How to find coordinates of TSS from 5pUTR and TTS from 3pUTR in transcriptome/ mRNA ?

Question

[isha.lily20]

Hello Researchers

Can you please tell me just the correct coordinates of TSS(1kb) from 5pUTR + & - strand and TTS(1kb) from 3pUTR + & - strand of transcriptome/ mRNA?

I only have data of 5pUTR= start & end coordinates and 3pUTR= start & end coordinates of rice transcriptome/ mRNA.

Thank you so much for the intellectual help.

Answer 1

[Carlo Yague]

Because in a bed/GTF/GFF file, "start" is always the leftmost coordinate regardless of strand, that means that:

• TSS (transcription start site) corresponds to the start of the 5'UTR for genes on the "+" strand and to the end of the 5'UTR for genes of the minus strand.

• TTS (transcription termination site) corresponds to the end of the 3'UTR for genes on the "+" strand and to the start of the 3'UTR for genes on the minus strand.

[isha.lily20]

Hello Carlo

means i can also take TSS from first exon from transcriptome data and TTS from exon end, is i am technically correct.

Thanks for suggestions