Ancient genomic architecture for mammalian olfactory receptor clusters

Table 2 Summary of UCSC pairwise alignments of OR genes

Pair of genomes compared^a	Total reference OR genes	ORs aligned in the net	ORs aligned to another OR^b	ORs aligned to a 'syntenic ortholog'^c	Number of chains containing 'syntenic orthologs'^d	Correlation between sequence similarity and chain length^e
Human versus mouse	765	760	651	379 (50%)	33	0.31
Human versus rat	765	763	671	307 (40%)	28	0.21
Human versus dog	765	764	611	391 (51%)	31	0.22
Human versus opossum	765	760	693	109 (14%)	25	0.2
Mouse versus human	1,228	1,222	1,055	376 (31%)	36	0.44
Mouse versus rat	1,228	1,226	1,095	911 (74%)	26	0.43
Mouse versus dog	1,228	1,224	998	395 (32%)	38	0.54
Mouse versus opossum	1,228	1,226	1,119	147 (12%)	30	0.4
Rat versus human	1,654	1,650	1,583	313 (19%)	29	0.22
Rat versus mouse	1,654	1,645	1,400	964 (58%)	32	0.49
Dog versus human	804	804	751	374 (47%)	26	0.26
Dog versus mouse	804	803	683	384 (48%)	36	0.42

^aOut of 20 possible comparisons between five species, only 12 are available at the UCSC alignment net [56]. A pairwise comparison is directed from a reference genome to a target genome, and is thus not symmetric. ^bWe filtered out alignments between an OR to a genomic segment that was mapped to 'chrUn' or 'random' (approximately 1% of all alignment pairs), was split between two separated genomic locations (approximately 7%), or did not overlap with any annotated OR from the collection described in Table 1 (approximately 3.5%). However, the overlooked segments may contain a genuine OR coding frame, and thus the counts are probably an underestimate for the ORs that have an orthologous counterpart. ^cThe number of alignments that satisfy the criteria of syntenic orthology. The fraction out of the total number of reference genes is given in parentheses. ^dThe total number of alignment chains that together contain all pairs of syntenic orthologs. Usually, each chain contains many such pairs and as such represents a unit of conservation. ^eCorrelation coefficient between the two properties used for defining syntenic orthology: length of the alignment chain from which the aligned gene pair is derived, and the percentage mutual DNA identity between the genes of this pair. Genes with higher identity tend to be in longer chains. OR, olfactory receptor; UCSC, University of California at Santa Cruz.

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