SPAC27D7.09c shows as removed, but it wasn't
Closed this issue · 6 comments
manulera commented
Changes in location:
revision user date chromosome systematic_id primary_name feature_type added_or_removedvalue
20110324 - 2011-03-24 I SPAC27D7.09c 3'UTR added complement(4523298..4523387)
20110324 - 2011-03-24 I SPAC27D7.09c 3'UTR removed complement(4523380..4523387)
20110324 - 2011-03-24 I SPAC27D7.09c 5'UTR added complement(4524540..4524731)
20110324 - 2011-03-24 I SPAC27D7.09c 5'UTR removed complement(4524542..4524743)
20110304 - 2011-03-04 I SPAC27D7.09c 5'UTR added complement(4524542..4524743)
20110304 - 2011-03-04 I SPAC27D7.09c 5'UTR removed complement(4524540..4524743)
20110204 - 2011-02-04 I SPAC27D7.09c 3'UTR added complement(4523380..4523387)
20110204 - 2011-02-04 I SPAC27D7.09c 5'UTR added complement(4524540..4524743)
20070620 - 2007-06-20 I SPAC27D7.09c CDS removed complement(4526425..4527576)
manulera commented
This error could occur because I was using synonyms for genes that were merged, but also:
revision user date systematic_id primary_name feature_type added_or_removed value
320 vw253 2012-03-18 SPCC794.07 lat1 CDS removed join(262881..262884,263093..264399)
manulera commented
Hi @ValWood. I noticed that some genes had two CDS associated with them in some revisions. See meu1. This is what caused the error that we saw in the call yesterday. Was this to represent two possible transcripts? Also note how this particular one was removed and added several times with identical coordinates.
revision user date chromosome systematic_id primary_name feature_type added_or_removed value
5819 mah79 2019-09-26 I SPAC1556.06 meu1 CDS added join(3802551..3804587,3804661..3804954)
svn_2 kmr44 2011-08-22 I SPAC1556.06 intron added 3804588..3804660
20110204 - 2011-02-04 I SPAC1556.06 3'UTR removed 3804955..3805271
20090904 - 2009-09-04 I SPAC1556.06 3'UTR added 3804955..3805271
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)
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)
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)
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)
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)
manulera commented
Oh now I see that this must have been used at some point to represent several transcripts for the same gene.
manulera commented
Before different systematic_ids were used for each gene
manulera commented
revision user date chromosome systematic_id primary_name feature_type added_or_removed value
5819 mah79 2019-09-26 I SPAC1556.06 meu1 CDS added join(3802551..3804587,3804661..3804954)
5819 mah79 2019-09-26 I SPAC1556.06.1 meu1 CDS removed join(3802551..3804587,3804661..3804954)
3755 vw253 2016-12-01 I SPAC1556.06.2 meu1-2 CDS removed join(3804582..3804587,3804661..3804954)
svn_2 kmr44 2011-08-22 I SPAC1556.06 intron added 3804588..3804660
20110324 - 2011-03-24 I SPAC1556.06.1 3'UTR removed 3804955..3805271
20110204 - 2011-02-04 I SPAC1556.06 3'UTR removed 3804955..3805271
20110204 - 2011-02-04 I SPAC1556.06.1 3'UTR added 3804955..3805271
20090904 - 2009-09-04 I SPAC1556.06 3'UTR added 3804955..3805271
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
manulera commented
This problem does not affect the generation of the alignment dictionary for allele_qc, because revisions where there are multiple removals or multiple additions of CDS are not included.