RT1-N1 (RT1 class Ib, locus N1) - Rat Genome Database

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Gene: RT1-N1 (RT1 class Ib, locus N1) Rattus norvegicus
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Symbol: RT1-N1
Name: RT1 class Ib, locus N1
RGD ID: 3498
Description: PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; autoimmune thyroiditis pathway; FOUND IN membrane (inferred); INTERACTS WITH ammonium chloride; benzene; bromobenzene
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MHTLL; RATMHTLL; RT1 class Ib gene H2-TL-like grc region; RT1 class Ib gene, H2-TL-like, grc region (N1)
Latest Assembly: GRCr8 - GRCr8 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release; Note: GeneID 24748, defined by M74822.1, was annotated on chromosome 20 of NCBI's build 4.1 of the rat genome. This accession represents one of three similar RT1-N genes from the r21 haplotype of the major histocompatibility complex. The reference assembly, derived from the n haplotype, contains only two related RT1-N genes. Based on PubMed ID 15060004, this locus is not found on the reference assembly, which instead contains RT1-N2, GeneID 360323. [17 Jun 2014]
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
UTH_Rnor_WKY_Bbb_1.0202,736,031 - 2,739,211 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
RGSC_v3.4202,785,625 - 2,788,804 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1202,785,851 - 2,789,031 (+)NCBI
Celera2071,983 - 75,162 (+)NCBICelera
Cytogenetic Map20p12NCBI


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. Genomic DNA sequence and organization of a TL-like gene in the grc-G/C region of the rat. Kirisits MJ, etal., Immunogenetics 1992;35(6):365-77.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Genomics

Markers in Region
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: NM_012646   ⟹   NP_036778
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
RGSC_v3.4202,785,625 - 2,788,804 (+)RGD
Celera2071,983 - 75,162 (+)RGD
Protein Sequences
Protein RefSeqs NP_036778 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000049883.4
RefSeq Acc Id: NP_036778   ⟸   NM_012646
- UniProtKB: Q31277 (UniProtKB/TrEMBL),   A0A8J8XQ64 (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)
Ensembl Genes ENSRNOG00000029386 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050159.4 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 24748 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-N1 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
TIGR TC216302
UniProt A0A8J8XQ64 ENTREZGENE, UniProtKB/TrEMBL
  Q31277 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-09-15 RT1-N1  RT1 class Ib, locus N1  RT1-N1  RT1 class Ib gene, H2-TL-like, grc region (N1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 RT1-N1  RT1 class Ib, locus H2-TL-like, grc region (N1)      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 RT1-N1  RT1 class Ib gene, H2-TL-like, grc region      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_transcript consists of eight exons characteristic of a class I gene 633917