Question: extract 3'UTR sequeunce from RNAseq data and genome reference
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gravatar for najibveto
4.2 years ago by
najibveto40
Korea, Republic Of
najibveto40 wrote:

hello everyone i did one experiment on microrna in epc cell which are derived from fathead minnow fish. i got the microrna sequences and now i need to do target prediction of microrna. the problem is there is a genome for fathead minnow but without annotation file, i checked the annotation file joined with the genome but doesn't contain any information about CDS or UTR positions. my idea is to use the transcriptome from this paper Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection and do as they did in the paper. but i don't know how to get the 3'utr from transcriptome .can someone help me for this task because i need it in my project and i am a phd student in molecular biology so my bioinformatics knowledge is limited. thanks for your help.

rna-seq genome • 1.2k views
ADD COMMENTlink written 4.2 years ago by najibveto40

Forgive me my ignorance about fish species, I only eat them. Do I understand it correctly that you want to determine 3' UTR sequences for your specie of interest (fathead minnow fish) by using the transcriptome of the carp described in the paper?

Essentially, you would want to look for the stopcodon in the transcripts (not sure if these are the same in fish as in human?) and determine the transcript par following that stop codon.

ADD REPLYlink written 4.2 years ago by WouterDeCoster43k

thanks for your advice, there isn't a tool to do this work?

ADD REPLYlink written 4.2 years ago by najibveto40

I'm not aware of a tool with that functionality, but that definitely doesn't mean it doesn't exist. Scripting something like this wouldn't be impossible.

ADD REPLYlink written 4.2 years ago by WouterDeCoster43k
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