RT1-T18 (RT1 class Ib, locus T18) - Rat Genome Database

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Pathways
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Gene: RT1-T18 (RT1 class Ib, locus T18) Rattus norvegicus
Analyze
Symbol: RT1-T18
Name: RT1 class Ib, locus T18
RGD ID: 1303092
Description: PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 6-propyl-2-thiouracil; ammonium chloride
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: VALIDATED
Previously known as: H-2 class I histocompatibility antigen, TLA(B) alpha chain-like; H2-T18; H2-T3; histocompatibility 2, T region locus 18; histocompatibility 2, T region locus 3; LOC108348140; MHC class Ib antigen; RanoTL; TL antigen; Tla
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,605,478 - 2,614,543 (+)NCBIGRCr8
mRatBN7.2202,605,261 - 2,608,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,605,265 - 2,608,909 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx202,699,563 - 2,703,220 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,704,522 - 2,708,183 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,641,679 - 2,645,340 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,113,026 - 3,114,031 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,115,840 - 3,123,100 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,217,007 - 5,231,707 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,754,269 - 2,758,358 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1202,754,495 - 2,758,585 (+)NCBI
Celera2056,895 - 60,365 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. Hyperconservation of the putative antigen recognition site of the MHC class I-b molecule TL in the subfamily Murinae: evidence that thymus leukemia antigen is an ancient mammalian gene. Davis BK, etal., J Immunol 2002 Dec 15;169(12):6890-9.
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:12477932   PMID:15060004  


Genomics

Variants

.
Variants in RT1-T18
64 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:284
Count of miRNA genes:189
Interacting mature miRNAs:206
Transcripts:ENSRNOT00000061395
Prediction methods:Microtar, 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


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001002821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060737 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH012206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH012207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY144125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC104719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000061395
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,118,709 - 3,123,100 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080406
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,118,837 - 3,122,637 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084324
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,115,840 - 3,116,058 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,605,265 - 2,608,909 (+)Ensembl
RefSeq Acc Id: NM_001002821   ⟹   NP_001002821
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,610,278 - 2,613,925 (+)NCBI
mRatBN7.2202,605,261 - 2,608,909 (+)NCBI
Rnor_6.0203,113,026 - 3,114,031 (+)NCBI
Rnor_5.0205,217,007 - 5,231,707 (+)NCBI
RGSC_v3.4202,754,269 - 2,758,358 (+)RGD
Celera2056,895 - 60,365 (+)RGD
Sequence:
RefSeq Acc Id: XM_063279362   ⟹   XP_063135432
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,771 - 2,614,543 (+)NCBI
RefSeq Acc Id: XM_063279363   ⟹   XP_063135433
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,791 - 2,614,543 (+)NCBI
RefSeq Acc Id: XM_063279364   ⟹   XP_063135434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,879 - 2,614,543 (+)NCBI
RefSeq Acc Id: XM_063279365   ⟹   XP_063135435
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,792 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060733
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,771 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060734
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,810 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060735
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,791 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060736
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,791 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060737
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,605,478 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060738
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,519 - 2,614,543 (+)NCBI
RefSeq Acc Id: XR_010060739
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,606,879 - 2,614,543 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001002821   ⟸   NM_001002821
- Peptide Label: precursor
- UniProtKB: Q6MFZ7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_063135432   ⟸   XM_063279362
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135433   ⟸   XM_063279363
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135435   ⟸   XM_063279365
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063135434   ⟸   XM_063279364
- Peptide Label: isoform X1
Protein Domains
Ig-like

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303092 AgrOrtholog
BioCyc Gene G2FUF-4829 BioCyc
Ensembl Genes ENSRNOG00000030666 Ensembl
  ENSRNOG00000062067 Ensembl
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
KEGG Report rno:406194 UniProtKB/TrEMBL
NCBI Gene 406194 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
PhenoGen RT1-T18 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030666 RatGTEx
  ENSRNOG00000062067 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt Q6MFZ7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 RT1-T18  RT1 class Ib, locus T18  LOC108348140  H-2 class I histocompatibility antigen, TLA(B) alpha chain-like  Data merged from RGD:11396749 737654 PROVISIONAL
2016-08-02 LOC108348140  H-2 class I histocompatibility antigen, TLA(B) alpha chain-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2009-09-11 RT1-T18  RT1 class Ib, locus T18  H2-T3  histocompatibility 2, T region locus 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-20 H2-T3  histocompatibility 2, T region locus 3  H2-T18  histocompatibility 2, T region locus 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED