RT1-T24-1 (RT1 class I, locus T24, gene 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: RT1-T24-1 (RT1 class I, locus T24, gene 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-T24-1
Name: RT1 class I, locus T24, gene 1
RGD ID: 1359499
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 located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be active in external side of plasma membrane and extracellular space; 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: H2-T24; histocompatibility 2, T region locus 24; RT1 class I, T24, gene 1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,766,304 - 2,779,680 (+)NCBIGRCr8
mRatBN7.2202,761,495 - 2,774,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,718,279 - 2,776,154 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx202,818,294 - 2,825,475 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,823,255 - 2,830,442 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,849,778 - 2,856,953 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,269,315 - 3,282,523 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,242,492 - 3,282,523 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,367,427 - 5,388,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,907,237 - 2,922,971 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1202,907,463 - 2,923,198 (+)NCBI
Celera20188,032 - 200,983 (+)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. Comparison of exon 5 sequences from 35 class I genes of the BALB/c mouse. Brorson KA, etal., J Exp Med 1989 Dec 1;170(6):1837-58.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15060004  


Genomics

Variants

.
Variants in RT1-T24-1
177 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000041502
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

Markers in Region
D20Yum33  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,766,460 - 2,766,623 (+)MAPPERmRatBN7.2
Rnor_6.0203,274,235 - 3,274,397NCBIRnor6.0
Rnor_5.0205,372,401 - 5,372,563UniSTSRnor5.0
RGSC_v3.4202,912,157 - 2,912,319UniSTSRGSC3.4
Celera20192,943 - 193,105UniSTS
Cytogenetic Map20p12UniSTS
BI298734  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,685,051 - 2,685,205 (+)MAPPERmRatBN7.2
mRatBN7.2202,761,943 - 2,762,097 (+)MAPPERmRatBN7.2
Rnor_6.0203,269,718 - 3,269,871NCBIRnor6.0
Rnor_6.0203,189,994 - 3,190,147NCBIRnor6.0
Rnor_5.0205,367,884 - 5,368,037UniSTSRnor5.0
Rnor_5.0205,288,160 - 5,288,313UniSTSRnor5.0
RGSC_v3.4202,830,285 - 2,830,438UniSTSRGSC3.4
RGSC_v3.4202,907,640 - 2,907,793UniSTSRGSC3.4
Celera20188,435 - 188,588UniSTS
Celera20115,465 - 115,618UniSTS
RH 3.4 Map2015.8UniSTS
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 1 1 1 1 2 1 5 2
Low 2 40 56 40 17 40 6 9 58 30 36 9 6
Below cutoff 2 2 2 16 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041502   ⟹   ENSRNOP00000050015
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,741,359 (+)Ensembl
Rnor_6.0 Ensembl203,242,492 - 3,282,523 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000061299   ⟹   ENSRNOP00000058011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,375 - 2,741,958 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000070903   ⟹   ENSRNOP00000064880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078110   ⟹   ENSRNOP00000075284
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,482 - 2,774,583 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078454   ⟹   ENSRNOP00000074530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082449   ⟹   ENSRNOP00000072021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,369 - 2,776,124 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089044   ⟹   ENSRNOP00000075312
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,356 - 2,741,958 (+)Ensembl
Rnor_6.0 Ensembl203,269,284 - 3,282,248 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116904   ⟹   ENSRNOP00000079819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,510 - 2,776,154 (+)Ensembl
RefSeq Acc Id: NM_001410263   ⟹   NP_001397192
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,766,304 - 2,779,680 (+)NCBI
mRatBN7.2202,761,495 - 2,774,871 (+)NCBI
RefSeq Acc Id: NM_001410264   ⟹   NP_001397193
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,766,304 - 2,779,680 (+)NCBI
mRatBN7.2202,761,495 - 2,774,871 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000075312   ⟸   ENSRNOT00000089044
RefSeq Acc Id: ENSRNOP00000050015   ⟸   ENSRNOT00000041502
RefSeq Acc Id: ENSRNOP00000079819   ⟸   ENSRNOT00000116904
RefSeq Acc Id: ENSRNOP00000072021   ⟸   ENSRNOT00000082449
RefSeq Acc Id: ENSRNOP00000075284   ⟸   ENSRNOT00000078110
RefSeq Acc Id: ENSRNOP00000064880   ⟸   ENSRNOT00000070903
RefSeq Acc Id: ENSRNOP00000058011   ⟸   ENSRNOT00000061299
RefSeq Acc Id: ENSRNOP00000074530   ⟸   ENSRNOT00000078454
RefSeq Acc Id: NP_001397192   ⟸   NM_001410263
- Peptide Label: isoform 1
- UniProtKB: Q6MG05 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001397193   ⟸   NM_001410264
- Peptide Label: isoform 2
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG05-F1-model_v2 AlphaFold Q6MG05 1-330 view protein structure

Transcriptome

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

Promoters
RGD ID:13701289
Promoter ID:EPDNEW_R11812
Type:multiple initiation site
Name:RT1-T24-1_1
Description:RT1 class I, locus T24, gene 1
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_6.0203,269,284 - 3,269,344EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359499 AgrOrtholog
BioCyc Gene G2FUF-4798 BioCyc
Ensembl Genes ENSRNOG00000032596 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061299.4 UniProtKB/TrEMBL
  ENSRNOT00000070903.3 UniProtKB/TrEMBL
  ENSRNOT00000078110.2 UniProtKB/TrEMBL
  ENSRNOT00000082449.2 UniProtKB/TrEMBL
  ENSRNOT00000089044.2 UniProtKB/TrEMBL
  ENSRNOT00000116904 ENTREZGENE
  ENSRNOT00000116904.1 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/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:361787 UniProtKB/TrEMBL
NCBI Gene 361787 ENTREZGENE
PANTHER HISTOCOMPATIBILITY 2, T REGION LOCUS 24 UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-T24-1 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032596 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K1X5_RAT UniProtKB/TrEMBL
  A0A0G2KA70_RAT UniProtKB/TrEMBL
  A0A0G2KA93_RAT UniProtKB/TrEMBL
  F1LXB3_RAT UniProtKB/TrEMBL
  M0R642_RAT UniProtKB/TrEMBL
  Q6MG05 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-T24-1  RT1 class I, locus T24, gene 1  RT1-T24-1  RT1 class I, T24, gene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-09-14 RT1-T24-1  RT1 class I, T24, gene 1  RT1-T24-1  histocompatibility 2, T region locus 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RT1-T24-1  histocompatibility 2, T region locus 24      Symbol and Name updated 1559027 APPROVED
2005-07-29 RT1-T24-1  histocompatibility 2, T region locus 24      Symbol and Name status set to provisional 70820 PROVISIONAL