[ensembl-dev] transcript coordinates via REST?

[Reece Hart]

Hi Andy-

Thanks for the reply.

I'm aware that the annotation is performed on the assembly and I'm a fan.
However, in my view there's always an implicit alignment -- even if a
trivial one -- whenever one has a change of a coordinate system e.g., from
genome to transcript.

The upshot of this is that GENCODE annotation reflects what occurs in the
> genome. Providing an alignment file would match the transcript models.
>

Is this *always* true? More correctly, my understanding was that the above
typical case had exceptions, which caused ENSTs to differ from the
underlying genome. Or, perhaps that used to be the case and I'm not
up-to-date with modern Ensembl practice?

Let's use a specific example: ALMS1, ENST00000264448, GRCh37 (for which I
have some data handy). This transcript contains both an indel and a
substitution with respect to the assembly. The ENST sequence and exon
structure (in e-75, at least) differ from the genome. How does this happen?
(Apologies, I don't have examples for GRCh38 handy.)

When bridging to the translational genetics community, it's imperative that
we use transcripts that are familiar in both structure and sequence. Since
one or both characteristics will differ from a reference genome for some
genes, it's unclear to me that we can rely solely on genome-based
annotations. In other words, it seems that some alignment file will always
be necessary to handle corner cases.

Do you agree? Am I missing something?

Thanks,
Reece
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