Table 2

Summary of UCSC pairwise alignments of OR genes

Pair of genomes compareda

Total reference OR genes

ORs aligned in the net

ORs aligned to another ORb

ORs aligned to a 'syntenic ortholog'c

Number of chains containing 'syntenic orthologs'd

Correlation between sequence similarity and chain lengthe


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.

Aloni et al. Genome Biology 2006 7:R88   doi:10.1186/gb-2006-7-10-r88

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