[maker-devel] maker exon result

[Jingjing Jin]

Dear all,

I have used maker to predict the gene model in my draft genome.

However, when I check the sequence for each exon, I find some of them just have start codon, without stop codon.

Is it reasonable for this?

Like in this example:

processed_tobacco_genome_sequences_c33    maker    gene    8916    12632    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9;Name=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9
processed_tobacco_genome_sequences_c33    maker    mRNA    8916    12632    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9;Name=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0|1|0.14|0.12|8|0|362
processed_tobacco_genome_sequences_c33    maker    exon    8916    9065    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:148;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    9089    9214    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:149;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    10232    10381    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:150;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    11216    11270    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:151;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    11336    11496    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:152;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    11513    11602    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:153;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    11903    12151    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:154;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    exon    12528    12632    .    +    .    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:exon:155;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    8916    9065    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    9089    9214    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    10232    10381    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    11216    11270    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    11336    11496    .    +    2    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    11513    11602    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    11903    12151    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1
processed_tobacco_genome_sequences_c33    maker    CDS    12528    12632    .    +    0    ID=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1:cds;Parent=maker-processed_tobacco_genome_sequences_c33-snap-gene-0.9-mRNA-1

ATGAAGGGCGCGATACGTACTACGATTCCAAAACCATCAGCATTGCCATTGAAGGTCTCAGAATTATCT
CCATCAGCTGATTCAGTACCCGTTCCAGCGTCTTTACAGGATGTCGAGGCGGGGAAGTTGATTGAGAAT
AATCCATCAGGGGTGATACAGAAGAATTGTTTCAGTATCTTGTTGAAATATTGGCTTCTAGAGTGTATG
ATGTAGCAATTGATTCCCCCTTGCAAAATGCAACTAAGCTTTCCAAGAAGCTTGGAGTTAACTTTTGGA
TCAAAAGAGAGGATATGCAGTCCGTATGTTTCTCCTCTCTTCTTTTTTTGATGTAGCATTTGCTTTAAC
TTAGAATTTGTGGTTTTAAACATACCATTAGAAAGGTATGGAGGTTGAGGATTAGGGTAGTAAAGTAGG
TAGTCTAGAGTGTTCATAACAGTAATATTGACAAGCAGTCTCGCTTTCCGTTGGTAGTAGGTTTTTATG
ACTAACCGTTATTTTCTTTCATTGTTGATCAACTTACTTTTGTTGTTTTTATTCTGCTTTTATATGGCT
TTTTGGTACTGTCCCTTCTTGTCTATATTTTCATTAATGTGGTGCTTATGCTTTTCTAAGCCGAGAGTT
TATTGGAAACAACTTTCATATCCTCACAAGGTAGGGGTAAGGTGTGCGTACACACTACCCTCCCCAGAC
TCTACGGTGTGGGATAATATTTAGTATGTTATTGTCGTTGTTGTTGTAAACGTTTTTTTTGTTGCTATC
AAAGCATGTTATTACGGGTAAAATAGAAACATTTAAAGTGAAAGAGTTTCCAAACGTAGGAAAGCTTTT
TTTTCTTTCGGAATACACCGAAAAAAGAAAGACTATCATTTAAGATAGAACAACAACAGCGACGGAGCT
AGCCTTCGACTTACTGGTTCGGCAGAACCCAATAATTTTGGCCCAAACTCTGTACTTGTACTAAAAAGC
TCACTTAATATGTATAAAAAGCCTAGTAATTAAGTTGCATTTTTTTCTTTCTAAAATCTAGAGCTCATA
AACTCAAAATTATGTCTCCGCCTCTGAACAATGGGGATATTATTCTACTTTTAACTATCTTAGATAAGT
TAATAATTGTTCTCTTTTTCAAACGTTTCTGCCTTGTATTATTGTGTAACTATTTATACTGTGTGGACG
CTTCAAAATGTTGTTGCGCCCGCGTCGGATCCTCAAAAAATATATATTTTGAGGATTCGACACGCACCC
GATGACCTTTTCGGAGAATTCGAGCAATATAGGTAACTAATATTGCTAGCTCATCAACTGGTGGTATTT
TTTAGGTGCTCTCATTCAAGCTTAGAGGAGCTTATAACATGATGACCAAACTCTCAAAGGAGCAATTAG
AAAGAGGGGTTATAACTGCTTCAGCTGGAAATCATGCACAAGGTGTTGCATTAGGTGCTCAGAGACTTA
AATGTACTGCTACGATTGTCATGCCTGTTACCACACCAGAGATCAAGGTAATTAGTTCTCTCCTGTTAA
TTTATCCTTCATGTTCGATTCATGTGAATCTAGTTGATCGGGCACTGAGTTTTACTAAAAAATGAAGAC
TTTCGGAACTTGGGAGCTTTAACATGCTGTAACATTTGTGTAGTTATAAGACTTTTGAAACTTATAGTC
TTAGTGGGTGTTTGGACATAAGAATTGTAAAGTTCCAAGAAAAGTGAAAAAAAATTCAAGTGAAAATGG
TATTTGAAAATTAGAGTTGTGTTTGGACATGAATATAATTTTAGGTTGTTTTTGAAGTTTTGTGAGTGA
TCTGACACAAATTTTGAAAAAACAACTTTTTGGAGTTTTTCAAATTTTCGAAAAATTCCAAAATGCATC
TTCAAGTGAAAATTGGAAATTATATGACCAAACGCTGATTTCGGGAAAAAAATTCGAAAAAATGTGAAA
ATTTTCTTATGTCCAAACGGGCTCTTAAATGCGTCATAACGTTTGTGTGGTTATAAAAGTCTCTCATCT
GAATAGGGTCACACAACTAAAACAGAGAGAACAAAATAATTCACTAAAAAAAAATTGGAACTAGCTACA
AACTTCGTCGCAAGTCTCGCTAAATCGCTCGTAGCTAATAGAATTTCTAGATAATTTGTTTAGCTTGTA
GCATGAAATTTTTCTATTTAGCAACAGAAGTAGTCTGTCGCTAATTCCTATTTTTTTAGTAGAAAGTAT
TGTGAAATTATTTGTTTTTCTAAAGGACCATTTTCTTTACAAATGAACAGATTGAAGCAGTTAAGAACT
TGGATGGTAATGTAGTTCTACAGGGTGACACATTTGATGAAGCTCAAGCACATGCTTTAAAGTTGGCTG
AAGATGAAGGTCTCACATTCATCCCGCCTTTCGATCACATCTTAAAGATATACATGCAGTATTTCTGCC
TGTAGGAGGAGGAGGTTTAATAGCTGGTGTTGCTGCATATTTCAAAAGGGTTGCTCCTCATACAAAGAT
TATAGGAGTTGAGCCATTTGGTGCAAGTTCAATGACACAGTCTTTGTACCACGGAATGAGAGTAAAGTT
AGAACAAGTTGATAATTTTGCAGATGGCGTAGCTGTTGCACTAGTTAGTTGGTGAAGAAACTTTCCGTC
TTTGCAAAGATTTAATAGACGGAATGGTCTTAGTCAGTAACGATGCTATTAGTGCAGCAGTAAAGGTTA
GCACGCACCATCTCCTAATGGTTTCAGATATGATCCGTCCAACCAGCCAAAATTGGTTAGAATAGGACG
GGTTGAACTATCAACCCAATCAATCACAGCCCAAATAACATTTATGTGGGTATATGACTCGCCCATTTA
TTAACTCAACCAATTTTGGTCCATTCAAATTCAGGCTAACCCGTCCACGTTTGACATTCATACTTTAGA
TGTGGATTAAAGTAACTTTCTTAAATTTCCCTCTGGTTTTGACATGTACTAGTTTGTGTTTGTGTGTGT
TTTGTTCTTTTTTTCAATAGGATGTGTACGACAAAGGAAGGAACATATTAGAGACATCAGGTGCACTCG
CCATAGCTGGAGCTGAAGCATACTGCAAATACTATGACATAAAGGGCGAAAACGTTGTAGCAATTGCTA
GTGGAGCCAATATGGACATCAGCAAACTAAAATTAGTCGTCGATTTAGCAGATATTGGTGGACAGAGGG
AAGCTCTGCTGGCTACTTTTATGCCAGAAGAACCAGGAAGCTTCAAAAAATTCTGCGAACTTGTGCGTT
ACTTAGAGCACTTAACAAGCATTTTAGCCAGAGTTTAAGTTATATACATCGTCGTCAGTGTAAGAAACT
TTTATACCGTCTTGATGGAGTAAAAATTTGTTACACTGACGTGTACATAACTTAAAACTTTTTTAGTTA
CTATATGATACTTTCTGTCTAAGAAACTGAAATATTGACTTGAATTACTGGTGGGACCTATGATTATTA
CCGAATTCAAGTACAGATATAACTCTGGAAGAAAACAAGCTCTAGTTCTGTACAGGTAATTAAAGTTCT
ATTCATTTTTAGAGGGGATGTTGGCTTCTCATTTTAGATTTGCTTTATTAGTTGTTAGGAAAAAAGAAA
TTACTTATTACATTCAATTTTTAGATTTTCTGTCAATTCATATTTCCTGAGAAGCCTGGAGCTTTAAGG
AAGTTCTTAGATGCTTTCAGCCCTCGATGGAATATAAGTTTGTTCCATTATCGTGAACAG


This is the sequence for this gene, the red color is for the first exon??

However, for this exon, I cannot found the stop codon???

I also find for some exon, there are several stop codon in one exon???

Does anyone have the same problem with me?
Or there is something wrong when I configure the maker file??

Thanks!

Jingjing




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