This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why we have exons that start and end at the same coordinate?!

Maybe I'm missing something, but why there are exons that the start and end are the same?!

Examples:

1   havana  exon    2768091 2768091 .   +   .   gene_id "ENSG00000285945"; gene_version "1"; transcript_id "ENST00000648684"; transcript_version "1"; exon_number "1"; gene_name "AC242022.2"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "AC242022.2-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003831437"; exon_version "1"; tag "basic";


17  ensembl exon    41624191    41624191    .   -   .   gene_id "ENSG00000128422"; gene_version "17"; transcript_id "ENST00000540235"; transcript_version "5"; exon_number "2"; gene_name "KRT17"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "KRT17-205"; transcript_source "ensembl"; transcript_biotype "protein_coding"; exon_id "ENSE00003733771"; exon_version "1"; tag "basic"; transcript_support_level "5";

Thanks

gtf exon grch38
• 1,735 views • link
updated by WouterDeCoster WouterDeCoster • written by Medhat Medhat

1 answer

Hmmm seems like an off-by-one error, as these exons are actually a single base long. But GTF is one-based so the coordinates indicate, indeed, a single nucleotide: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

• 0 views • link
written by WouterDeCoster WouterDeCoster

I see, thanks!

• 0 views • link
written by Medhat Medhat

Log in to answer this question.

More posts like this