RT1-M2 (RT1 class Ib, locus M2) - Rat Genome Database

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Gene: RT1-M2 (RT1 class Ib, locus M2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-M2
Name: RT1 class Ib, locus M2
RGD ID: 3493
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 active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including Stevens-Johnson syndrome; asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (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 17beta-estradiol; 17beta-estradiol 3-benzoate; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RT1 class Ib gene, locus M2
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr820984,174 - 986,762 (+)NCBIGRCr8
mRatBN7.220978,918 - 981,510 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl20978,935 - 981,723 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx201,004,207 - 1,006,431 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,007,665 - 1,009,887 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.020972,795 - 975,035 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0201,337,242 - 1,339,488 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl201,337,149 - 1,339,488 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0201,328,649 - 1,330,895 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera201,717,719 - 1,719,942 (+)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 major histocompatibility complex of the rat (Rattus norvegicus). Gunther E and Walter L, Immunogenetics 2001 Sep;53(7):520-42.
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
Additional References at PubMed
PMID:15045471   PMID:15060004  


Genomics

Variants

.
Variants in RT1-M2
28 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:78
Count of miRNA genes:65
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000041074
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
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
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
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
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat


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
nervous system
renal system
reproductive system
respiratory system
9 7 23 33 80 79 48 25 48 6 146 70 13 14 35 31

Sequence


Ensembl Acc Id: ENSRNOT00000041074   ⟹   ENSRNOP00000043659
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl20978,935 - 981,723 (+)Ensembl
Rnor_6.0 Ensembl201,337,149 - 1,339,488 (-)Ensembl
RefSeq Acc Id: NM_001001717   ⟹   NP_001001717
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr820984,174 - 986,762 (+)NCBI
mRatBN7.220978,918 - 981,510 (+)NCBI
Rnor_6.0201,337,242 - 1,339,488 (-)NCBI
Rnor_5.0201,328,649 - 1,330,895 (-)NCBI
Celera201,717,719 - 1,719,942 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001001717 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ81309 (Get FASTA)   NCBI Sequence Viewer  
  EDL84641 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000043659
  ENSRNOP00000043659.4
RefSeq Acc Id: NP_001001717   ⟸   NM_001001717
- Peptide Label: precursor
- UniProtKB: Q6W9J5 (UniProtKB/TrEMBL),   F1LW75 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000043659   ⟸   ENSRNOT00000041074
Protein Domains
Ig-like   MHC class I-like antigen recognition-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6W9J5-F1-model_v2 AlphaFold Q6W9J5 1-344 view protein structure

Transcriptome

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

Promoters
RGD ID:13701264
Promoter ID:EPDNEW_R11788
Type:single initiation site
Name:RT1-M2_1
Description:RT1 class Ib, locus M2
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_6.0201,339,505 - 1,339,565EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3493 AgrOrtholog
BioCyc Gene G2FUF-5040 BioCyc
Ensembl Genes ENSRNOG00000049590 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041074 ENTREZGENE
  ENSRNOT00000041074.6 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:24988 UniProtKB/TrEMBL
NCBI Gene 24988 ENTREZGENE
PANTHER HISTOCOMPATIBILITY 2, M REGION LOCUS 2 UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-M2 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049590 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A6KR48_RAT UniProtKB/TrEMBL
  F1LW75 ENTREZGENE
  Q6W9J5 ENTREZGENE, UniProtKB/TrEMBL
  Q95IU1_RAT UniProtKB/TrEMBL
UniProt Secondary F1LW75 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-11 RT1-2.5  RT1 class Ib, locus M2  RT1-M2  RT1 class Ib gene, locus M2  Name updated 625702 APPROVED
2002-06-10 RT1-M2  RT1 class Ib gene, locus M2      Symbol and Name status set to approved 70586 APPROVED