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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Dear all,<br>
<br>
I have used maker to predict the gene model in my draft genome.<br>
<br>
However, when I check the sequence for each exon, I find some of them just have start codon, without stop codon.
<br>
<br>
Is it reasonable for this?<br>
<br>
Like in this example:<br>
<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
<br>
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<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><i><b><span style="color:red">ATGAAGGGCGCGATACGTACTACGATTCCAAAACCATCAGCATTGCCATTGAAGGTCTCAGAATTATCT</span></b></i></p>
<i><b></b></i>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><i><b><span style="color:red">CCATCAGCTGATTCAGTACCCGTTCCAGCGTCTTTACAGGATGTCGAGGCGGGGAAGTTGATTGAGAAT</span></b></i></p>
<i><b></b></i>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><i><b><span style="color:red">AATCCATCAGGG</span></b></i>GTGATACAGAAGAATTGTTTCAGTATCTTGTTGAAATATTGGCTTCTAGAGTGTATG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">ATGTAGCAATTGATTCCCCCTTGCAAAATGCAACTAAGCTTTCCAAGAAGCTTGGAGTTAACTTTTGGA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TCAAAAGAGAGGATATGCAGTCCGTATGTTTCTCCTCTCTTCTTTTTTTGATGTAGCATTTGCTTTAAC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTAGAATTTGTGGTTTTAAACATACCATTAGAAAGGTATGGAGGTTGAGGATTAGGGTAGTAAAGTAGG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TAGTCTAGAGTGTTCATAACAGTAATATTGACAAGCAGTCTCGCTTTCCGTTGGTAGTAGGTTTTTATG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">ACTAACCGTTATTTTCTTTCATTGTTGATCAACTTACTTTTGTTGTTTTTATTCTGCTTTTATATGGCT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTTGGTACTGTCCCTTCTTGTCTATATTTTCATTAATGTGGTGCTTATGCTTTTCTAAGCCGAGAGTT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TATTGGAAACAACTTTCATATCCTCACAAGGTAGGGGTAAGGTGTGCGTACACACTACCCTCCCCAGAC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TCTACGGTGTGGGATAATATTTAGTATGTTATTGTCGTTGTTGTTGTAAACGTTTTTTTTGTTGCTATC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AAAGCATGTTATTACGGGTAAAATAGAAACATTTAAAGTGAAAGAGTTTCCAAACGTAGGAAAGCTTTT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTTCTTTCGGAATACACCGAAAAAAGAAAGACTATCATTTAAGATAGAACAACAACAGCGACGGAGCT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AGCCTTCGACTTACTGGTTCGGCAGAACCCAATAATTTTGGCCCAAACTCTGTACTTGTACTAAAAAGC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TCACTTAATATGTATAAAAAGCCTAGTAATTAAGTTGCATTTTTTTCTTTCTAAAATCTAGAGCTCATA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AACTCAAAATTATGTCTCCGCCTCTGAACAATGGGGATATTATTCTACTTTTAACTATCTTAGATAAGT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TAATAATTGTTCTCTTTTTCAAACGTTTCTGCCTTGTATTATTGTGTAACTATTTATACTGTGTGGACG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">CTTCAAAATGTTGTTGCGCCCGCGTCGGATCCTCAAAAAATATATATTTTGAGGATTCGACACGCACCC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GATGACCTTTTCGGAGAATTCGAGCAATATAGGTAACTAATATTGCTAGCTCATCAACTGGTGGTATTT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTAGGTGCTCTCATTCAAGCTTAGAGGAGCTTATAACATGATGACCAAACTCTCAAAGGAGCAATTAG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AAAGAGGGGTTATAACTGCTTCAGCTGGAAATCATGCACAAGGTGTTGCATTAGGTGCTCAGAGACTTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AATGTACTGCTACGATTGTCATGCCTGTTACCACACCAGAGATCAAGGTAATTAGTTCTCTCCTGTTAA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTATCCTTCATGTTCGATTCATGTGAATCTAGTTGATCGGGCACTGAGTTTTACTAAAAAATGAAGAC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTCGGAACTTGGGAGCTTTAACATGCTGTAACATTTGTGTAGTTATAAGACTTTTGAAACTTATAGTC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTAGTGGGTGTTTGGACATAAGAATTGTAAAGTTCCAAGAAAAGTGAAAAAAAATTCAAGTGAAAATGG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TATTTGAAAATTAGAGTTGTGTTTGGACATGAATATAATTTTAGGTTGTTTTTGAAGTTTTGTGAGTGA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TCTGACACAAATTTTGAAAAAACAACTTTTTGGAGTTTTTCAAATTTTCGAAAAATTCCAAAATGCATC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTCAAGTGAAAATTGGAAATTATATGACCAAACGCTGATTTCGGGAAAAAAATTCGAAAAAATGTGAAA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">ATTTTCTTATGTCCAAACGGGCTCTTAAATGCGTCATAACGTTTGTGTGGTTATAAAAGTCTCTCATCT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GAATAGGGTCACACAACTAAAACAGAGAGAACAAAATAATTCACTAAAAAAAAATTGGAACTAGCTACA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AACTTCGTCGCAAGTCTCGCTAAATCGCTCGTAGCTAATAGAATTTCTAGATAATTTGTTTAGCTTGTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GCATGAAATTTTTCTATTTAGCAACAGAAGTAGTCTGTCGCTAATTCCTATTTTTTTAGTAGAAAGTAT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TGTGAAATTATTTGTTTTTCTAAAGGACCATTTTCTTTACAAATGAACAGATTGAAGCAGTTAAGAACT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TGGATGGTAATGTAGTTCTACAGGGTGACACATTTGATGAAGCTCAAGCACATGCTTTAAAGTTGGCTG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AAGATGAAGGTCTCACATTCATCCCGCCTTTCGATCACATCTTAAAGATATACATGCAGTATTTCTGCC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TGTAGGAGGAGGAGGTTTAATAGCTGGTGTTGCTGCATATTTCAAAAGGGTTGCTCCTCATACAAAGAT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TATAGGAGTTGAGCCATTTGGTGCAAGTTCAATGACACAGTCTTTGTACCACGGAATGAGAGTAAAGTT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AGAACAAGTTGATAATTTTGCAGATGGCGTAGCTGTTGCACTAGTTAGTTGGTGAAGAAACTTTCCGTC</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTGCAAAGATTTAATAGACGGAATGGTCTTAGTCAGTAACGATGCTATTAGTGCAGCAGTAAAGGTTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GCACGCACCATCTCCTAATGGTTTCAGATATGATCCGTCCAACCAGCCAAAATTGGTTAGAATAGGACG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GGTTGAACTATCAACCCAATCAATCACAGCCCAAATAACATTTATGTGGGTATATGACTCGCCCATTTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTAACTCAACCAATTTTGGTCCATTCAAATTCAGGCTAACCCGTCCACGTTTGACATTCATACTTTAGA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TGTGGATTAAAGTAACTTTCTTAAATTTCCCTCTGGTTTTGACATGTACTAGTTTGTGTTTGTGTGTGT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTGTTCTTTTTTTCAATAGGATGTGTACGACAAAGGAAGGAACATATTAGAGACATCAGGTGCACTCG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">CCATAGCTGGAGCTGAAGCATACTGCAAATACTATGACATAAAGGGCGAAAACGTTGTAGCAATTGCTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">GTGGAGCCAATATGGACATCAGCAAACTAAAATTAGTCGTCGATTTAGCAGATATTGGTGGACAGAGGG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AAGCTCTGCTGGCTACTTTTATGCCAGAAGAACCAGGAAGCTTCAAAAAATTCTGCGAACTTGTGCGTT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">ACTTAGAGCACTTAACAAGCATTTTAGCCAGAGTTTAAGTTATATACATCGTCGTCAGTGTAAGAAACT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTTATACCGTCTTGATGGAGTAAAAATTTGTTACACTGACGTGTACATAACTTAAAACTTTTTTAGTTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">CTATATGATACTTTCTGTCTAAGAAACTGAAATATTGACTTGAATTACTGGTGGGACCTATGATTATTA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">CCGAATTCAAGTACAGATATAACTCTGGAAGAAAACAAGCTCTAGTTCTGTACAGGTAATTAAAGTTCT</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">ATTCATTTTTAGAGGGGATGTTGGCTTCTCATTTTAGATTTGCTTTATTAGTTGTTAGGAAAAAAGAAA</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">TTACTTATTACATTCAATTTTTAGATTTTCTGTCAATTCATATTTCCTGAGAAGCCTGGAGCTTTAAGG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">AAGTTCTTAGATGCTTTCAGCCCTCGATGGAATATAAGTTTGTTCCATTATCGTGAACAG</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">This is the sequence for this gene, the red color is for the first exon??</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">However, for this exon, I cannot found the stop codon???</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">I also find for some exon, there are several stop codon in one exon???</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">Does anyone have the same problem with me?<br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">Or there is something wrong when I configure the maker file??</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">Thanks!</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt">Jingjing</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt"><br>
</p>
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