Getting the mRNA sequence from genome annotation

Question

[colin.kern]

From my understanding, if an annotated gene from Ensembl, UCSC, etc. is marked as being on the positive strand, that means its sense strand is the exact sequence from the assembly fasta file, and so the mRNA sequence is a copy of the genome assembly sequence for the exon regions (except with uracil replacement). For a gene on the negative strand, then, the reverse complement of the fasta sequence needs to be used to get the mRNA sequence. Is this correct, or do I have this backwards?

Answer 1

[benformatics]

Yes that is correct assuming you want the exonic sequence in 5' to 3' order relative to the mRNA. Also note RNA-editing or alternative splicing may change the sequence from the genome reference.

Answer 2

[swbarnes2]

Realistically, if you want a transcript from an annotated organism in ensembl, just get the transcript. Transcripts and exons are always returned in the desired orientation, no matter what strand the transcript is on.