Table 1
Identification of gene structure of RabbitCCL2,-7,-11,-8,-13,-1genes 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”.

van der Loo et al. BMC Genetics 2012 13:72   doi:10.1186/1471-2156-13-72

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