PolyA site/signal feature from NCBI GenBank File

Question

[vsivaranjanipriya]

Hi all,

I need to extract PolyA site/signal feature from GBK (GenBank) file for current release. Unfortunately, current release of NCBI GBK files do not have this feature. Can anyone suggest me where to get this feature..??

Answer 1

[Siva]

GENCODE has PolyA annotation in GTF/GFF3 format. I believe they are manually curated.

http://www.gencodegenes.org/releases/21.html

[vsivaranjanipriya]

Thank You for your reply..:) but I need RefSeq IDs/genome position rather than Ensembl.. How can I map Ensembl genome position to Refseq position??

[Siva]

I believe you should be able to link Ensembl gene IDs to RefSeq IDs using BioMart. Please search older threads (for example Refseq From Ensembl?)

[vsivaranjanipriya]

I used BioMart to map ENST ids to RefSeq ids, but there is problem with co-ordinates.. The co-ordinates are different for considerable amount of entries between ENSTs and RefSeq..