RT1-S2 (RT1 class Ib, locus S2) - Rat Genome Database

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Gene: RT1-S2 (RT1 class Ib, locus S2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-S2
Name: RT1 class Ib, locus S2
RGD ID: 1595920
Description: Predicted to be involved in antigen processing and presentation of peptide antigen via MHC class I and immune response. Predicted to be located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be part of MHC class I protein complex; INTERACTS WITH acetamide; amphetamine; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RT1 class Ib gene H2-TL-like(S2); RT1 class Ib gene, H2-TL-like; RT1 class Ib gene, H2-TL-like(S2); RT1 class Ib, locus H2-TL-like (S2); RT1 class Ib, locus H2-TL-like (S2) (mapped); RT1-S2_mapped; RT1.S1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,655,054 - 2,664,895 (+)NCBIGRCr8
mRatBN7.2202,650,233 - 2,651,654 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,649,964 - 2,652,027 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx202,735,459 - 2,736,880 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,740,420 - 2,741,841 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,744,720 - 2,768,350 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,152,073 - 3,165,871 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,155,652 - 3,157,088 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,253,818 - 5,255,239 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,794,349 - 2,795,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2080,707 - 82,128 (+)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. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
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:1300431   PMID:9089092  


Genomics

Variants

.
Variants in RT1-S2
87 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:124
Interacting mature miRNAs:136
Transcripts:ENSRNOT00000042882
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
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
AW523891  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,651,964 - 2,652,065 (+)MAPPERmRatBN7.2
Rnor_6.0203,157,384 - 3,157,484NCBIRnor6.0
Rnor_5.0205,255,550 - 5,255,650UniSTSRnor5.0
RGSC_v3.4202,796,081 - 2,796,181UniSTSRGSC3.4
Celera2082,439 - 82,539UniSTS
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 3 9 1 10 1 2 1 7
Low 10 22 14 9 14 8 9 9 26 26 4 8
Below cutoff 11 10 10 10 2 35 6 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042882   ⟹   ENSRNOP00000041765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,649,964 - 2,652,027 (+)Ensembl
Rnor_6.0 Ensembl203,155,652 - 3,157,073 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082880   ⟹   ENSRNOP00000068581
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,655,116 - 2,657,520 (+)Ensembl
Rnor_6.0 Ensembl203,156,170 - 3,157,088 (+)Ensembl
RefSeq Acc Id: NM_001008857   ⟹   NP_001008857
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,655,054 - 2,656,475 (+)NCBI
mRatBN7.2202,650,233 - 2,651,654 (+)NCBI
Rnor_6.0203,155,652 - 3,157,073 (+)NCBI
Rnor_5.0205,253,818 - 5,255,239 (+)NCBI
RGSC_v3.4202,794,349 - 2,795,770 (+)RGD
Celera2080,707 - 82,128 (+)RGD
Sequence:
RefSeq Acc Id: XM_063278970   ⟹   XP_063135040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,655,054 - 2,664,895 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001008857 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135040 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84048 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000041765
  ENSRNOP00000041765.2
Reference Protein Sequences
RefSeq Acc Id: NP_001008857   ⟸   NM_001008857
- Peptide Label: precursor
- UniProtKB: Q6MFZ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068581   ⟸   ENSRNOT00000082880
RefSeq Acc Id: ENSRNOP00000041765   ⟸   ENSRNOT00000042882
RefSeq Acc Id: XP_063135040   ⟸   XM_063278970
- Peptide Label: isoform X1
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MFZ9-F1-model_v2 AlphaFold Q6MFZ9 1-176 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)
AGR Gene RGD:1595920 AgrOrtholog
BioCyc Gene G2FUF-4820 BioCyc
Ensembl Genes ENSRNOG00000029001 Ensembl
  ENSRNOG00000032664 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042882 ENTREZGENE
  ENSRNOT00000042882.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 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_a_C UniProtKB/TrEMBL
KEGG Report rno:24994 UniProtKB/TrEMBL
NCBI Gene 24994 ENTREZGENE
PANTHER MHC CLASS I-RELATED UniProtKB/TrEMBL
  MHC CLASS IB T9-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I_C UniProtKB/TrEMBL
PhenoGen RT1-S2 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029001 RatGTEx
  ENSRNOG00000032664 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt Q6MFZ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-S2  RT1 class Ib, locus S2  RT1-S2  RT1 class Ib, locus H2-TL-like (S2)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-12 RT1-S2  RT1 class Ib, locus H2-TL-like (S2)  RT1-S2_mapped  RT1 class Ib, locus H2-TL-like (S2) (mapped)  Data merged from RGD:3505 737654 APPROVED
2006-11-20 RT1-S2  RT1 class Ib, locus H2-TL-like (S2)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-S2_mapped  RT1 class Ib, locus H2-TL-like (S2)(mapped)  RT1-S2  RT1 class Ib, locus H2-TL-like (S2)  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2004-02-11 RT1-2.5  RT1 class Ib, locus H2-TL-like (S2)  RT1-S2  RT1 class Ib gene, H2-TL-like(S2)  Name updated 625702 APPROVED
2002-06-10 RT1-S2  RT1 class Ib gene, H2-TL-like      Symbol and Name status set to approved 70586 APPROVED