Dear Friends, Hi. ( I'm not native in English so, be ready for some possible language flaws).
As you know, there are about 481 ultra-conserved elements that are very similar among Human, rat, mouse and some fishes (http://www.ncbi.nlm.nih.gov/pubmed/15131266 ).
I have the RNA-seq data of a non-model vertebrate (so, there is no reference genome for it) and de novo transcriptome assembly of it and I want to check
1- first, if these ultra conserved 200 bp elements is exist in this species, too.
2- and secondly, what is the percentage of the similarity of the related sequence of my species to the sequence of each element in human
Can the RNA-seq data (and de novo assembly) could be used for these purposes ? How?
Thank you in advance