RT1-T24-3 (RT1 class I, locus T24, gene 3) - Rat Genome Database

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Gene: RT1-T24-3 (RT1 class I, locus T24, gene 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-T24-3 (Ensembl: RT1-T24-4)
Name: RT1 class I, locus T24, gene 3 (Ensembl:RT1 class I, locus T24, gene 4)
RGD ID: 1624211
Description: INVOLVED IN antigen processing and presentation of peptide antigen via MHC class I (inferred); immune system process (inferred); FOUND IN lumenal side of endoplasmic reticulum membrane (inferred); membrane (inferred); MHC class I protein complex (inferred); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 17beta-estradiol 3-benzoate
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RT1 class I, T24, gene 3
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,723,043 - 2,752,691 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl202,723,049 - 2,730,857 (+)EnsemblGRCr8
mRatBN7.2202,718,210 - 2,730,604 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,718,279 - 2,776,154 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx202,770,185 - 2,809,487 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,775,145 - 2,814,446 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,801,652 - 2,840,970 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,226,010 - 3,257,254 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,226,313 - 3,233,694 (+)Ensemblrn6Rnor6.0
Rnor_5.0205,324,458 - 5,336,132 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4202,864,012 - 2,871,315 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera20145,036 - 152,339 (+)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. 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-T24-3
891 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:49
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000070903
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
BI284484  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,725,313 - 2,725,503 (+)MAPPERmRatBN7.2
Rnor_6.0203,233,394 - 3,233,583NCBIRnor6.0
Rnor_5.0205,331,560 - 5,331,749UniSTSRnor5.0
RGSC_v3.4202,871,015 - 2,871,204UniSTSRGSC3.4
Celera20152,039 - 152,228UniSTS
RH 3.4 Map2015.8UniSTS
Cytogenetic Map20p12UniSTS
RH131520  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,725,366 - 2,725,579 (+)MAPPERmRatBN7.2
Rnor_6.0203,233,447 - 3,233,659NCBIRnor6.0
Rnor_5.0205,331,613 - 5,331,825UniSTSRnor5.0
RGSC_v3.4202,871,068 - 2,871,280UniSTSRGSC3.4
Celera20152,092 - 152,304UniSTS
RH 3.4 Map2052.42UniSTS
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 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000041502   ⟹   ENSRNOP00000050015
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,741,359 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000061299   ⟹   ENSRNOP00000058011
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,375 - 2,741,958 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000070903   ⟹   ENSRNOP00000064880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
Rnor_6.0 Ensembl203,226,360 - 3,233,694 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000078110   ⟹   ENSRNOP00000075284
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,482 - 2,774,583 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000078454   ⟹   ENSRNOP00000074530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,718,279 - 2,725,613 (+)Ensembl
Rnor_6.0 Ensembl203,230,052 - 3,232,793 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082449   ⟹   ENSRNOP00000072021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,369 - 2,776,124 (+)Ensembl
Rnor_6.0 Ensembl203,226,352 - 3,232,428 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000089044   ⟹   ENSRNOP00000075312
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,734,356 - 2,741,958 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092423   ⟹   ENSRNOP00000075787
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,226,313 - 3,233,367 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000116904   ⟹   ENSRNOP00000079819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,761,510 - 2,776,154 (+)Ensembl
RefSeq Acc Id: NM_001166403   ⟹   NP_001159875
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,125 - 2,730,428 (+)NCBI
mRatBN7.2202,718,310 - 2,725,614 (+)NCBI
Rnor_6.0203,226,391 - 3,233,694 (+)NCBI
Rnor_5.0205,324,458 - 5,336,132 (+)NCBI
RGSC_v3.4202,864,012 - 2,871,315 (+)RGD
Celera20145,036 - 152,339 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098963   ⟹   XP_038954891
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,043 - 2,734,553 (+)NCBI
mRatBN7.2202,718,210 - 2,730,604 (+)NCBI
RefSeq Acc Id: XM_063279400   ⟹   XP_063135470
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,043 - 2,730,428 (+)NCBI
RefSeq Acc Id: XM_063279401   ⟹   XP_063135471
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,043 - 2,752,691 (+)NCBI
RefSeq Acc Id: XM_063279402   ⟹   XP_063135472
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,043 - 2,730,428 (+)NCBI
RefSeq Acc Id: XM_063279403   ⟹   XP_063135473
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,723,043 - 2,729,560 (+)NCBI
RefSeq Acc Id: NP_001159875   ⟸   NM_001166403
- UniProtKB: A0A0G2K8A4 (UniProtKB/TrEMBL),   F7EZJ6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000064880   ⟸   ENSRNOT00000070903
Ensembl Acc Id: ENSRNOP00000075787   ⟸   ENSRNOT00000092423
Ensembl Acc Id: ENSRNOP00000072021   ⟸   ENSRNOT00000082449
Ensembl Acc Id: ENSRNOP00000074530   ⟸   ENSRNOT00000078454
RefSeq Acc Id: XP_038954891   ⟸   XM_039098963
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8A4 (UniProtKB/TrEMBL),   F7EZJ6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000079819   ⟸   ENSRNOT00000116904
Ensembl Acc Id: ENSRNOP00000050015   ⟸   ENSRNOT00000041502
Ensembl Acc Id: ENSRNOP00000075284   ⟸   ENSRNOT00000078110
Ensembl Acc Id: ENSRNOP00000075312   ⟸   ENSRNOT00000089044
Ensembl Acc Id: ENSRNOP00000058011   ⟸   ENSRNOT00000061299
RefSeq Acc Id: XP_063135471   ⟸   XM_063279401
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8A4 (UniProtKB/TrEMBL),   F7EZJ6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135470   ⟸   XM_063279400
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8A4 (UniProtKB/TrEMBL),   F7EZJ6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135472   ⟸   XM_063279402
- Peptide Label: isoform X2
- UniProtKB: M0R642 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135473   ⟸   XM_063279403
- Peptide Label: isoform X3
Protein Domains
Ig-like   MHC class I-like antigen recognition-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K8A4-F1-model_v2 AlphaFold A0A0G2K8A4 1-316 view protein structure

Transcriptome

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

Promoters
RGD ID:13701288
Promoter ID:EPDNEW_R11810
Type:initiation region
Name:RT1-T24-3_1
Description:RT1 class I, locus T24, gene 3
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_6.0203,226,360 - 3,226,420EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1624211 AgrOrtholog
BioCyc Gene G2FUF-4804 BioCyc
Ensembl Genes ENSRNOG00000032596 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000045924 Ensembl
Ensembl Transcript ENSRNOT00000078454 ENTREZGENE
  ENSRNOT00000078454.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
InterPro Ig-like_dom 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:414788 UniProtKB/TrEMBL
NCBI Gene 414788 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
PhenoGen RT1-T24-3 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032596 RatGTEx
  ENSRNOG00000045924 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2K8A4 ENTREZGENE, UniProtKB/TrEMBL
  F7EZJ6 ENTREZGENE
  M0R642 ENTREZGENE
  Q6MG04_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-T24-3  RT1 class I, locus T24, gene 3  RT1-T24-3  RT1 class I, T24, gene 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-05-03 RT1-T24-3  RT1 class I, T24, gene 3      Symbol and Name status set to provisional 70820 PROVISIONAL