Handling of multi-transcript genes
Closed this issue · 1 comments
kimrutherford commented
Hi Manu. Sorry for making so many new issues.
I think the multi-transcript genes aren't being handled correctly:
20060219 - 2006-02-19 I SPAC1556.06.1 meu1 CDS added join(3802551..3804587,3804661..3804954)
20060219 - 2006-02-19 I SPAC1556.06.2 meu2 CDS added join(3804582..3804587,3804661..3804954)
20060219 - 2006-02-19 I SPAC1556.06 CDS removed join(3803451..3805487,3805561..3805854)
20060219 - 2006-02-19 I SPAC1556.06 CDS removed join(3805482..3805487,3805561..3805854)
20060517 - 2006-05-17 I SPAC1556.06.1 meu1 CDS removed join(3802551..3804587,3804661..3804954)
20060517 - 2006-05-17 I SPAC1556.06.2 meu2 CDS removed join(3804582..3804587,3804661..3804954)
20060517 - 2006-05-17 I SPAC1556.06 CDS added join(3803451..3805487,3805561..3805854)
20060517 - 2006-05-17 I SPAC1556.06 CDS added join(3805482..3805487,3805561..3805854)
20060626 - 2006-06-26 I SPAC1556.06.1 meu1 CDS added join(3803451..3805487,3805561..3805854)
20060626 - 2006-06-26 I SPAC1556.06.2 meu2 CDS added join(3805482..3805487,3805561..3805854)
20060626 - 2006-06-26 I SPAC1556.06 CDS removed join(3803451..3805487,3805561..3805854)
20060626 - 2006-06-26 I SPAC1556.06 CDS removed join(3805482..3805487,3805561..3805854)
20060701 - 2006-07-01 I SPAC1556.06.1 meu1 CDS removed join(3803451..3805487,3805561..3805854)
20060701 - 2006-07-01 I SPAC1556.06.2 meu2 CDS removed join(3805482..3805487,3805561..3805854)
20060701 - 2006-07-01 I SPAC1556.06 CDS added join(3803451..3805487,3805561..3805854)
20060701 - 2006-07-01 I SPAC1556.06 CDS added join(3805482..3805487,3805561..3805854)
20060905 - 2006-09-05 I SPAC1556.06.1 meu1 CDS added join(3803451..3805487,3805561..3805854)
20060905 - 2006-09-05 I SPAC1556.06.2 meu2 CDS added join(3805482..3805487,3805561..3805854)
20060905 - 2006-09-05 I SPAC1556.06 CDS removed join(3803451..3805487,3805561..3805854)
20060905 - 2006-09-05 I SPAC1556.06 CDS removed join(3805482..3805487,3805561..3805854)
3755 vw253 2016-12-01 I SPAC1556.06.2 meu1-2 CDS removed join(3804582..3804587,3804661..3804954)
5819 mah79 2019-09-26 I SPAC1556.06.1 meu1 CDS removed join(3802551..3804587,3804661..3804954)
5819 mah79 2019-09-26 I SPAC1556.06 meu1 CDS added join(3802551..3804587,3804661..3804954)
manulera commented
embl file before listed changes:
FT CDS join(3803451..3805487,3805561..3805854)
FT /colour=2
FT /gene="meu1"
FT /gene="SPAC1556.06"
FT /product="meiotic expression upregulated (PMID 11376151);
FT leucine zipper; NLS (predicted) (PMID 11376151); coiled-
FT coil (region); no apparent orthologs"
FT /fasta_file="fasta/c1556.tab.seq.00001.out"
FT /note="alternative splice form meu2 (PMID 11376151);"
FT CDS join(3805482..3805487,3805561..3805854)
FT /colour=2
FT /gene="meu2"
FT /gene="SPAC1556.06b"
FT /product="meiotic expression upregulated (PMID 11376151);
FT NLS (predicted) (PMID 11376151); no apparent orthologs"
FT /fasta_file="fasta/c1556.tab.seq.00028.out"
FT /note="alternative splice form meu1 (PMID 11376151)"
embl file at 20060219
FT CDS join(3802551..3804587,3804661..3804954)
FT /colour=8
FT /gene="meu1"
FT /gene="SPAC1556.06"
FT /gene="SPAC1556.06.1"
FT /primary_name="meu1"
FT /systematic_id="SPAC1556.06.1"
FT /synonym="SPAC1556.06a"
FT /synonym="SPAC1556.06"
FT /product="sequence orphan; meiotic expression upregulated
FT (PMID 11376151)"
FT /controlled_curation="term=leucine zipper; date=20060605"
FT /controlled_curation="term=NLS; qualifier=predicted;
FT db_xref=PMID:11376151; date=20060605"
FT /controlled_curation="term=coiled-coil; qualifier=region;
FT date=20060605"
FT /controlled_curation="term=alternative splicing;
FT db_xref=PMID:11376151; date=20060605"
FT /shared_id="SPAC1556.06"
FT /other_transcript="SPAC1556.06.2"
FT /fasta_file="fasta/chromosome1.contig.seq.01557.out"
FT CDS join(3804582..3804587,3804661..3804954)
FT /colour=8
FT /gene="meu2"
FT /gene="SPAC1556.06"
FT /gene="SPAC1556.06.2"
FT /gene="SPAC1556.06b"
FT /primary_name="meu2"
FT /systematic_id="SPAC1556.06.2"
FT /synonym="SPAC1556.06b"
FT /synonym="SPAC1556.06"
FT /product="sequence orphan; meiotic expression upregulated
FT (PMID 11376151)"
FT /controlled_curation="term=NLS; qualifier=predicted;
FT db_xref=PMID:11376151; date=20060605"
FT /controlled_curation="term=alternative splicing;
FT db_xref=PMID:11376151; date=20060605"
FT /shared_id="SPAC1556.06"
FT /other_transcript="SPAC1556.06.1"
FT /fasta_file="fasta/chromosome1.contig.seq.01558.out"
Then at 20060517:
FT CDS join(3803451..3805487,3805561..3805854)
FT /colour=2
FT /gene="meu1"
FT /gene="SPAC1556.06"
FT /product="meiotic expression upregulated (PMID 11376151);
FT leucine zipper; NLS (predicted) (PMID 11376151); coiled-
FT coil (region); no apparent orthologs"
FT /fasta_file="fasta/c1556.tab.seq.00001.out"
FT /note="alternative splice form meu2 (PMID 11376151);"
FT CDS join(3805482..3805487,3805561..3805854)
FT /colour=2
FT /gene="meu2"
FT /gene="SPAC1556.06b"
FT /product="meiotic expression upregulated (PMID 11376151);
FT NLS (predicted) (PMID 11376151); no apparent orthologs"
FT /fasta_file="fasta/c1556.tab.seq.00028.out"
FT /note="alternative splice form meu1 (PMID 11376151)"
I was also surprised, but it did happen like this!