[maker-devel] duplicate exons?

[Uma Maheswari]

Hi Carson,

When I was trying to load the Maker-2.27 results into ensembl, I found 
that few hundreds of genes with 'duplicate exons' . When I looked in the 
gff file, I found cases like this, where the exons are not actually 
duplicated but have two Parents with same mRNA ID. This can be a 
potential alternate transcript, attached to the same transcript by mistake?

Many thanks
Uma





3       maker   gene    524271  525467  .       -       .       
ID=augustus_masked-3-processed-gene-6.179;Name=augustus_masked-3-processed-gene-6.179
3       maker   mRNA    524271  525467  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1;Parent=augustus_masked-3-processed-gene-6.179;Name=augustus_masked-3-processed-gene-6.179-mRNA-1;_AED=0.50;_eAED=0.63;_QI=1476|0.33|0.75|1|0|0.25|4|0|406
3       maker   exon    524271  524480  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:573;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   exon    524538  525182  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:572;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1,augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   exon    524271  525467  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:571;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   CDS     524538  524903  .       -       0       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   CDS     524538  525182  .       -       0       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   CDS     524271  524480  .       -       0       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   five_prime_UTR  524271  525467  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1
3       maker   five_prime_UTR  524904  525182  .       -       .       
ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=augustus_masked-3-processed-gene-6.179-mRNA-1