<i>In Silico</i>method for identification of MHC class I-like molecules in whole genomes

Reinink, Peter; Rhijn, van

doi:10.1101/046607

Cited by 1 publication

(6 citation statements)

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Section: Cd1 Loci In Less Well Studied Mammalian Genomesmentioning

confidence: 99%

“…In mice, a chromosomal rearrangement caused the separation of the CD1 and MR1 genes, which are located on chromosome 3 and chromosome 1, respectively (Dascher and Brenner 2003 ). In the available assembled primate data, MR1 and CD1 are located on the same chromosome, but in other mammals that were studied, like cow and pig, they are not (Goldfinch et al 2010 ; Reinink and Van Rhijn 2016 ).…”

Section: Chromosomal Location and Gene Structure Of Cd1 And Mr1mentioning

confidence: 99%

“…Later, one functional gene for CD1d was described (Looringh van Beeck et al 2009 ), and one gene of unknown functionality for CD1a (Van Rhijn and Moody 2015 ). The guinea pig CD1 locus has not been mapped, but while the genome is being updated and assembled, even more CD1 genes have been identified in guinea pig (Reinink and Van Rhijn 2016 ). The first attempt to define the bovine CD1 locus was based on an early draft of the bovine genome and identified one CD1a gene, five CD1b genes, two CD1d genes, and a CD1e gene.…”

Section: Cd1 In Humans and Common Research Farm And Companion Animamentioning

confidence: 99%

“…Therefore, to get an indication of the total number of CD1 genes in a species, searches using the basic local alignment search tool (BLAST) or collection of annotated genes in genomes provide more reliable information than expressed sequence tags or cDNA databases. Table 1 shows numbers of CD1 genes obtained from whole genomes of 15 mammals, including less well studied species like alpaca, dolphin, elephant, two bat species, panda, and sloth (Reinink and Van Rhijn 2016 ). Of note, BLAST-based searches reveal functional genes and pseudogenes.…”

Section: Cd1 Loci In Less Well Studied Mammalian Genomesmentioning

confidence: 99%

“… For each of the indicated mammalian genomes, a list of CD1 and MR1 genes as determined by BLAST-based searches was merged with a list of Ensembl-annotated CD1 and MR1 genes when available (adapted from (Reinink and Van Rhijn 2016 )). Redundancies (genes with identical genomic location) were removed a The dolphin and sloth genomes are not completely assembled and consist of relatively small contigs, which may have led to the fragmentation of CD1 or MR1 genes and subsequent failure of identification …”

Section: Cd1 Loci In Less Well Studied Mammalian Genomesmentioning

confidence: 99%

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Mammalian CD1 and MR1 genes

Reinink

Rhijn

2016

Immunogenetics

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All higher vertebrates share the fundamental components of the adaptive immune system: the B cell receptor, the T cell receptor, and classical MHC proteins. At a more detailed level, their immune systems vary considerably, especially with respect to the non-polymorphic MHC class I-like proteins. In mammals, the CD1 family of lipid-presenting proteins is encoded by clusters of genes of widely divergent sizes and compositions. Another MHC class I-like protein, MR1, is typically encoded by a single gene that is highly conserved among species. Based on mammalian genomes and the available data on cellular expression profiles and protein structure, we review MR1 genes and families of CD1 genes in modern mammals from a genetic and functional perspective. Understanding the CD1 and MR1 systems across animal species provides insights into the specialized functions of the five types of CD1 proteins and facilitates careful consideration of animal models for human diseases in which immune responses to lipids and bacterial metabolites play a role.

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Section: Cd1 Loci In Less Well Studied Mammalian Genomesmentioning

confidence: 99%