RT1-M5 (RT1 class Ib, locus M5) - Rat Genome Database

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Gene: RT1-M5 (RT1 class Ib, locus M5) Rattus norvegicus
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Symbol: RT1-M5
Name: RT1 class Ib, locus M5
RGD ID: 1595816
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; INTERACTS WITH 6-propyl-2-thiouracil; aflatoxin B1; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Hla-f; LOC499400; major histocompatibility complex, class I, F; MHC class Ib antigen RT1.M5 long isoform; MHC class Ib antigen RT1.M5 short isoform; RGD1560260; RT1 class Ib gene, locus M5; RT1 class Ib, locus M5 (mapped); RT1-M5_mapped; RT1.M5; similar to RT1 class I, M5
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,551,751 - 1,554,015 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl201,549,836 - 1,558,362 (-)EnsemblGRCr8
mRatBN7.2201,546,496 - 1,548,948 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,546,511 - 1,548,775 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx201,599,901 - 1,602,165 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,603,397 - 1,605,661 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,544,793 - 1,547,057 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,038,158 - 2,040,422 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl202,038,158 - 2,040,422 (-)Ensemblrn6Rnor6.0
Rnor_5.0204,078,537 - 4,080,801 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4201,638,276 - 1,640,540 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera202,254,856 - 2,257,120 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse:




Disease 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. HLA-B27 subtypes in Turkish patients with ankylosing spondylitis and healthy controls. Acar M, etal., Rheumatol Int. 2012 Oct;32(10):3103-5. Epub 2011 Sep 17.
2. 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.
3. Lack of association of HLA-B*51 with a severe disease course in Behcet's disease. Gul A, etal., Rheumatology (Oxford). 2001 Jun;40(6):668-72.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. Clinical phenotype is related to HLA genotype in the peripheral arthropathies of inflammatory bowel disease. Orchard TR, etal., Gastroenterology. 2000 Feb;118(2):274-8.
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Novel HLA B*2714 and B*2708 allele associations in seronegative spondarthritis patients and haemophilia patients with chronic synovitis in India. Shankarkumar U, etal., Tissue Antigens. 2003 Aug;62(2):175-8.
Additional References at PubMed
PMID:11685465   PMID:15060004   PMID:18324395  


Genomics

Comparative Map Data
RT1-M5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,551,751 - 1,554,015 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl201,549,836 - 1,558,362 (-)EnsemblGRCr8
mRatBN7.2201,546,496 - 1,548,948 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,546,511 - 1,548,775 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx201,599,901 - 1,602,165 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,603,397 - 1,605,661 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,544,793 - 1,547,057 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,038,158 - 2,040,422 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl202,038,158 - 2,040,422 (-)Ensemblrn6Rnor6.0
Rnor_5.0204,078,537 - 4,080,801 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4201,638,276 - 1,640,540 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera202,254,856 - 2,257,120 (-)NCBICelera
Cytogenetic Map20p12NCBI
H2-M5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391737,294,677 - 37,308,847 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1737,294,953 - 37,300,429 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381736,983,785 - 36,997,955 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1736,984,061 - 36,989,537 (-)Ensemblmm10GRCm38
MGSCv371737,123,800 - 37,126,449 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361736,595,031 - 36,597,557 (-)NCBIMGSCv36mm8
Celera1740,410,376 - 40,413,023 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1719.16NCBI

Variants

.
Variants in RT1-M5
13 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000052311
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
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
7 10 93 43 38 13 16 13 6 80 41 1 74 19 43 25 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000052311   ⟹   ENSRNOP00000045665
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl201,551,751 - 1,558,362 (-)Ensembl
mRatBN7.2 Ensembl201,546,511 - 1,548,775 (-)Ensembl
Rnor_6.0 Ensembl202,038,158 - 2,040,422 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000080237   ⟹   ENSRNOP00000073221
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl202,038,158 - 2,040,080 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000082965   ⟹   ENSRNOP00000069692
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl202,038,158 - 2,040,080 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120325   ⟹   ENSRNOP00000098015
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl201,549,836 - 1,558,362 (-)Ensembl
RefSeq Acc Id: NM_001048045   ⟹   NP_001041510
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,551,751 - 1,554,015 (-)NCBI
mRatBN7.2201,546,511 - 1,548,775 (-)NCBI
Rnor_6.0202,038,158 - 2,040,422 (-)NCBI
Rnor_5.0204,078,537 - 4,080,801 (-)NCBI
RGSC_v3.4201,638,276 - 1,640,540 (-)ENTREZGENE
Celera202,254,856 - 2,257,120 (-)ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001168353   ⟹   NP_001161825
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,551,751 - 1,554,015 (-)NCBI
mRatBN7.2201,546,511 - 1,548,775 (-)NCBI
Rnor_6.0202,038,158 - 2,040,422 (-)NCBI
Rnor_5.0204,078,537 - 4,080,801 (-)NCBI
RGSC_v3.4201,638,276 - 1,640,540 (-)ENTREZGENE
Celera202,254,856 - 2,257,120 (-)ENTREZGENE
Sequence:
RefSeq Acc Id: NP_001041510   ⟸   NM_001048045
- Peptide Label: isoform 2 precursor
- UniProtKB: Q0PKT2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001161825   ⟸   NM_001168353
- Peptide Label: isoform 1 precursor
- UniProtKB: F1MAR7 (UniProtKB/TrEMBL),   Q0PKT2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000069692   ⟸   ENSRNOT00000082965
Ensembl Acc Id: ENSRNOP00000073221   ⟸   ENSRNOT00000080237
Ensembl Acc Id: ENSRNOP00000045665   ⟸   ENSRNOT00000052311
Ensembl Acc Id: ENSRNOP00000098015   ⟸   ENSRNOT00000120325
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MAR7-F1-model_v2 AlphaFold F1MAR7 1-357 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:1595816 AgrOrtholog
BioCyc Gene G2FUF-4985 BioCyc
Ensembl Genes ENSRNOG00000033136 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000052311 ENTREZGENE
  ENSRNOT00000052311.6 UniProtKB/TrEMBL
  ENSRNOT00000120325 ENTREZGENE
  ENSRNOT00000120325.2 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
NCBI Gene RT1-M5 ENTREZGENE
PANTHER HISTOCOMPATIBILITY 2, M REGION LOCUS 5 UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-M5 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033136 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0ABK0L3I7_RAT UniProtKB/TrEMBL
  F1MAR7 ENTREZGENE, UniProtKB/TrEMBL
  O77979_RAT UniProtKB/TrEMBL
  Q0PKT2 ENTREZGENE, UniProtKB/TrEMBL
  Q6MFY1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-21 RT1-M5  RT1 class Ib, locus M5  Hla-f  major histocompatibility complex, class I, F  Data merged from RGD:1560260 737654 APPROVED
2008-04-30 RGD1560260  similar to RT1 class I, M5   RGD1560260_predicted  similar to RT1 class I, M5 (predicted)  'predicted' is removed 2292626 APPROVED
2007-04-12 RT1-M5  RT1 class Ib, locus M5  RT1-M5_mapped  RT1 class Ib, locus M5 (mapped)  Data merged from RGD:3496 737654 APPROVED
2006-11-20 RT1-M5_mapped  RT1 class Ib, locus M5(mapped)  RT1-M5  RT1 class Ib, locus M5  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-M5  RT1 class Ib, locus M5      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-07 RGD1560260_predicted  similar to RT1 class I, M5 (predicted)  LOC499400  similar to RT1 class I, M5  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499400  similar to RT1 class I, M5      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-2.5  RT1 class Ib, locus M5  RT1-M5  RT1 class Ib gene, locus M5  Name updated 625702 APPROVED
2002-06-10 RT1-M5  RT1 class Ib gene, locus M5      Symbol and Name status set to approved 70586 APPROVED