATED 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 ENSRNOG00000038999 RatGTEx
  ENSRNOG00000050210 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K1E1 ENTREZGENE, UniProtKB/TrEMBL
  A0A2P1NRX9_RAT UniProtKB/TrEMBL
  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