RT1-CE16 (RT1 class I, locus CE16) - Rat Genome Database

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Gene: RT1-CE16 (RT1 class I, locus CE16) Rattus norvegicus
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Symbol: RT1-CE16
Name: RT1 class I, locus CE16
RGD ID: 1359403
Description: Predicted to enable several functions, including TAP complex binding activity; beta-2-microglobulin 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; positive regulation of T cell activation; and regulation of lymphocyte mediated immunity. Predicted to act upstream of or within antigen processing and presentation. Predicted to be located in several cellular components, including Golgi medial cisterna; cell surface; and endoplasmic reticulum exit site. Predicted to be part of MHC class I peptide loading complex and MHC class I protein complex; PARTICIPATES IN interleukin-12 signaling pathway; allograft rejection pathway; antigen processing and presentation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: class I histocompatibility antigen, Non-RT1.A alpha-1 chain-like; LOC103690108; mature MHC class I alpha heavy chain; MHC class Ib alpha chain; MHC class Ib molecule; MHC class Ib, RT1-Uav1; MHC class Ib, RT1-Uc; MHC class Ib, RT1-Ulv1; RT1 class I histocompatibility antigen, AA alpha chain-like; RT1 class I, CE16; RT1 class I, CE16 precursor, RT1-Un; RT1-Uav1; RT1-Uc; RT1-Ulv1; RT1.Cg
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,257,109 - 3,260,747 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,257,123 - 3,279,563 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0203,791,412 - 3,796,550 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,791,407 - 3,794,027 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0205,857,676 - 5,876,456 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera20685,595 - 688,522 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin G1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
beryllium sulfate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
brinzolamide  (ISO)
bupropion  (ISO)
butanal  (ISO)
butyric acid  (ISO)
caffeine  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefoxitin  (ISO)
ceric oxide  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
corn oil  (EXP)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
D-penicillamine  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diflunisal  (ISO)
disodium selenite  (ISO)
diuron  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
erythromycin A  (ISO)
etoposide  (ISO)
fenofibrate  (ISO)
ferroheme b  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
gentamycin  (EXP)
heme b  (ISO)
hydralazine  (ISO)
ifosfamide  (ISO)
ivermectin  (ISO)
ketorolac  (ISO)
lead diacetate  (EXP,ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
malathion  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
minocycline  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium dichromate  (ISO)
quercitrin  (ISO)
silicon dioxide  (EXP)
sodium arsenite  (ISO)
starch  (EXP)
sunitinib  (ISO)
tebufenpyrad  (ISO)
terbinafine  (ISO)
tetrachloromethane  (EXP,ISO)
thalidomide  (ISO)
thimerosal  (ISO)
ticlopidine  (ISO)
titanium dioxide  (ISO)
topiramate  (ISO)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
trimellitic anhydride  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
zidovudine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:3839199   PMID:8881041   PMID:12477932   PMID:29531166  


Genomics

Comparative Map Data
RT1-CE16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,257,109 - 3,260,747 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,257,123 - 3,279,563 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0203,791,412 - 3,796,550 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,791,407 - 3,794,027 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0205,857,676 - 5,876,456 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera20685,595 - 688,522 (-)NCBICelera
Cytogenetic Map20p12NCBI
HLA-A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38629,942,532 - 29,945,870 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl629,941,260 - 29,949,572 (+)EnsemblGRCh38hg38GRCh38
GRCh37629,910,309 - 29,913,647 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36630,018,310 - 30,021,633 (+)NCBINCBI36Build 36hg18NCBI36
Build 34630,018,309 - 30,021,632NCBI
Celera631,508,544 - 31,511,881 (+)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef629,655,296 - 29,712,161 (+)NCBIHuRef
CHM1_1629,857,559 - 29,915,772 (+)NCBICHM1_1
T2T-CHM13v2.0629,806,459 - 29,809,798 (+)NCBIT2T-CHM13v2.0
H2-Q1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,539,503 - 35,547,118 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,539,381 - 35,544,075 (+)EnsemblGRCm39 Ensembl
GRCm381735,320,525 - 35,328,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,320,405 - 35,325,099 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,457,503 - 35,462,044 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,928,615 - 34,933,472 (+)NCBIMGSCv36mm8
MGSCv361734,433,669 - 34,438,526 (+)NCBIMGSCv36mm8
Cytogenetic Map17B1NCBI
cM Map1718.63NCBI

Variants

.
Variants in RT1-CE16
318 total Variants

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
H2-D1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,908,501 - 4,908,657 (+)MAPPERmRatBN7.2
Rnor_6.0205,417,603 - 5,417,758NCBIRnor6.0
Rnor_5.0207,477,747 - 7,477,902UniSTSRnor5.0
RGSC_v3.4205,059,871 - 5,060,026UniSTSRGSC3.4
Celera206,492,138 - 6,492,293UniSTS
Celera20685,255 - 685,411UniSTS
Celera205,715,355 - 5,715,511UniSTS
Cytogenetic Map20p12UniSTS


Expression


Sequence


RefSeq Acc Id: ENSRNOT00000049310   ⟹   ENSRNOP00000040885
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,537,809 - 3,541,790 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000049540   ⟹   ENSRNOP00000039605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,791,407 - 3,793,985 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000060980   ⟹   ENSRNOP00000057699
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,257,123 - 3,279,563 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086293   ⟹   ENSRNOP00000074183
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,791,840 - 3,794,027 (-)Ensembl
RefSeq Acc Id: NM_001008839   ⟹   NP_001008839
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,257,109 - 3,260,747 (-)NCBI
Rnor_5.0205,857,676 - 5,876,456 (-)NCBI
Celera20685,595 - 688,522 (-)RGD
Sequence:
RefSeq Acc Id: NP_001008839   ⟸   NM_001008839
- Peptide Label: precursor
- UniProtKB: Q6MG28 (UniProtKB/TrEMBL),   A0A2P1NRY6 (UniProtKB/TrEMBL),   P79589 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039605   ⟸   ENSRNOT00000049540
RefSeq Acc Id: ENSRNOP00000074183   ⟸   ENSRNOT00000086293
RefSeq Acc Id: ENSRNOP00000040885   ⟸   ENSRNOT00000049310
RefSeq Acc Id: ENSRNOP00000057699   ⟸   ENSRNOT00000060980
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

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-4741 BioCyc
Ensembl Genes ENSRNOG00000047706 Ensembl
  ENSRNOG00000065254 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060980 ENTREZGENE
  ENSRNOT00000060980.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7365633 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
  MHC_I_a_C UniProtKB/TrEMBL
KEGG Report rno:414819 UniProtKB/TrEMBL
MGC_CLONE MGC:109587 IMAGE-MGC_LOAD
NCBI Gene 414819 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
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-CE16 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047706 RatGTEx
  ENSRNOG00000065254 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A2P1NRY6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8YPS9_RAT UniProtKB/TrEMBL
  P79589 ENTREZGENE, UniProtKB/TrEMBL
  Q5FVF6_RAT UniProtKB/TrEMBL
  Q6MG28 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 RT1-CE16  RT1 class I, locus CE16  LOC103690108  class I histocompatibility antigen, Non-RT1.A alpha-1 chain-like  Data merged from RGD:9113230 737654 PROVISIONAL
2014-08-25 LOC103690108  class I histocompatibility antigen, Non-RT1.A alpha-1 chain-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-09-15 RT1-CE16  RT1 class I, locus CE16  RT1-CE16  RT1 class I, CE16  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 RT1-CE16  RT1 class I, CE16      Symbol and Name status set to provisional 70820 PROVISIONAL