5 prime & 3 prime end of the gene in GTF

Question

[anu014]

Hello Biostars!

This one is just a basic question which is confusing me a lot. I've a GENCODE GTF & I'm pasting a record from it here:

chr15   HAVANA  gene    34341713    34343177    .   -   .   gene_id "ENSG00000182117.5"; gene_type "protein_coding"; gene_name "NOP10"; level 1; havana_gene "OTTHUMG00000129440.3";

So does the start of gene here (34341713) is 5' end & end of the gene (34343177) is 3' end?

Please help me out.. Thanks :)

Answer 1

[GenoMax]

This gene is on the - (reverse) strand where as the genomic co-ordinates in GTF are referencing the + (forward) strand. So you can think about which of those numbers should be the 5'-end.

[anu014]

So start of gene is always 5' end weather the gene is on reverse or forward ??

[Emily]

No, the start is the lower coordinate, the end is the higher coordinate. The 5' of the gene is the start for forward strand gene, abd the end for reverse strand genes.

[anu014]

Thanks Emily for answering.