Mapping old Ensembl transcript to a newer one

Question

[nadne]

I have a bunch of human Ensembl transcript ids from an old release, that I want to find the ids in the current version.

For example, the transcript: ENST00000360913, is was removed since release 76. But If I BLAST its sequence, I can find a 100% match for another transcript in the current release (80): ENST00000585580.

Is there a way to do it automatically?

Is there a resource of mapping such ids?

Answer 1

[Alexander Skates]

The two transcripts are distinct transcripts that code for the same protein (see the archived Ensembl browser 75), meaning what you are doing isn't strictly mapping it to a newer version of the transcript, but to an entirely different transcript.

If you want to do this programmatically, you could probably implement a solution using biomaRt in R. I've put together a solution that works for the example you've given, though I haven't tested it with any others. It should give you an idea of how to go about this, if nothing else:

library(biomaRt)

#transcript IDs to "convert"
transcript.ids <- "ENST00000360913"

# define biomart objects, current and archived
mart.current <- useMart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
mart.archive <- useMart(host="feb2014.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL",
                        dataset="hsapiens_gene_ensembl")

# query biomart for the CCDS ID, shared by the two transcripts
archive.results <- getBM(attributes=c("ccds","transcript_biotype","ensembl_transcript_id"),
                         filters="ensembl_transcript_id",values=transcript.ids,mart=mart.archive)
current.results <- getBM(attributes=c("ensembl_transcript_id","transcript_biotype","ccds"),
                         filters="ccds",values=archive.results$ccds,mart=mart.current)

mapped <- merge(archive.results,current.results,by=c("ccds","transcript_biotype"),
                suffixes=c("_archived","_current"))

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