Multiple Hits In Blat For Hox Genes

Question

[anuragm]

I am trying to identify homologous regions among the hox genes across vertebrate clades using data from UCSC browser. I used the BLAT tool to find the corresponding region in other taxa by taking the hoxa1 (and 8kbp on either side of it) for Xenopus and performing BLAT of this region against other sequences. However, I find multiple hits ( ~20) ranging from 80-100% similarity for almost all the different taxa. What could be the possible explanation behind it, as I expect very few matches when I am trying to BLAT a sequence thats almost 20kbp long against a genome. Is there anything I am doing wrong ?

Answer 1

[dario.garvan]

The genes in the HOX cluster are essential for normal development. Presumably, there are enhancers or transcription factor binding sites near the genes, which are conserved because they are under evolutionary pressure. If you use the Genome Browser and look at the Mammalian Conservation track in this area, you'll notice that the sequence conservation is high far outside of HoxA1, as well as in it.