Dear Community, I am a cell-biologist and not very familiar with bioinformatics... I have cloned a novel isoform/transcript variant of a protein and my advisor (who is not familiar with bio-informatics as well) asked me to investigate the species and tissue expression pattern of this isoform using database searches.... I have cloned this isoform from mouse kidney and obtained the sequence - but I have no idea how to proceed or how to generate "typical" graphs to show such information...
Regarding the existence/evolution of this isoform in other species: my initial thought was to download all the transcript variants of this gene in different species (human, mouse, drosophila, elegans) from NCBI's RefSeq DB and to align all those sequences to my sequence... I dont know, if this is a good way.... this may work/produce some useful results, but what I would really like to do is to present the evolutionary development of this sequence across the different species in some kind of phylogenetic tree... maybe someone could give me some hints or recommend a paper??? ... or do you think, that my idea is somehow "bad" or "unprofessional"???
Regarding the species-specific tissue expression: how to do such a thing???? Should I search UniGene and GEO and manually generate excel-data like this: "isoform X" (blast-related similarity to my isoform: 50%) is predominantly expressed in Drosophila melanogaster tissue X"???? To me, this sounds very "nooby" or "unprofessionell"....maybe someone could teach me how to manage such things in a more professional way?
I am really thankful for any hints and help!!! Thanks a lot - this is really important to me and I really urgently need professional help!!!!!!!!! Thanks!!!!!!!!!!