RT1-M1-5 (RT1 class I, M1, gene 5) - Rat Genome Database

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Gene: RT1-M1-5 (RT1 class I, M1, gene 5) Rattus norvegicus
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Symbol: RT1-M1-5 (Ensembl: AABR07072807.1)
Name: RT1 class I, M1, gene 5 (Ensembl:RT1 class I, M1, 5)
RGD ID: 1587041
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; INTERACTS WITH 1,2-dimethylhydrazine; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: H2-M9; histocompatibility 2, M region locus 9; LOC680842; similar to RT1 class I, M1, gene 2
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8201,863,437 - 1,867,022 (+)NCBIGRCr8
mRatBN7.2201,858,608 - 1,860,708 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl201,811,604 - 1,860,708 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx201,899,979 - 1,902,070 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0201,903,483 - 1,905,576 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0201,856,620 - 1,858,705 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0202,355,975 - 2,358,994 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0204,386,402 - 4,388,502 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4201,945,294 - 1,947,394 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera202,566,434 - 2,568,524 (+)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

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15060004  


Genomics

Variants

.
Variants in RT1-M1-5
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:26
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000038725
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 (mRatBN7.2)
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)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
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
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
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


Sequence


Ensembl Acc Id: ENSRNOT00000038725   ⟹   ENSRNOP00000086567
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl201,811,604 - 1,860,708 (+)Ensembl
RefSeq Acc Id: NM_001168332   ⟹   NP_001161804
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,863,823 - 1,865,923 (+)NCBI
mRatBN7.2201,858,608 - 1,860,708 (+)NCBI
Rnor_6.0202,355,975 - 2,358,075 (+)NCBI
Rnor_5.0204,386,402 - 4,388,502 (+)NCBI
RGSC_v3.4201,945,294 - 1,947,394 (+)RGD
Celera202,566,434 - 2,568,524 (+)RGD
Sequence:
RefSeq Acc Id: XM_063279503   ⟹   XP_063135573
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8201,863,437 - 1,867,022 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001161804 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135573 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE84056 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000086567.1
RefSeq Acc Id: NP_001161804   ⟸   NM_001168332
- Peptide Label: precursor
- UniProtKB: A0A8I6GE62 (UniProtKB/TrEMBL),   Q6MFZ1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000086567   ⟸   ENSRNOT00000038725
RefSeq Acc Id: XP_063135573   ⟸   XM_063279503
- Peptide Label: isoform X1
- UniProtKB: Q6MFZ1 (UniProtKB/TrEMBL)
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)
BioCyc Gene G2FUF-4955 BioCyc
Ensembl Genes ENSRNOG00000028035 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038725.7 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:680842 UniProtKB/TrEMBL
NCBI Gene 680842 ENTREZGENE
PANTHER CLASS IB MHC ANTIGEN QA-2-RELATED UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-M1-5 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028035 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6GE62 ENTREZGENE, UniProtKB/TrEMBL
  Q6MFZ1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-21 H2-M9  histocompatibility 2, M region locus 9  RT1-M1-5  RT1 class I, M1, gene 5  Data merged from RGD:1624208 737654 APPROVED
2008-03-05 H2-M9  histocompatibility 2, M region locus 9  LOC680842  similar to RT1 class I, M1, gene 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-05-03 RT1-M1-5  RT1 class I, M1, gene 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680842  similar to RT1 class I, M1, gene 2      Symbol and Name status set to provisional 70820 PROVISIONAL