RT1-O1 (RT1 class Ib, locus O1) - Rat Genome Database

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Pathways
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Gene: RT1-O1 (RT1 class Ib, locus O1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-O1
Name: RT1 class Ib, locus O1
RGD ID: 3501
Description: Predicted to be involved in antigen processing and presentation of peptide antigen via MHC class I. 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; PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Qlikea; RATQLIKEA; RT1 class Ib gene H2-Q-like grc region; RT1 class Ib gene, H2-Q-like, grc region; RT1 class Ib, locus H2-Q-like, grc region; RT1-O
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,659,937 - 2,662,341 (+)NCBIGRCr8
mRatBN7.2202,655,116 - 2,657,520 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,655,116 - 2,657,520 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx202,740,349 - 2,742,753 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,745,310 - 2,747,712 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,771,819 - 2,774,223 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,160,535 - 3,162,939 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,162,039 - 3,162,939 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,258,701 - 5,261,105 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,799,232 - 2,801,636 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1202,798,404 - 2,805,038 (+)NCBI
Celera2085,590 - 87,994 (+)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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Genomic structure and organization of a Q-like gene in the GRC-G/C region of the rat. Rushton JJ, etal., Eur J Immunogenet 1994 Jun;21(3):189-98.
Additional References at PubMed
PMID:15060004  


Genomics

Variants

.
Variants in RT1-O1
46 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:178
Count of miRNA genes:125
Interacting mature miRNAs:135
Transcripts:ENSRNOT00000048036
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
D20Wox5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,658,895 - 2,659,158 (+)MAPPERmRatBN7.2
Rnor_6.0203,164,315 - 3,164,577NCBIRnor6.0
Rnor_6.0203,142,216 - 3,142,492NCBIRnor6.0
Rnor_5.0205,262,481 - 5,262,743UniSTSRnor5.0
Rnor_5.0205,240,382 - 5,240,658UniSTSRnor5.0
RGSC_v3.4202,780,205 - 2,781,189UniSTSRGSC3.4
RGSC_v3.4202,803,012 - 2,804,073UniSTSRGSC3.4
Celera2089,370 - 89,630UniSTS
RH 3.4 Map2015.8UniSTS
RH 3.4 Map2015.8RGD
RH 2.0 Map200.0RGD
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
Low 2 5 20 4 19 4 15 3 13 10
Below cutoff 1 9 11 11 11 6 8 24 21 20 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042882   ⟹   ENSRNOP00000041765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,649,964 - 2,652,027 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000048036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,162,039 - 3,162,939 (+)Ensembl
RefSeq Acc Id: NM_001008856   ⟹   NP_001008856
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,659,937 - 2,662,341 (+)NCBI
mRatBN7.2202,655,116 - 2,657,520 (+)NCBI
Rnor_6.0203,160,535 - 3,162,939 (+)NCBI
Rnor_5.0205,258,701 - 5,261,105 (+)NCBI
RGSC_v3.4202,799,232 - 2,801,636 (+)RGD
Celera2085,590 - 87,994 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008856 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84047 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000068581
  ENSRNOP00000068581.2
Reference Protein Sequences
RefSeq Acc Id: NP_001008856   ⟸   NM_001008856
- UniProtKB: Q6MG00 (UniProtKB/TrEMBL),   A0A0G2JT60 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000041765   ⟸   ENSRNOT00000042882
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:3501 AgrOrtholog
BioCyc Gene G2FUF-4818 BioCyc
Ensembl Genes ENSRNOG00000029001 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000032664 Ensembl
Ensembl Transcript ENSRNOT00000082880 ENTREZGENE
  ENSRNOT00000082880.2 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
KEGG Report rno:24751 UniProtKB/TrEMBL
NCBI Gene 24751 ENTREZGENE
PANTHER CLASS IB MHC ANTIGEN QA-2-RELATED UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
PhenoGen RT1-O1 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 A0A0G2JT60 ENTREZGENE
  Q6MG00 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A0G2JT60 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-O1  RT1 class Ib, locus O1  RT1-O  RT1 class Ib, locus H2-Q-like, grc region  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 RT1-2.5  RT1 class Ib, locus H2-Q-like, grc region  RT1-O  RT1 class Ib gene, H2-Q-like, grc region  Name updated 625702 APPROVED
2002-06-10 RT1-O  RT1 class Ib gene, H2-Q-like, grc region      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a alpha 3 domain, transmembrane region, cytoplasmic domain 633921