Question: mRNA positions from vcf
gravatar for jindal.aashi21
15 months ago by
jindal.aashi2110 wrote:

Hi everyone,

I am processing a vcf file from ExAC browser (release 1.0) with hg19 as human reference genome. I want to identify only those mutations which occur at mRNA positions. Is there any field/column in vcf that can give me that information.

For now, I tried to use "BIOTYPE" field from vcf. I selected only those positions for which "BIOTYPE=Protein_coding". However, when cross-checking these positions with exon start/stop positions from USCS browser, some of these are marked as non-coding RNA. How is this possible or "BIOTYPE=protein_coding" does not give me the right information about RNA type?

Example: 138593 position in chr1 in vcf is marked with BIOTYPE=protein_coding. This position is part of LOC729737 gene. When I look for this position in ucsc file, it is marked as non-coding RNA (as per ucsc kgXref table).

snp exac vcf exome • 271 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 15 months ago by jindal.aashi2110

See here:

DESCRIPTION: SubName: Full=Uncharacterized protein;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.
ADD REPLYlink modified 15 months ago • written 15 months ago by ATpoint40k


Thanks for your response. May you please explain this more.

ADD REPLYlink written 15 months ago by jindal.aashi2110

What is unclear? The page summarizing LOC729737 and there you see that based on Ensembl automatic analysis pipeline there is some yet not verified evidence for a protein-coding gene.

ADD REPLYlink written 15 months ago by ATpoint40k

Also check the Ensembl genome browser to see if there are any other annotated transcripts in your location of interest. UCSC and/or other sources sometime exclude potential isoforms that don't have as much supporting data.

ADD REPLYlink written 15 months ago by benformatics2.0k
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