Hi,
When you look up an mRNA seq of a certain gene, it says "complete cds" on NCBI. This means that only the coding sequence is given, right?
When you compare this mRNA seq to a NCBI TSA (transcriptome shotgun assembly), it is often much shorter. Does this mean that in the TSA, also 3'UTRs are present ?
Thanks!
What does CDS fields say? Does it start at 1 and end equals the length of the sequence? If yes then this is only the coding sequence. If not- then it has UTRs.
It would help to paste a link to an example, but in general the above should help you figure it out.
In the NCBI mRNA entry, the phrase "complete cds" states that the CDS is completely captured on the sequence. There may be an extra of UTR sequence. You'll find out if you check the CDS coordinates in the annotation section.
TSA is based on shotgun mRNA sequencing. It contains CDS as well as UTR sequences (5p and 3p). However, the TSA contigs often are fragmented such that only parts, e.g. a terminal portion of CDS plus 3pUTR, are represented.
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