How to sequence a gene along with its 3' and 5' UTR

Question

[Shahzad]

Dear All I have a gene transferred into a plant (cotton) chromosome. I want to know the upstream and downstream DNA sequences present with this gene. Please guide me the possible procedure/s by which I can get this information and specially is there any possibility that NGS can help in this matter. If anymore information is needed please ask.

BEST REGARDS

[Carlo Yague]

Do you want the flanking DNA regions (not part of the transcript) or the UTRs which are part of the gene and are transcribed ?

[Shahzad]

I want the sequences of flanking DNA regions(upstream and downstream) to know the place of this Gene in a chromosome.

[christopher medway]

If you know the sequence of your inserted gene, you could try "cycle sequencing" by designing a single primer at the end of your gene that will read into the flank (and then do the same for the start).

[Shahzad]

Thank you all for these wise suggestions.

Answer 1

[Carlo Yague]

NGS can definitely help if you do genome sequencing. This thread may give you some ideas on how to proceed with the data.

[Shahzad]

please also let me know if there is Any other technique which can earmark the transformed gene's position in chromosome so I can get the up and downstream DNA sequences?