Supplementary Material for: Sequencing and genomic annotation of the chicken <i>(Gallus gallus)</i> Hox clusters, and mapping of evolutionarily conserved regions
2007-08-02T00:00:00Z (GMT) by
Hox genes encode transcription factors that are involved in the regulation of normal development and are mutated in some diseases and malformations. Chicken <i>HOX</i> genes have been extensively studied in the chick limb and other developmental models. To date while the chicken <i>HOXA </i>cluster has been completely sequenced many other chicken <i>HOX</i> genes are known only from partial mRNAs or unfinished genome assemblies. Furthermore, although a finished sequence of the <i>HOXA</i> cluster is available, the sequence has not yet been annotated. We have therefore manually annotated the available <i>HOX</i> sequences and improved the sequences by sequencing PCR fragments that bridge existing gaps in the genome sequences. These sequences complement the published sequences, including the currently incomplete WashUC Gallus_gallus-2.1 build, to give an improved coverage of the cluster. We used phylogenetic footprinting to map the genomic location of 398 Ultra Conserved Regions in the<i> HOX</i> complex 248 of which do not overlap with any known annotated coding exon. These included the hox-related microRNAs miR-10 and miR-196. The chicken <i>HOX</i> clusters appear to be broadly comparable to their human counterparts. A few human orthologues were not recovered from the chicken, presumably because of incomplete sequence.