Pseudogenization of the MCP-2/CCL8 chemokine gene in European rabbit (genus Oryctolagus), but not in species of Cottontail rabbit (Sylvilagus) and Hare (Lepus)

Table 1 Identification of gene structure of Rabbit CCL2,-7,-11,-8,-13,-1 genes based on Human orthologs

*CHEMOKINE*			P	GenB			sense
Species	orcu^$	orcu^$			Hosa^*	Hosa^*
*CCL2*
hnmRNA	216	2031			227	2153
CDS-ex1	287	362	0.86	v	300	375	+
CDS-ex2	1066	1183	1.00	v	1172	1289	+
CDS-ex3	1534	1717	0.89	v	1627	1777	+
*CCL7*
hnmRNA	11534	13840			15171	17187
CDS-ex1	11603	11678	0.99	v	15241	15316	+
CDS-ex2	12913	13030	1.00	-	16096	16213	+
CDS-ex3	13429	13534	1.00	-	16647	16752	+
*CCL11*
hnmRNA	19375	22120			30618	33130
CDS-ex1	19509	19584	0.89	- v	30759	30834	+
CDS-ex2	20714	20822	1.00	v v	32046	32157	+
CDS-ex3	21217	21322	1.00	v v	32535	32640	+
*CCL8-like*
pseudogene	47126	49449			63997	66352
CDS-ex1	47576	47641		-	64452	64527	+
CDS-ex2	48337	48455		-	65219	65336	+
CDS-ex3	48872	48977		-	65752	65857	+
*CCL13*
hnmRNA	71995	73927			101402	103560
CDS-ex1	72083	72158	1.00	-	101477	101552	+
CDS-ex2	72902	73016	1.00	-	102425	102539	+
CDS-ex3	73361	73457	1.00	-	102976	103081	+
*complCCL1*
hnmRNA	74930	77383			105330	108183	-
CDS-ex3	75053	75155	1.00	-	105509	105611	-
CDS-ex2	76180	76291	1.00	-	106735	106846	-
CDS-ex1	77337	77412	0.91	-	108036	108111	-

^$): pos 1 corresponds to position 23720000 of NC_013687.1.
^*): pos 1 corresponds to position 32582070 of NC_000017.1.
The Rabbit genome fragment R-MCPgb containing the CCL2 and CCL1 genes is compared to its Human correlate according to the alignment in Additional file 5. The identification of the Rabbit orthologs of the Human CCL genes based on sequence similarity was checked for consistency using Genscan [29], which furthermore provided estimates of the quality of intron splice sites (values varying between 0 and 1 are shown under the heading “P”). Positions of transcription initiator and termination sites were estimated by homology with Human. The exons annotated in the GenBank feature file of the Rabbit sequence (Additional file 1) are marked “v” under “GenB”.

ISSN: 2730-6844