[ensembl-dev] (v80) "RefSeq_gene_name" DBLink missing for ACKR1?

Luke Goodsell Luke.Goodsell at ogt.com
Tue Jul 21 10:15:12 BST 2015

Hi EnsEMBL Devs,

Querying an  external transcript adaptor for 'NM_002036.3' or 'NM_001122951.2' (transcripts of ACKR1/DARC) and calling get_all_DBEntries or get_all_DBLinks on either the returned transcript or the transcripts' gene objects returns nothing in v80, but in v75 it returns the expected RefSeq_gene_name links.

Have the DBLinks/Entries been intentionally removed, is this in error, or have I missed something?

Example code below.

Kind regards,


use strict;
use warnings;

use Bio::EnsEMBL::Registry;

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

                -host => 'ensembldb.ensembl.org',
                -user => 'anonymous',

my $external_transcript_adaptor = $registry->get_adaptor( 'Human', 'otherfeatures', 'Transcript' );

foreach my $query ('NM_002036.3', 'NM_001122951.2') {
                print "q: " . $query . "\n";

                my $transcript = $external_transcript_adaptor->fetch_by_stable_id($query);

                print "  t: " . $transcript->stable_id . "\n";

                foreach my $dbe (
                                @{ $transcript->get_Gene->get_all_DBEntries() },
                                @{ $transcript->get_all_DBEntries() },
                                @{ $transcript->get_Gene->get_all_DBLinks() },
                                @{ $transcript->get_all_DBLinks() }
                ) {
                                printf "    XREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();
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