RT1-T24-4 (RT1 class I, locus T24, gene 4) - Rat Genome Database

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Gene: RT1-T24-4 (RT1 class I, locus T24, gene 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-T24-4
Name: RT1 class I, locus T24, gene 4
RGD ID: 1598233
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 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H2-T24; histocompatibility 2, T region locus 24; MGC112931; MHC class I RT1.O type 149 processed pseudogene; RT1 class I, T24, gene 4; RT1-149
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,689,329 - 2,749,848 (+)NCBIGRCr8
mRatBN7.2202,684,515 - 2,747,878 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,684,515 - 2,692,511 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0203,189,457 - 3,197,457 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,189,473 - 3,197,457 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,287,081 - 5,348,200 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,829,748 - 2,837,748 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera20114,928 - 122,928 (+)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
Additional References at PubMed
PMID:7672818   PMID:12477932  


Genomics

Variants

.
Variants in RT1-T24-4
2348 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:78
Count of miRNA genes:75
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000047439
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
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
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
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
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
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
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
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
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
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat

Markers in Region
D20Yum31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,688,499 - 2,688,678 (+)MAPPERmRatBN7.2
Rnor_6.0203,193,442 - 3,193,620NCBIRnor6.0
Rnor_5.0205,291,608 - 5,291,786UniSTSRnor5.0
RGSC_v3.4202,833,733 - 2,833,911UniSTSRGSC3.4
Celera20118,913 - 119,091UniSTS
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
RH131544  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0205,353,773 - 5,353,981NCBIRnor5.0
Rnor_5.020127,246 - 127,454NCBIRnor5.0
Rnor_5.0205,299,230 - 5,299,438NCBIRnor5.0
RGSC_v3.4202,893,229 - 2,893,436UniSTSRGSC3.4
RGSC_v3.4202,841,356 - 2,841,563UniSTSRGSC3.4
Celera20174,037 - 174,244UniSTS
RH 3.4 Map2015.8UniSTS
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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC098866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC158853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM045430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L40364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000047439   ⟹   ENSRNOP00000043387
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,684,515 - 2,692,511 (+)Ensembl
Rnor_6.0 Ensembl203,189,473 - 3,197,457 (+)Ensembl
RefSeq Acc Id: NM_001008826   ⟹   NP_001008826
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,333 - 2,697,333 (+)NCBI
mRatBN7.2202,684,515 - 2,692,515 (+)NCBI
Rnor_6.0203,189,457 - 3,197,457 (+)NCBI
Rnor_5.0205,287,081 - 5,348,200 (+)NCBI
RGSC_v3.4202,829,748 - 2,837,748 (+)RGD
Celera20114,928 - 122,928 (+)RGD
Sequence:
RefSeq Acc Id: XM_063279389   ⟹   XP_063135459
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,749,650 (+)NCBI
RefSeq Acc Id: XM_063279390   ⟹   XP_063135460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,749,650 (+)NCBI
RefSeq Acc Id: XM_063279391   ⟹   XP_063135461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,738,891 - 2,749,848 (+)NCBI
RefSeq Acc Id: XM_063279392   ⟹   XP_063135462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,697,333 (+)NCBI
RefSeq Acc Id: XM_063279393   ⟹   XP_063135463
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,749,650 (+)NCBI
RefSeq Acc Id: XM_063279394   ⟹   XP_063135464
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,739,237 - 2,749,848 (+)NCBI
RefSeq Acc Id: XM_063279395   ⟹   XP_063135465
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,697,333 (+)NCBI
RefSeq Acc Id: XM_063279396   ⟹   XP_063135466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,738,888 - 2,749,848 (+)NCBI
RefSeq Acc Id: XM_063279397   ⟹   XP_063135467
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,689,329 - 2,697,333 (+)NCBI
RefSeq Acc Id: XM_063279398   ⟹   XP_063135468
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,738,790 - 2,749,848 (+)NCBI
RefSeq Acc Id: NP_001008826   ⟸   NM_001008826
- UniProtKB: Q4G002 (UniProtKB/TrEMBL),   A6KT56 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000043387   ⟸   ENSRNOT00000047439
RefSeq Acc Id: XP_063135460   ⟸   XM_063279390
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063135459   ⟸   XM_063279389
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135463   ⟸   XM_063279393
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063135465   ⟸   XM_063279395
- Peptide Label: isoform X7
- UniProtKB: Q6MG03 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135462   ⟸   XM_063279392
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063135467   ⟸   XM_063279397
- Peptide Label: isoform X9
RefSeq Acc Id: XP_063135468   ⟸   XM_063279398
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063135466   ⟸   XM_063279396
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063135461   ⟸   XM_063279391
- Peptide Label: isoform X3
- UniProtKB: A0A0G2KA93 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135464   ⟸   XM_063279394
- Peptide Label: isoform X6
- UniProtKB: F1LXB3 (UniProtKB/TrEMBL)
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4G002-F1-model_v2 AlphaFold Q4G002 1-373 view protein structure

Transcriptome

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

Promoters
RGD ID:13701285
Promoter ID:EPDNEW_R11809
Type:initiation region
Name:RT1-T24-4_1
Description:RT1 class I, locus T24, gene 4
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_6.0203,189,473 - 3,189,533EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598233 AgrOrtholog
BioCyc Gene G2FUF-4813 BioCyc
Ensembl Genes ENSRNOG00000032596 UniProtKB/TrEMBL
  ENSRNOG00000042905 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047439.6 UniProtKB/TrEMBL
  ENSRNOT00000061299.4 UniProtKB/TrEMBL
  ENSRNOT00000089044.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7380738 IMAGE-MGC_LOAD
  IMAGE:7936214 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_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:414784 UniProtKB/TrEMBL
MGC_CLONE MGC:112931 IMAGE-MGC_LOAD
  MGC:188366 IMAGE-MGC_LOAD
NCBI Gene 414784 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-T24-4 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032596 RatGTEx
  ENSRNOG00000042905 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2KA93 ENTREZGENE, UniProtKB/TrEMBL
  A6KT56 ENTREZGENE, UniProtKB/TrEMBL
  F1LXB3 ENTREZGENE, UniProtKB/TrEMBL
  Q4G002 ENTREZGENE, UniProtKB/TrEMBL
  Q6MG03 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-T24-4  RT1 class I, locus T24, gene 4  RT1-T24-4  RT1 class I, T24, gene 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-09-11 RT1-T24-4  RT1 class I, T24, gene 4  H2-T24  histocompatibility 2, T region locus 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 H2-T24  histocompatibility 2, T region locus 24  RT1-149  RT1-149 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 RT1-149  RT1-149 protein      Symbol and Name status set to provisional 70820 PROVISIONAL