Olfactory receptors (ORs) are the largest protein family in the mammalian genome. They underlie the recognition ofodorants and the initiation of olfactory sensory signals. HORDE is a free online source, which integrates extensive information on human ORs. It aims at supplying a global overview on the evolution, structure and function of this entire gene superfamily. Such overview includes information about OR genomic organization, their orthologues in other mammals, and a nomenclature system which reflects the relevant phylogeny.
HORDE #41 was constructed using fast and automated data-mining of the human genome. This included the following steps:
- The human genome was searched for novel ORs with BLAT (Kent, W.J. Genome Res 12: 656-664, 2002) using HORDE #40 OR sequence entries as queries.
- All hit locations were then extracted from the human genome sequence and translated into proteins. Genes with a premature stop codons were defined as pseudo genes, and retranslated using FASTY.
- All resultant novel proteins were aligned against a multiple alignment of 400 human and mouse ORs. This was done to determine the optimal ATG position at the 5' of the gene, and the Stop codon at the 3'.
HORDE #41 contains 11 novel ORs.
All HORDE's routines, including the data mining procedures are written in Perl.
Genes and clusters: HORDE #41 contains 855 human OR genes, of which 391 have full open reading frame. The OR genes are present on practically all human chromosomes, with the apparent exception of chromosomes 20 and Y. Chromosome 11 is by far the richest in OR genes (Fig 1). Most of the ORs are distributed in genomic clusters, with a typical intergenic distance of 19.2+/-14 kb. Only 48 ORs are singletons (of which 37 are pseudogenes). We have formally divided the OR repertoire into clusters, using a cutoff of maximal intergenic distance of 100 kb. HORDE #41 contains 135 clusters ranging in size from 0.35-1502 kb, and containing up to 98 ORs per cluster (Fig 2). Clusters are labeled as xx\@yy where xx specify stands for the chromosome and yy for the coordinate (in Mb).
Single Nucleotide Polymorphisms: SNPs in human ORs were extracted from dbSNP and UCSC genome browser. HORDE #41 contains 3395 SNPs, of which 1111 are synonymous, and 508 is non-synonymous. A distribution of the SNPs count per OR is shown in Fig 3
Orthologs: To allow orthologues-paralogues comparisons, HORDE includes information on ORs from other species. Current HORDE's non-human ORs are listed in Table 1
The Nomenclature system for members of the OR gene superfamily is based on a divergence evolutionary model (Glusman, G., Yanai, I., Rubin, I. and Lancet, D., The complete human olfactory subgenome, Genome Research 11:685-702 2001) . The nomenclature terms are accepted as official gene symbols by the HUGO Gene Nomenclature Committee ( HGNC). The symbols consist of a root 'OR', followed by family numeral, subfamily letter(s), and a numeral representing the individual gene within subfamily. For example, OR3A1 is an OR gene of family 3, subfamily A and OR7E12P is an OR pseudogene of family 7 subfamily E.
If you wish to link to particular OR card, just use
http://bip.weizmann.ac.il/cgi-bin/HORDE/showGene.pl?symbol=XXX (with XXX being the OR gene symbol).
Official URL of HORDE: http://bioportal.weizmann.ac.il/HORDE/.
Publications: Safran M, Chalifa-Caspi V, Shmueli
O, Olender T, Lapidot M, Rosen N, Shmoish M, Peter Y,
Glusman G, Feldmesser E, Adato A, Peter I, Khen M, Atarot T, Groner Y, Lancet D.
Olender T, Feldmesser E, Atarot T, Eisenstein M, Lancet D.
The olfactory receptor universe--from whole genome analysis to structure and evolution.
Genet Mol Res. 2004 Dec 30;3(4):545-53.