Question: 5 prime & 3 prime end of the gene in GTF
0
gravatar for anu014
7 days ago by
anu014120
India
anu014120 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 7 days ago • written 7 days ago by anu014120
1
gravatar for genomax
7 days ago by
genomax37k
United States
genomax37k 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 1 day ago • written 7 days ago by genomax37k

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

ADD REPLYlink written 7 days ago by anu014120
1

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 1 day ago by Emily_Ensembl13k

Thanks Emily for answering.

ADD REPLYlink written 18 hours ago by anu014120
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