get the 3utr of gene using transcriptome and genome
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7.2 years ago
najibveto ▴ 110

hello i am working on fish called fathead minnow and by looking in NCBI found the genome assembly and the transcriptome assembly pf this fish, plus the closed relative to it is the zebrafish. i have one gene of interest called the TP53i11, the zebrafish have it and i need to know the sequence of it in fathead minnow based on this approach:

  1. i will retrieve the cds of gene from zebrafish and blastx against the transcriptome of fathead minnow
  2. after getting the homologue gene in fathead minnow i will look for the 3utr based on blastn against the transcriptome of fathead minnow. what do you think about this approach? should i blast also against the genome of fathead minnow? thanks for your help.
genome transciptome gene 3utr • 1.3k views
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