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PolyA site/signal feature from NCBI GenBank File

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..??

genome gene
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updated by Siva Siva • written by vsivaranjanipriya • vsivaranjanipriya

1 answer

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

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

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written by Siva Siva

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??

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written by vsivaranjanipriya • vsivaranjanipriya

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?)

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written by Siva Siva

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..

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written by vsivaranjanipriya • vsivaranjanipriya

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