RT1-S3 (RT1 class Ib, locus S3) - Rat Genome Database

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Gene: RT1-S3 (RT1 class Ib, locus S3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-S3
Name: RT1 class Ib, locus S3
RGD ID: 735037
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 part of MHC class I protein complex. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including arthritis (multiple); asthma (multiple); eye disease (multiple); inner ear disease (multiple); and vasculitis (multiple). Orthologous to several human genes including HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-F (major histocompatibility complex, class I, F); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BM1; BM1av1; H2-T23; histocompatibility 2, T region locus 23; MHC class Ib RT1.S3; RT-BM1; RT1 class Ib gene(BM!); RT1 class Ib, locus BM1; RT1-BM1; RT1.S3; RTBM1
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,675,463 - 2,680,229 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.2202,670,654 - 2,675,411 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,670,709 - 2,675,411 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx202,756,137 - 2,760,852 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,761,097 - 2,765,812 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,787,603 - 2,792,318 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,176,124 - 3,180,825 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,176,107 - 3,179,818 (+)Ensemblrn6Rnor6.0
Rnor_5.0205,274,209 - 5,278,991 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4202,815,943 - 2,820,644 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera20101,124 - 105,825 (+)NCBICelera
RGSC_v3.1202,816,244 - 2,820,867 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
membrane  (IEA)

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 major histocompatibility complex of the rat (Rattus norvegicus). Gunther E and Walter L, Immunogenetics 2001 Sep;53(7):520-42.
3. Comparison of RT-BM1 sequences from six different rat major histocompatibility complex haplotypes reveals limited variation, and alternate splicing in the 3' untranslated region. Lau P, etal., Immunogenetics 2000 Feb;51(2):148-53.
4. A rat class I cDNA clone with an Alu-like sequence and mapping to two genes in RT1.C/E. Parker KE, etal., Immunogenetics 1990;31(3):211-4.
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Structural organization, sequence analysis, and physical mapping of the Grc-linked class Ib gene RT1.S3 in the rat. Salgar SK, etal., Immunogenetics 1998 Jun;48(1):76-81.
9. Genetic variants in the major histocompatibility complex class I and class II genes are associated with diisocyanate-induced Asthma. Yucesoy B, etal., J Occup Environ Med. 2014 Apr;56(4):382-7. doi: 10.1097/JOM.0000000000000138.
Additional References at PubMed
PMID:1538753   PMID:9427624   PMID:9486650   PMID:9754572   PMID:10799855   PMID:12411439   PMID:16474394   PMID:17179229   PMID:18083576   PMID:18339401   PMID:18448674   PMID:20458337  
PMID:21795542   PMID:23335510   PMID:25631937   PMID:28676677   PMID:30087334   PMID:30134159  


Genomics

Variants

.
Variants in RT1-S3
84 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:44
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000001036
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
AI411411  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0205,318,820 - 5,319,005NCBIRnor5.0
Rnor_5.020111,341 - 111,526NCBIRnor5.0
Rnor_5.0205,277,514 - 5,277,699NCBIRnor5.0
RGSC_v3.4202,819,168 - 2,819,352UniSTSRGSC3.4
RGSC_v3.4202,858,276 - 2,858,460UniSTSRGSC3.4
Celera20139,300 - 139,484UniSTS
Celera20104,349 - 104,533UniSTS
Cytogenetic Map20p12UniSTS
H2-T23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,671,177 - 2,672,392 (+)MAPPERmRatBN7.2
Rnor_6.0203,176,592 - 3,177,806NCBIRnor6.0
Rnor_5.0205,274,758 - 5,275,972UniSTSRnor5.0
RGSC_v3.4202,816,411 - 2,817,625UniSTSRGSC3.4
Celera20101,592 - 102,806UniSTS
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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000001036   ⟹   ENSRNOP00000001036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,670,709 - 2,675,411 (+)Ensembl
Rnor_6.0 Ensembl203,176,107 - 3,179,818 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082116   ⟹   ENSRNOP00000073220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,178,250 - 3,179,674 (+)Ensembl
RefSeq Acc Id: NM_001008886   ⟹   NP_001008886
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,675,528 - 2,680,229 (+)NCBI
mRatBN7.2202,670,709 - 2,675,411 (+)NCBI
Rnor_6.0203,176,124 - 3,180,825 (+)NCBI
Rnor_5.0205,274,209 - 5,278,991 (+)NCBI
RGSC_v3.4202,815,943 - 2,820,644 (+)RGD
Celera20101,124 - 105,825 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255917   ⟹   XP_006255979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,675,463 - 2,680,229 (+)NCBI
mRatBN7.2202,670,654 - 2,674,395 (+)NCBI
Rnor_6.0203,176,130 - 3,180,825 (+)NCBI
Rnor_5.0205,274,209 - 5,278,991 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001008886   ⟸   NM_001008886
- Peptide Label: precursor
- UniProtKB: F1LQF2 (UniProtKB/TrEMBL),   O78105 (UniProtKB/TrEMBL),   O78106 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255979   ⟸   XM_006255917
- Peptide Label: isoform X1
- UniProtKB: F1LQF2 (UniProtKB/TrEMBL),   O78105 (UniProtKB/TrEMBL),   O78106 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000073220   ⟸   ENSRNOT00000082116
Ensembl Acc Id: ENSRNOP00000001036   ⟸   ENSRNOT00000001036
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LQF2-F1-model_v2 AlphaFold F1LQF2 1-365 view protein structure

Transcriptome

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

Promoters
RGD ID:13701284
Promoter ID:EPDNEW_R11808
Type:initiation region
Name:RT1-S3_1
Description:RT1 class Ib, locus S3
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_6.0203,176,135 - 3,176,195EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735037 AgrOrtholog
BioCyc Gene G2FUF-4816 BioCyc
Ensembl Genes ENSRNOG00000000777 Ensembl
  ENSRNOG00000085024 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000120072 ENTREZGENE
  ENSRNOT00000120072.3 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_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:294228 UniProtKB/TrEMBL
NCBI Gene 294228 ENTREZGENE
PANTHER H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-37 ALPHA CHAIN UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-S3 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000777 RatGTEx
  ENSRNOG00000085024 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6AQ52_RAT UniProtKB/TrEMBL
  F1LQF2 ENTREZGENE
  O78105 ENTREZGENE, UniProtKB/TrEMBL
  O78106 ENTREZGENE
  Q9QUQ2_RAT UniProtKB/TrEMBL
UniProt Secondary O78106 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-11 RT1-S3  RT1 class Ib, locus S3  H2-T23  histocompatibility 2, T region locus 23  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 H2-T23  histocompatibility 2, T region locus 23  RT1-S3  RT1 class Ib, locus S3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 RT1-S3  RT1 class Ib, locus S3  RT1-BM1  RT1 class Ib, locus BM1  Data merged from RGD:3525 737654 APPROVED
2005-01-12 RT1-S3  RT1 class Ib, locus S3  RT1.S3  MHC class Ib RT1.S3  Symbol and Name updated 1299863 APPROVED
2004-02-11 RT1-BM1  RT1 class Ib, locus BM1  RTBM1  RT1 class Ib gene(BM!)  Symbol and Name updated 625702 APPROVED
2002-06-10 RTBM1  RT1 class Ib gene      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression by northern blot, expression was found in spleen, thymus and testis, but not liver 1299621
gene_homology appears to be an ortholog of the mouse H2-T23 gene which encodes the Qa-1 class 1 MHC molecule 1299621
gene_transcript alternative splicing in the 3' untranslated region gives rise to two different transcripts; the alternative splicing may be involved in regulating the stability of the mRNA 1299620