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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">For my understanding, the prediction gene model should be connect different exon together.<br>
<br>
For each exon of a gene, I think it should have a start codon and stop codon. However, it may be wrong.<br>
<br>
However, when I check some gene model from maker prediction, some exon of one gene, I cannot find stop codon for it. Like the example I give, the red color is the first exon. However, the last 3 NT is not a stop codon.<br>
<br>
Even for last 3 NT for last exon, it is also not a stop codon.<br>
<br>
Is it reasonable?<br>
<br>
Thanks!<br>
<br>
Jingjing<br>
<br>
<br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF529417"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Daniel Ence [dence@genetics.utah.edu]<br>
<b>Sent:</b> Thursday, June 20, 2013 7:06 PM<br>
<b>To:</b> Jingjing Jin; maker-devel@yandell-lab.org<br>
<b>Subject:</b> RE: maker exon result<br>
</font><br>
</div>
<div></div>
<div>
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi Jingjing,
<div><br>
</div>
<div>It's really hard to find the stop codon in the nucleotide sequence that you sent. I think most people determine the presence of a stop codon in a gene by viewing the annotations and sequence in some kind of viewer. The one that I use the most is Apollo,
but many people also like gbrowse and igv. </div>
<div><br>
</div>
<div>When you view gene models in Apollo, the start codons are highlighted in green and the stop codons are highlighted in red. Sometimes MAKER couldn't find the stop or start codon for a gene, and in those cases, the end of the gene model is marked with an
orange arrow. </div>
<div><br>
</div>
<div>I hope that I understood your question. Feel free to reply back on the mailing list if I didn't.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Daniel<br>
<div><br>
<div class="BodyFragment"><font size="2">
<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
</font></div>
</div>
<div style="font-family:Times New Roman; color:#000000; font-size:16px">
<hr tabindex="-1">
<div id="divRpF188077" style="direction:ltr"><font color="#000000" face="Tahoma" size="2"><b>From:</b> maker-devel [maker-devel-bounces@yandell-lab.org] on behalf of Jingjing Jin [jjin01@mail.rockefeller.edu]<br>
<b>Sent:</b> Thursday, June 20, 2013 2:22 PM<br>
<b>To:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> [maker-devel] maker exon result<br>
</font><br>
</div>
<div></div>
<div>
<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>
<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>
<br>
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