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10

Yes, of course. Exons are not limited to the protein coding regions. Many UTRs are in exons. In fact, you even have various cases of UTRs being multiple exons, and being spliced. What is strange in your file is not so much that you have exons beyond the stop codon, but that you also have them marked as CDS (coding sequence). That isn't possible, no. While ...

7

Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.

2

Okay well, because you're using HYPHY, you're going to need a gene tree of every gene you intend to analyze. This requires you to understand the homology relationships between the genomes at hand. Depending on your project, you might already have a list of homologs you're trying to analyze, or you can start from scratch. If starting from scratch, you will ...

2

If you need a 3-column BED, you can just use standard Unix tools: curl ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gtf.gz \ | gzip -dc \ | grep -wFf list.txt \ | awk -vFS="\t" '$3=="exon"{print$1"\t"($4-1)"\t"$5"\t"$9}' > out-3.bed If you need a 12-column BED: # install k8 and paftools.js curl -L http://bit.... 2 You could grab exons via Gencode v27 (hg38) GFF annotations and convert them to BED via BEDOPS convert2bed/gff2bed:$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gff3.gz \ | gunzip --stdout - \ | awk '\$3 == "exon"' \ | convert2bed -i gff - \ > exons.bed Then use grep to filter exons ...

2

Although the explanation that UTR (untranscribed) regions can consist of multiple exons covers most situations, I think it is good to mention stop codon readthrough. This would result in a CDS (coding sequence) part of your mRNA (messenger RNA) after a stop codon. However, following the gff3 format specification, this should probably be encoded differently,...

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