RT1-N2 (RT1 class Ib, locus N2) - Rat Genome Database

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Gene: RT1-N2 (RT1 class Ib, locus N2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: RT1-N2
Name: RT1 class Ib, locus N2
RGD ID: 1595850
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-E (major histocompatibility complex, class I, E); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cell surface antigen; MHC class I TL-like; RT1 class Ib gene, H2-TL-like, grc region; RT1 class Ib gene, H2-TL-like, grc region(N2); RT1 class Ib gene, H2-TL-like, grc region(N2) (mapped); RT1-N2_mapped
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8202,645,980 - 2,650,260 (+)NCBIGRCr8
mRatBN7.2202,641,157 - 2,645,439 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl202,641,202 - 2,644,900 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx202,726,683 - 2,730,075 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0202,731,648 - 2,735,040 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0202,713,803 - 2,717,194 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0203,146,579 - 3,150,852 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,146,856 - 3,150,852 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0205,244,741 - 5,250,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4202,785,625 - 2,789,016 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2071,983 - 75,374 (+)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 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  


Genomics

Variants

.
Variants in RT1-N2
54 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:103
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000050159
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

Markers in Region
RH127521  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2202,644,998 - 2,645,184 (+)MAPPERmRatBN7.2
Rnor_6.0203,150,418 - 3,150,603NCBIRnor6.0
Rnor_5.0205,248,584 - 5,248,769UniSTSRnor5.0
RGSC_v3.4202,789,115 - 2,789,300UniSTSRGSC3.4
Celera2075,473 - 75,658UniSTS
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
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 musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 1 5 5 2 5 3 15 14 2
Low 1 25 19 19 19 1 62 11 17
Below cutoff 8 9 8 1 8 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001008854 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006255938 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BX883048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L23127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M74822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000050159   ⟹   ENSRNOP00000049883
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,641,202 - 2,644,900 (+)Ensembl
Rnor_6.0 Ensembl203,146,856 - 3,150,397 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084770   ⟹   ENSRNOP00000074505
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,149,114 - 3,150,852 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086026   ⟹   ENSRNOP00000075415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl202,641,202 - 2,644,688 (+)Ensembl
Rnor_6.0 Ensembl203,148,665 - 3,150,421 (+)Ensembl
RefSeq Acc Id: NM_001008854   ⟹   NP_001008854
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,646,330 - 2,649,721 (+)NCBI
mRatBN7.2202,641,509 - 2,644,900 (+)NCBI
Rnor_6.0203,146,928 - 3,150,319 (+)NCBI
Rnor_5.0205,244,741 - 5,250,054 (+)NCBI
RGSC_v3.4202,785,625 - 2,789,016 (+)RGD
Celera2071,983 - 75,374 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255938   ⟹   XP_006256000
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,984 - 2,650,260 (+)NCBI
mRatBN7.2202,641,160 - 2,645,439 (+)NCBI
Rnor_6.0203,146,582 - 3,150,852 (+)NCBI
Rnor_5.0205,244,741 - 5,250,054 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601671   ⟹   XP_017457160
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,985 - 2,650,260 (+)NCBI
mRatBN7.2202,641,161 - 2,645,439 (+)NCBI
Rnor_6.0203,146,962 - 3,150,852 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098781   ⟹   XP_038954709
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,984 - 2,650,260 (+)NCBI
mRatBN7.2202,641,160 - 2,645,439 (+)NCBI
RefSeq Acc Id: XM_039098782   ⟹   XP_038954710
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,980 - 2,650,260 (+)NCBI
mRatBN7.2202,641,161 - 2,645,439 (+)NCBI
RefSeq Acc Id: XM_039098783   ⟹   XP_038954711
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,993 - 2,650,260 (+)NCBI
mRatBN7.2202,641,173 - 2,645,439 (+)NCBI
RefSeq Acc Id: XM_039098784   ⟹   XP_038954712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,983 - 2,648,163 (+)NCBI
mRatBN7.2202,641,157 - 2,643,189 (+)NCBI
RefSeq Acc Id: XM_039098785   ⟹   XP_038954713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,984 - 2,648,163 (+)NCBI
mRatBN7.2202,641,158 - 2,643,192 (+)NCBI
RefSeq Acc Id: XM_063279192   ⟹   XP_063135262
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,980 - 2,650,260 (+)NCBI
RefSeq Acc Id: XM_063279193   ⟹   XP_063135263
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,993 - 2,650,260 (+)NCBI
RefSeq Acc Id: XR_010060712
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8202,645,983 - 2,650,260 (+)NCBI
RefSeq Acc Id: NP_001008854   ⟸   NM_001008854
- Peptide Label: precursor
- UniProtKB: Q6MFZ8 (UniProtKB/TrEMBL),   V5ISG7 (UniProtKB/TrEMBL),   R9Q796 (UniProtKB/TrEMBL),   E9PSW1 (UniProtKB/TrEMBL),   L7N647 (UniProtKB/TrEMBL),   Q31279 (UniProtKB/TrEMBL),   A0A8J8XQ64 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256000   ⟸   XM_006255938
- Peptide Label: isoform X1
- UniProtKB: Q6MFZ8 (UniProtKB/TrEMBL),   V5ISG7 (UniProtKB/TrEMBL),   R9Q796 (UniProtKB/TrEMBL),   E9PSW1 (UniProtKB/TrEMBL),   L7N647 (UniProtKB/TrEMBL),   Q31279 (UniProtKB/TrEMBL),   A0A8J8XQ64 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457160   ⟸   XM_017601671
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000074505   ⟸   ENSRNOT00000084770
RefSeq Acc Id: ENSRNOP00000075415   ⟸   ENSRNOT00000086026
RefSeq Acc Id: ENSRNOP00000049883   ⟸   ENSRNOT00000050159
RefSeq Acc Id: XP_038954712   ⟸   XM_039098784
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954713   ⟸   XM_039098785
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954709   ⟸   XM_039098781
- Peptide Label: isoform X1
- UniProtKB: R9Q796 (UniProtKB/TrEMBL),   V5ISG7 (UniProtKB/TrEMBL),   E9PSW1 (UniProtKB/TrEMBL),   L7N647 (UniProtKB/TrEMBL),   Q31279 (UniProtKB/TrEMBL),   Q6MFZ8 (UniProtKB/TrEMBL),   A0A8J8XQ64 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954710   ⟸   XM_039098782
- Peptide Label: isoform X1
- UniProtKB: R9Q796 (UniProtKB/TrEMBL),   V5ISG7 (UniProtKB/TrEMBL),   E9PSW1 (UniProtKB/TrEMBL),   L7N647 (UniProtKB/TrEMBL),   Q31279 (UniProtKB/TrEMBL),   Q6MFZ8 (UniProtKB/TrEMBL),   A0A8J8XQ64 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954711   ⟸   XM_039098783
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063135262   ⟸   XM_063279192
- Peptide Label: isoform X1
- UniProtKB: A0A8J8XQ64 (UniProtKB/TrEMBL),   E9PSW1 (UniProtKB/TrEMBL),   L7N647 (UniProtKB/TrEMBL),   Q31279 (UniProtKB/TrEMBL),   Q6MFZ8 (UniProtKB/TrEMBL),   R9Q796 (UniProtKB/TrEMBL),   V5ISG7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135263   ⟸   XM_063279193
- Peptide Label: isoform X2
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MFZ8-F1-model_v2 AlphaFold Q6MFZ8 1-377 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:1595850 AgrOrtholog
BioCyc Gene G2FUF-4821 BioCyc
Ensembl Genes ENSRNOG00000029386 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050159 ENTREZGENE
  ENSRNOT00000050159.4 UniProtKB/TrEMBL
  ENSRNOT00000086026.2 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_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:360323 UniProtKB/TrEMBL
NCBI Gene 360323 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-N2 PhenoGen
PRINTS MHCCLASSI UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029386 RatGTEx
SMART IGc1 UniProtKB/TrEMBL
Superfamily-SCOP MHC_I/II-like_Ag-recog UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt A0A0G2KAJ0_RAT UniProtKB/TrEMBL
  A0A8J8XQ64 ENTREZGENE, UniProtKB/TrEMBL
  E9PSW1 ENTREZGENE
  L7N647 ENTREZGENE
  Q31279 ENTREZGENE
  Q6MFZ8 ENTREZGENE, UniProtKB/TrEMBL
  R9Q796 ENTREZGENE
  V5ISG7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary E9PSW1 UniProtKB/TrEMBL
  L7N647 UniProtKB/TrEMBL
  Q31279 UniProtKB/TrEMBL
  R9Q796 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-N2  RT1 class Ib, locus N2  RT1-N2  RT1 class Ib gene, H2-TL-like, grc region(N2)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-04-12 RT1-N2  RT1 class Ib gene, H2-TL-like, grc region(N2)  RT1-N2_mapped  RT1 class Ib gene, H2-TL-like, grc region(N2) (mapped)  Data merged from RGD:3499 737654 APPROVED
2006-11-20 RT1-N2_mapped  RT1 class Ib gene, H2-TL-like, grc region(N2)(mapped)  RT1-N2  RT1 class Ib gene, H2-TL-like, grc region(N2)  Symbol set to symbol_mapped, name set to name (mapped) 1582166 APPROVED
2006-11-20 RT1-N2  RT1 class Ib gene, H2-TL-like, grc region(N2)      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 RT1-N2  RT1 class Ib, locus H2-TL-like, grc region (N2)      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-N2  RT1 class Ib gene, H2-TL-like, grc region      Symbol and Name status set to approved 70586 APPROVED