RT1-CE1 (RT1 class I, locus 1) - Rat Genome Database

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Gene: RT1-CE1 (RT1 class I, locus 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-CE1
Name: RT1 class I, locus 1 (Ensembl:RT1 class I, locus1)
RGD ID: 1595869
Description: Predicted to enable beta-2-microglobulin binding activity; peptide antigen binding activity; and signaling receptor binding activity. Predicted to be involved in several processes, including positive regulation of gene expression; regulation of leukocyte mediated cytotoxicity; and regulation of lymphocyte activation. Predicted to act upstream of or within antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent; inner ear development; and natural killer cell mediated immunity. Predicted to be located in cell surface and plasma membrane. Predicted to be part of MHC class I protein complex and MHC class Ib protein complex. Predicted to be active in external side of plasma membrane and extracellular space. 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-H (major histocompatibility complex, class I, H (pseudogene)); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC102554995; MHC class I protein; RT1 class I, CE1; RT1 class I, CE12; RT1 class I, locus CE1; RT1 class I, locus1; RT1-C/E1; RT1-CE12; uncharacterized LOC102554995
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,560,455 - 3,564,428 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2203,555,779 - 3,559,487 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,555,782 - 3,559,486 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx203,480,890 - 3,484,114 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,489,036 - 3,492,235 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0203,539,571 - 3,542,801 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0204,638,235 - 4,792,390 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,638,663 - 4,943,564 (-)Ensemblrn6Rnor6.0
Rnor_5.0206,869,762 - 6,872,656 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4203,594,767 - 3,598,018 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,466,195 - 4,469,448 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse:




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

Biological Process

Cellular Component

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:9916694   PMID:12817008   PMID:29531166  


Genomics

Variants

.
Variants in RT1-CE1
565 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:58
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000047779, ENSRNOT00000061027
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


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 12 64 157 91 90 59 92 59 6 351 189 11 136 79 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000049310   ⟹   ENSRNOP00000040885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,638,663 - 4,943,564 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000061027   ⟹   ENSRNOP00000057743
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,638,720 - 4,792,283 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000089657
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,790,122 - 4,791,867 (-)Ensembl
RefSeq Acc Id: NM_001008832   ⟹   NP_001008832
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,839 - 3,564,090 (-)NCBI
mRatBN7.2203,556,163 - 3,559,417 (-)NCBI
Rnor_6.0204,638,235 - 4,792,390 (-)NCBI
Rnor_5.0206,869,762 - 6,872,656 (-)NCBI
RGSC_v3.4203,594,767 - 3,598,018 (-)RGD
Celera204,466,195 - 4,469,448 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098654   ⟹   XP_038954582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,428 (-)NCBI
mRatBN7.2203,555,779 - 3,559,486 (-)NCBI
RefSeq Acc Id: XM_063279100   ⟹   XP_063135170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,166 (-)NCBI
RefSeq Acc Id: XM_063279101   ⟹   XP_063135171
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,427 (-)NCBI
RefSeq Acc Id: XM_063279102   ⟹   XP_063135172
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,165 (-)NCBI
RefSeq Acc Id: XM_063279103   ⟹   XP_063135173
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,120 (-)NCBI
RefSeq Acc Id: XM_063279104   ⟹   XP_063135174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,563,900 (-)NCBI
RefSeq Acc Id: XM_063279105   ⟹   XP_063135175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,564,118 (-)NCBI
RefSeq Acc Id: XM_063279106   ⟹   XP_063135176
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,560,455 - 3,563,966 (-)NCBI
RefSeq Acc Id: NP_001008832   ⟸   NM_001008832
- Peptide Label: precursor
- UniProtKB: Q861Q4 (UniProtKB/TrEMBL),   A0A2P1NRX5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057743   ⟸   ENSRNOT00000061027
Ensembl Acc Id: ENSRNOP00000040885   ⟸   ENSRNOT00000049310
RefSeq Acc Id: XP_038954582   ⟸   XM_039098654
- Peptide Label: isoform X1
- UniProtKB: A0A2P1NRX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135171   ⟸   XM_063279101
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K4S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135170   ⟸   XM_063279100
- Peptide Label: isoform X2
- UniProtKB: A0A2P1NRX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135172   ⟸   XM_063279102
- Peptide Label: isoform X4
- UniProtKB: A0A2P1NRX5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135173   ⟸   XM_063279103
- Peptide Label: isoform X5
- UniProtKB: O62933 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135175   ⟸   XM_063279105
- Peptide Label: isoform X6
- UniProtKB: O62933 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135176   ⟸   XM_063279106
- Peptide Label: isoform X6
- UniProtKB: O62933 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135174   ⟸   XM_063279104
- 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

Promoters
RGD ID:13701368
Promoter ID:EPDNEW_R11887
Type:single initiation site
Name:RT1-CE1_2
Description:RT1 class I, locus1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11900  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0204,792,276 - 4,792,336EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595869 AgrOrtholog
BioCyc Gene G2FUF-4668 BioCyc
Ensembl Genes ENSRNOG00000030712 Ensembl
  ENSRNOG00000050183 Ensembl
  ENSRNOG00000071235 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000120404 ENTREZGENE
  ENSRNOT00000120404.2 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_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:309603 UniProtKB/TrEMBL
NCBI Gene 309603 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-CE1 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030712 RatGTEx
  ENSRNOG00000050183 RatGTEx
  ENSRNOG00000071235 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K4S5 ENTREZGENE
  A0A2P1NRX5 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L3M9_RAT UniProtKB/TrEMBL
  O62933 ENTREZGENE, UniProtKB/TrEMBL
  Q861Q4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2025-01-27 RT1-CE1  RT1 class I, locus 1  RT1-CE1  RT1 class I, locus1  Name changed 629549 APPROVED
2015-07-29 RT1-CE1  RT1 class I, locus1  LOC102554995  uncharacterized LOC102554995  Data merged from RGD:7500633 737654 PROVISIONAL
2013-12-17 LOC102554995  uncharacterized LOC102554995      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-09-15 RT1-CE1  RT1 class I, locus1  RT1-CE1  RT1 class I, CE1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 RT1-CE1  RT1 class I, CE1      Symbol and Name status set to provisional 70820 PROVISIONAL