RGD Reference Report - The genomic sequence and comparative analysis of the rat major histocompatibility complex. - Rat Genome Database

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The genomic sequence and comparative analysis of the rat major histocompatibility complex.

Authors: Hurt, P  Walter, L  Sudbrak, R  Klages, S  Muller, I  Shiina, T  Inoko, H  Lehrach, H  Gunther, E  Reinhardt, R  Himmelbauer, H 
Citation: Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
RGD ID: 1300431
Pubmed: PMID:15060004   (View Abstract at PubMed)
PMCID: PMC383307   (View Article at PubMed Central)
DOI: DOI:10.1101/gr.1987704   (Journal Full-text)

We have determined the sequence of a 4-Mb interval on rat chromosome 20p12 that encompasses the rat major histocompatibility complex (MHC). This is the first report of a finished sequence for a segment of the rat genome and constitutes one of the largest contiguous sequences thus far for rodent genomes in general. The rat MHC is, next to the human MHC, the second mammalian MHC sequenced to completion. Our analysis has resulted in the identification of at least 220 genes located within the sequenced interval. Although gene content and order are well conserved in the class II and class III gene intervals as well as the framework gene regions, profound rat-specific features were encountered within the class I gene regions, in comparison to human and mouse. Class I region-associated differences were found both at the structural level, the number, and organization of class I genes and gene families, and, in a more global context, in the way that evolution worked to shape the present-day rat MHC.

Gene Ontology Annotations    Click to see Annotation Detail View

Biological Process
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
G protein-coupled receptor signaling pathway  TAS 1300431 RGD 

Molecular Function
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
olfactory receptor activity  TAS 1300431 RGD 

Objects Annotated

Genes (Rattus norvegicus)
Or5v1b  (olfactory receptor family 5 subfamily V member 1B)

Objects referenced in this article
Gene Arrb2-ps arrestin, beta 2, pseudogene Rattus norvegicus
Gene Btnl3 butyrophilin-like 3 Rattus norvegicus
Gene Cyp21a1 cytochrome P450, family 21, subfamily a, polypeptide 1 Rattus norvegicus
Gene Cyp21a1-ps cytochrome P450, family 21, subfamily a, polypeptide 1, pseudogene Rattus norvegicus
Gene E230034O05Rik E230034O05Rik gene Rattus norvegicus
Gene Egfl8 EGF-like-domain, multiple 8 Rattus norvegicus
Gene G4 G4 protein Rattus norvegicus
Gene Lst1 leukocyte specific transcript 1 Rattus norvegicus
Gene Ly6g5b lymphocyte antigen 6 family member G5B Rattus norvegicus
Gene Ly6g5c lymphocyte antigen 6 family member G5C Rattus norvegicus
Gene Ly6g6c lymphocyte antigen 6 family member G6C Rattus norvegicus
Gene Ly6g6d lymphocyte antigen 6 family member G6D Rattus norvegicus
Gene Ly6g6e lymphocyte antigen 6 family member G6E Rattus norvegicus
Gene Ly6g6f lymphocyte antigen 6 family member G6F Rattus norvegicus
Gene Mpig6b megakaryocyte and platelet inhibitory receptor G6b Rattus norvegicus
Gene Mucl3 mucin like 3 Rattus norvegicus
Gene Npc1l1 NPC1 like intracellular cholesterol transporter 1 Rattus norvegicus
Gene Or10c1 olfactory receptor family 10 subfamily C member 1 Rattus norvegicus
Gene Or11a4 olfactory receptor family 11 subfamily A member 4 Rattus norvegicus
Gene Or12d14c olfactory receptor family 12 subfamily D member 14C Rattus norvegicus
Gene Or12d17 olfactory receptor family 12 subfamily D member 17 Rattus norvegicus
Gene Or12d2 olfactory receptor family 12 subfamily D member 2 Rattus norvegicus
Gene Or12d2b olfactory receptor family 12 subfamily D member 2B Rattus norvegicus
Gene Or12d2c olfactory receptor family 12 subfamily D member 2C Rattus norvegicus
Gene Or1o1 olfactory receptor family 1 subfamily O member 1 Rattus norvegicus
Gene Or1o11 olfactory receptor family 1 subfamily O member 11 Rattus norvegicus
Gene Or1o2 olfactory receptor family 1 subfamily O member 2 Rattus norvegicus
Gene Or1o2d-ps1 olfactory receptor family 1 subfamily O member 2D, pseudogene 1 Rattus norvegicus
Gene Or1o2e olfactory receptor family 1 subfamily O member 2E Rattus norvegicus
Gene Or1o2f-ps1 olfactory receptor family 1 subfamily O member 2F, pseudogene 1 Rattus norvegicus
Gene Or2h1 olfactory receptor family 2 subfamily H member 1 Rattus norvegicus
Gene Or2h1b olfactory receptor family 2 subfamily H member 1B Rattus norvegicus
Gene Or2h1c-ps1 olfactory receptor family 2 subfamily H member 1C, pseudogene 1 Rattus norvegicus
Gene Or2h2 olfactory receptor family 2 subfamily H member 2 Rattus norvegicus
Gene Or2h2c olfactory receptor family 2 subfamily H member 2C Rattus norvegicus
Gene Ppt2 palmitoyl-protein thioesterase 2 Rattus norvegicus
Gene Prr3 proline rich 3 Rattus norvegicus
Gene Ralgdsl2 ral guanine nucleotide dissociation stimulator like 2 Rattus norvegicus
Gene Ring1 ring finger protein 1 Rattus norvegicus
Gene RT1-CE6 RT1 class I, locus CE6 Rattus norvegicus
Gene RT1-M1-4 RT1 class I, locus M1, gene 4 Rattus norvegicus
Gene RT1-M3-1 RT1 class Ib, locus M3, gene 1 Rattus norvegicus
Gene RT1-N2 RT1 class Ib, locus N2 Rattus norvegicus
Gene RT1-N3 RT1 class Ib, locus N3 Rattus norvegicus
Gene RT1-S2 RT1 class Ib, locus S2 Rattus norvegicus
Gene RT1-T24-2 RT1 class I, locus T24, gene 2 Rattus norvegicus
Gene Sapcd1 suppressor APC domain containing 1 Rattus norvegicus

Additional Information