Question: 5 prime & 3 prime end of the gene in GTF
1
gravatar for anu014
22 months ago by
anu014170
India
anu014170 wrote:

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 :)

ADD COMMENTlink modified 22 months ago • written 22 months ago by anu014170
1
gravatar for genomax
22 months ago by
genomax71k
United States
genomax71k wrote:

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.

ADD COMMENTlink modified 22 months ago • written 22 months ago by genomax71k

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

ADD REPLYlink written 22 months ago by anu014170
2

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.

ADD REPLYlink written 22 months ago by Emily_Ensembl19k

Thanks Emily for answering.

ADD REPLYlink written 22 months ago by anu014170
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