How to download human mRNA sequences with STOP codon annotation?

Question

[supertech]

How to download human mRNA sequences with STOP codon annotation? How can I do that on the TableBrowser or download it from any other database?

[Ram]

You're going to need the GTF file to locate stop codons.

grep 'gene_name "BRCA1";' gencode.v33.annotation.gtf | grep 'transcript_type "protein_coding";' | awk -F"\t" '$3=="stop_codon"'

grep 'transcript_id "ENST00000357654.9";' gencode.v33.annotation.gtf | awk -F"\t" '$3=="stop_codon"'

chr17   HAVANA  stop_codon   43045678   43045680        .       -       0       gene_id "ENSG00000012048.23"; transcript_id "ENST00000357654.9"; gene_type "protein_coding"; gene_name "BRCA1"; transcript_type "protein_coding"; transcript_name "BRCA1-203"; exon_number 23; exon_id "ENSE00001814242.1"; level 2; protein_id "ENSP00000350283.3"; transcript_support_level "1"; hgnc_id "HGNC:1100"; tag "basic"; tag "MANE_Select"; tag "appris_alternative_2"; tag "CCDS"; ccdsid "CCDS11453.1"; havana_gene "OTTHUMG00000157426.16"; havana_transcript "OTTHUMT00000348798.4";

[supertech]

I have not downloaded any reference sequence or annotation yet. That is something I need to do also.

How to extract STP codon information from a GTF file. I see only 9 columns in GTF file format; two of them start and stop, and I am not sure what they are referring to. I need this information to calculate RNA-seq coverage around STOP codons. Thanks.

[Ram]

The Start and Stop are position information for each GTF feature. Where the feature in question (column 3) is stop_codon, the stop codon starts at position Start and ends at position Stop, spanning three bases.

You're going to need to map each such stop codon entry to a transcript ID, as stop codons are transcript specific, not gene specific.