RT1-N3 (RT1 class Ib, locus N3) - Rat Genome Database

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Gene: RT1-N3 (RT1 class Ib, locus N3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-N3
Name: RT1 class Ib, locus N3
RGD ID: 1598370
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; PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: RT1 class Ib gene, H2-TL-like, grc region (N3); RT1 class Ib gene, H2-TL-like, grc region (N3) (mapped); RT1-N3_mapped
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,666,469 - 2,670,355 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl202,666,464 - 2,670,348 (+)EnsemblGRCr8
mRatBN7.2202,659,132 - 2,665,536 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,661,584 - 2,665,530 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx202,747,065 - 2,750,926 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,752,025 - 2,755,886 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,778,533 - 2,782,394 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,166,793 - 3,170,945 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,167,079 - 3,170,945 (+)Ensemblrn6Rnor6.0
Rnor_5.0205,263,747 - 5,269,117 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4202,806,583 - 2,810,443 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2092,118 - 95,945 (+)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. 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 genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
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:1300431   PMID:8168848   PMID:12477932  


Genomics

Variants

.
Variants in RT1-N3
64 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:235
Count of miRNA genes:158
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000001035
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
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
D20Yum84  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8202,666,035 - 2,666,278 (+)Marker Load Pipeline
mRatBN7.2202,661,216 - 2,661,459 (+)MAPPERmRatBN7.2
Rnor_6.0203,166,636 - 3,166,874NCBIRnor6.0
Rnor_5.0205,264,802 - 5,265,040UniSTSRnor5.0
RGSC_v3.4202,806,132 - 2,806,372UniSTSRGSC3.4
Celera2091,689 - 91,907UniSTS
Cytogenetic Map20p12UniSTS
RH140239  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,644,376 - 2,644,590 (+)MAPPERmRatBN7.2
mRatBN7.2202,664,853 - 2,665,068 (+)MAPPERmRatBN7.2
Rnor_6.0203,170,269 - 3,170,483NCBIRnor6.0
Rnor_6.0203,149,796 - 3,150,009NCBIRnor6.0
Rnor_5.0205,268,435 - 5,268,649UniSTSRnor5.0
Rnor_5.0205,247,962 - 5,248,175UniSTSRnor5.0
RGSC_v3.4202,809,767 - 2,809,981UniSTSRGSC3.4
RGSC_v3.4202,788,493 - 2,788,706UniSTSRGSC3.4
Celera2074,851 - 75,064UniSTS
Celera2095,269 - 95,483UniSTS
RH 3.4 Map2015.8UniSTS
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 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000001035   ⟹   ENSRNOP00000001035
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl202,666,464 - 2,670,347 (+)Ensembl
mRatBN7.2 Ensembl202,661,584 - 2,665,493 (+)Ensembl
Rnor_6.0 Ensembl203,167,079 - 3,170,945 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000084770   ⟹   ENSRNOP00000074505
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl202,666,474 - 2,670,348 (+)Ensembl
mRatBN7.2 Ensembl202,661,602 - 2,665,530 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115132   ⟹   ENSRNOP00000083689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,661,645 - 2,665,314 (+)Ensembl
RefSeq Acc Id: NM_001008855   ⟹   NP_001008855
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,666,489 - 2,670,349 (+)NCBI
mRatBN7.2202,661,670 - 2,665,530 (+)NCBI
Rnor_6.0203,167,085 - 3,170,945 (+)NCBI
Rnor_5.0205,263,747 - 5,269,117 (+)NCBI
RGSC_v3.4202,806,583 - 2,810,443 (+)RGD
Celera2092,118 - 95,945 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255908   ⟹   XP_006255970
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,666,471 - 2,670,355 (+)NCBI
mRatBN7.2202,660,206 - 2,665,536 (+)NCBI
Rnor_6.0203,166,793 - 3,170,474 (+)NCBI
Rnor_5.0205,263,747 - 5,269,117 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255909   ⟹   XP_006255971
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,666,471 - 2,669,941 (+)NCBI
mRatBN7.2202,660,206 - 2,665,122 (+)NCBI
Rnor_6.0203,166,793 - 3,170,537 (+)NCBI
Rnor_5.0205,263,747 - 5,269,117 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098420   ⟹   XP_038954348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,666,469 - 2,670,355 (+)NCBI
mRatBN7.2202,659,132 - 2,665,536 (+)NCBI
RefSeq Acc Id: XM_039098421   ⟹   XP_038954349
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,666,473 - 2,670,355 (+)NCBI
mRatBN7.2202,660,193 - 2,665,536 (+)NCBI
RefSeq Acc Id: NP_001008855   ⟸   NM_001008855
- UniProtKB: A0A023GRW5 (UniProtKB/TrEMBL),   Q6MG01 (UniProtKB/TrEMBL),   V9HVV1 (UniProtKB/TrEMBL),   G5EBE1 (UniProtKB/TrEMBL),   H7C829 (UniProtKB/TrEMBL),   I1SB24 (UniProtKB/TrEMBL),   L7N646 (UniProtKB/TrEMBL),   Q31280 (UniProtKB/TrEMBL),   U3KRG4 (UniProtKB/TrEMBL),   F6PT03 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255971   ⟸   XM_006255909
- Peptide Label: isoform X4
- UniProtKB: F6PT03 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255970   ⟸   XM_006255908
- Peptide Label: isoform X1
- UniProtKB: F6PT03 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000001035   ⟸   ENSRNOT00000001035
RefSeq Acc Id: XP_038954348   ⟸   XM_039098420
- Peptide Label: isoform X2
- UniProtKB: F6PT03 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954349   ⟸   XM_039098421
- Peptide Label: isoform X3
- UniProtKB: F6PT03 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000083689   ⟸   ENSRNOT00000115132
Ensembl Acc Id: ENSRNOP00000074505   ⟸   ENSRNOT00000084770
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MG01-F1-model_v2 AlphaFold Q6MG01 1-393 view protein structure

Transcriptome

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

Promoters
RGD ID:13701283
Promoter ID:EPDNEW_R11807
Type:initiation region
Name:RT1-N3_1
Description:RT1 class Ib, locus N3
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_6.0203,167,083 - 3,167,143EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598370 AgrOrtholog
BioCyc Gene G2FUF-4817 BioCyc
Ensembl Genes ENSRNOG00000000795 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001035 ENTREZGENE
  ENSRNOT00000001035.7 UniProtKB/TrEMBL
  ENSRNOT00000084770 ENTREZGENE
  ENSRNOT00000084770.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9090368 IMAGE-MGC_LOAD
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:24750 UniProtKB/TrEMBL
MGC_CLONE MGC:187288 IMAGE-MGC_LOAD
NCBI Gene 24750 ENTREZGENE
PANTHER HISTOCOMPATIBILITY 2, T REGION LOCUS 10-RELATED UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/TrEMBL
Pfam C1-set UniProtKB/TrEMBL
  MHC_I UniProtKB/TrEMBL
PhenoGen RT1-N3 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000795 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A023GRW5 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K881_RAT UniProtKB/TrEMBL
  F6PT03 ENTREZGENE
  G5EBE1 ENTREZGENE
  H7C829 ENTREZGENE
  I1SB24 ENTREZGENE
  L7N646 ENTREZGENE
  Q31280 ENTREZGENE
  Q6MG01 ENTREZGENE, UniProtKB/TrEMBL
  U3KRG4 ENTREZGENE
  V9HVV1 ENTREZGENE
UniProt Secondary F6PT03 UniProtKB/TrEMBL
  G5EBE1 UniProtKB/TrEMBL
  H7C829 UniProtKB/TrEMBL
  I1SB24 UniProtKB/TrEMBL
  L7N646 UniProtKB/TrEMBL
  Q31280 UniProtKB/TrEMBL
  U3KRG4 UniProtKB/TrEMBL
  V9HVV1 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-N3  RT1 class Ib, locus N3  RT1-N3  RT1 class Ib gene, H2-TL-like, grc region (N3)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-12 RT1-N3  RT1 class Ib gene, H2-TL-like, grc region (N3)  RT1-N3_mapped  RT1 class Ib gene, H2-TL-like, grc region (N3) (mapped)  Data merged from RGD:3500 737654 APPROVED
2006-11-20 RT1-N3  RT1 class Ib gene, H2-TL-like, grc region (N3)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 RT1-N3_mapped  RT1 class Ib gene, H2-TL-like, grc region (N3)(mapped)  RT1-N3  RT1 class Ib gene, H2-TL-like, grc region (N3)  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2004-02-11 RT1-N3  RT1 class Ib, locus H2-TL-like, grc region (N3)      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-N3  RT1 class Ib gene, H2-TL-like, grc region      Symbol and Name status set to approved 70586 APPROVED