[ensembl-dev] (v80) External transcript adaptor for IGHG1 returns malformed stable_id

[Luke Goodsell]

Hi Ensembl Devs,

When using Ensembl v80 and calling get_all_Transcripts against a gene gathered from an external gene adaptor queried for 'IGHG1', the stable ID of the transcript that is returned is malformed. It is

'NC_000014.9:IGHG1:u_t_1'

whereas I would expect

'NC_000014.9'

Up to now, all transcripts I have queried this way have had standard refseq IDs, occasionally suffixed with '_dupl\d+'.

Is my expectation incorrect, or is there an error in the database?

A demonstration script is below.

Kind regards,
Luke

#!/usr/bin/perl

use strict;
use warnings;

use Bio::EnsEMBL::Registry;

my $query = 'IGHG1';

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
                                                -host => 'ensembldb.ensembl.org',
                                                -user => 'anonymous',
);

my $external_gene_adaptor = $registry->get_adaptor( 'Human', 'otherfeatures', 'Gene' );

my $genes = $external_gene_adaptor->fetch_all_by_external_name($query);

foreach my $gene (@{ $genes }) {
                print "g: " . $gene->stable_id . "\n";

                foreach my $transcript (@{ $gene->get_all_Transcripts() }) {
                                print "t: " . $transcript->stable_id . "\n";
                }
}


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