Question: 5 prime & 3 prime end of the gene in GTF
1
gravatar for anu014
3 months ago by
anu014140
India
anu014140 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 3 months ago • written 3 months ago by anu014140
1
gravatar for genomax
3 months ago by
genomax42k
United States
genomax42k 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 3 months ago • written 3 months ago by genomax42k

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

ADD REPLYlink written 3 months ago by anu014140
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 3 months ago by Emily_Ensembl14k

Thanks Emily for answering.

ADD REPLYlink written 3 months ago by anu014140
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