diff --git a/lib/EnsEMBL/REST/Model/Lookup.pm b/lib/EnsEMBL/REST/Model/Lookup.pm
index 5a4be424de52a341b4cfa15a6e301b85fab0d7f1..d91189b677f4b9054c716f0aaea9eb5c7ada5f53 100755
--- a/lib/EnsEMBL/REST/Model/Lookup.pm
+++ b/lib/EnsEMBL/REST/Model/Lookup.pm
@@ -515,6 +515,7 @@ sub features_as_hash {
if (lc($object_type) eq 'transcript') {
$features->{is_canonical} = $obj->is_canonical;
$features->{length} = $obj->length;
+ $features->{gencode_primary} = $obj->gencode_primary; # boolean value for having GENCODE Primary attrib
}
if (lc($object_type) eq 'gene') {
$features->{canonical_transcript} = $obj->canonical_transcript->stable_id.".".$obj->canonical_transcript->version;
diff --git a/t/lookup.t b/t/lookup.t
index 820367f3f5ac1a01ac30f48e452b161097c1c0f7..8df6b036699f00d5bb123bda9dfaec8c2f7a5139 100644
--- a/t/lookup.t
+++ b/t/lookup.t
@@ -109,7 +109,7 @@ $full_response = {
%{$condensed_response},
Parent => 'ENSG00000176515', start => 1080164, end => 1105181, strand => 1, version => 1, seq_region_name => '6', assembly_name => 'GRCh37',
biotype => 'protein_coding', display_name => 'AL033381.1-201', logic_name => 'ensembl', source => 'ensembl',
- is_canonical => 1, length => 3435,
+ is_canonical => 1, length => 3435, gencode_primary => 0,
};
cmp_deeply(json_GET("/lookup/$basic_id",'lookup transcript'), $full_response, 'Full response contains all Transcript information');
@@ -151,7 +151,7 @@ $full_response = {
%{$condensed_response},
Parent => 'ENSG00000164379', start => 1312675, end => 1314992, strand => 1, version => 2, seq_region_name => '6', assembly_name => 'GRCh37',
biotype => 'protein_coding', display_name => 'FOXQ1-001', logic_name => 'ensembl_havana_transcript', source => 'ensembl',
- is_canonical => 1, length => 2318,
+ is_canonical => 1, length => 2318, gencode_primary => 1,
};
cmp_deeply(json_GET("/lookup/$basic_id",'lookup transcript'), $full_response, 'Full response contains all Transcript information');
diff --git a/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt b/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
index c669dfc410beb0c65043d85e7107f4a63f3ca12f..32a0b673b3a471b22f3f16fb906f594b00fc85ea 100755
--- a/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
+++ b/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
@@ -230,3 +230,4 @@
405 ref_length Golden Path Length Length of the primary assembly
406 total_length Base Pairs Total length of the assembly
535 MANE_Select MANE Select v0.92 MANE Select (v0.92) is the preliminary release (phase 7) of the MANE Select data set. The Matched Annotation from NCBI and EMBL-EBI project (MANE) is a collaboration between Ensembl-GENCODE and RefSeq to select a default transcript per human protein coding locus that is representative of biology, well-supported, expressed and conserved. This transcript set matches GRCh38 and is 100% identical between RefSeq and Ensembl-GENCODE for 5' UTR, CDS, splicing and 3' UTR.
+576 gencode_primary GENCODE primary annotation Gencode Primary replaces Gencode Basic for protein coding genes as the set of the most biologically relevant transcripts. Protein coding transcripts are compared to MANE Select or to Ensembl Canonical where MANE Select is not yet defined. The features (exons and introns) that are novel to the reference transcript are filtered and assessed for biological relevance using conservation and expression data. The transcripts having the filtered features are retained for the set. For noncoding genes, the Gencode Primary set is identical to the Gencode Basic set.
diff --git a/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt b/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt
index ca623c8e1793818defa4af1110be4d42332d137b..dd58dc46adc3a115f58a41f3736e7fb055ee5079 100755
--- a/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt
+++ b/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt
@@ -272,3 +272,4 @@
1385028 52 Havana
1385028 53 v@somewhere.com
1384971 535 NM_033260.4
+1384971 576 GENCODE primary
\ No newline at end of file