Help with mRNA region annotation
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5.1 years ago
Neu ▴ 10

Hi, I have mRNA region of interest (mRNA_start-mRNA_end) and I want to find whether it is falling in cds and/or utr(s). The file is as below. How can I do this?

mRNA    mRNA_start  mRNA_end    5utr    cds 3utr
ENST00000000442.10  2170       2215     UTR5:1-171  CDS:172-1443    UTR3:1444-2215
sequence gene R • 1.0k views
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not sure if the example you provide makes sense ... unless the mRNA start /end are genomic coordinates and the CDS one are transcript coordinates. Is that the case?

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No Sir, I have just corrected the example. I have a region of mRNA (i.e. that is interacting with another mRNA). I want to know whether it is falling in UTRs and or CDS.

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ok, in that case I'm confused: how can the start of you mRNA be larger then the start of the CDS? Or is what is denoted in the mRNA_start/end fields the region of interaction you are talking about?

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Sir, Here mRNA-start means start of the fragment or region of mRNA for which I am interested. What I mean is the fragment of mRNA starting from 2178 to 2215 is a 3UTR/5UTR or CDS. Thank you

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if the info that is present in your example is relevant, it will be definitely in the 3prime UTR

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5.1 years ago

You have answer from your statements itself as you mentioned the CDS:172-1443, then beyond these limits you should have UTRs at 5' and 3' ends of your mRNA as you have also given the UTRs positions. If you wish to confirm, you should also have genomic sequence to align your mRNA using tools like splign from NCBI to see whether your mRNA falling within CDS region starting from first codon ATG of exon1 with further exons. If you don't have genomic DNA, just do BLASTN analysis in NCBI or other genome database of the species of your interest to download the genomic sequence of the gene of interest also, then proceed with splign tool for exon intron boundary/coordinate prediction to findout whether your mRNA falling within the CDS or it has 5' and 3' UTR as well.

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