<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; ">To further illustrate this I've highlighted the location of all CDS entries. You need to cut them out, string them together linearly, and only then can you translate. There is a start codon for the merged CDS then all open reading frame following that, but no stop codon so this is a partial transcript. Sometimes the gene predictors do not find a likely stop and a partial model scores better. You can force MAKER to try and find a stop even when the gene predictor (snap, augustus, etc.) doesn't by setting always_complete=1 in the maker_opts.ctl file. Keep in mind that this is just a forced canonical completion.</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><br></div><div><div><font class="Apple-style-span" face="Courier" color="#ff0000">ATGAAGGGCGCGATACGTACTACGATTCCAAAACCATCAGCATTGCCATTGAAGGTCTCA</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">GAATTATCTCCATCAGCTGATTCAGTACCCGTTCCAGCGTCTTTACAGGATGTCGAGGCG</font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">GGGAAGTTGATTGAGAATAATCCATCAGGG</font>gtgatacagaagaattgtttcag<font class="Apple-style-span" color="#ff0000">TATCTTG</font></font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">TTGAAATATTGGCTTCTAGAGTGTATGATGTAGCAATTGATTCCCCCTTGCAAAATGCAA</font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">CTAAGCTTTCCAAGAAGCTTGGAGTTAACTTTTGGATCAAAAGAGAGGATATGCAGTCC</font>g</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tatgtttctcctctcttctttttttgatgtagcatttgctttaacttagaatttgtggtt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttaaacataccattagaaaggtatggaggttgaggattagggtagtaaagtaggtagtct</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">agagtgttcataacagtaatattgacaagcagtctcgctttccgttggtagtaggttttt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">atgactaaccgttattttctttcattgttgatcaacttacttttgttgtttttattctgc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttttatatggctttttggtactgtcccttcttgtctatattttcattaatgtggtgctta</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tgcttttctaagccgagagtttattggaaacaactttcatatcctcacaaggtaggggta</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aggtgtgcgtacacactaccctccccagactctacggtgtgggataatatttagtatgtt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">attgtcgttgttgttgtaaacgttttttttgttgctatcaaagcatgttattacgggtaa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aatagaaacatttaaagtgaaagagtttccaaacgtaggaaagcttttttttctttcgga</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">atacaccgaaaaaagaaagactatcatttaagatagaacaacaacagcgacggagctagc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">cttcgacttactggttcggcagaacccaataattttggcccaaactctgtacttgtacta</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aaaagctcacttaatatgtataaaaagcctagtaattaagttgcatttttttctttctaa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aatctagagctcataaactcaaaattatgtctccgcctctgaacaatggggatattattc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tacttttaactatcttagataagttaataattgttctctttttcaaacgtttctgccttg</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tattattgtgtaactatttatactgtgtggacgcttcaaaatgttgttgcgcccgcgtcg</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gatcctcaaaaaatatatattttgaggattcgacacgcacccgatgaccttttcggagaa</font></div><div><font class="Apple-style-span" face="Courier">ttcgagcaatataggtaactaatattgctagctcatcaactggtggtattttttag<font class="Apple-style-span" color="#ff0000">GTGC</font></font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">TCTCATTCAAGCTTAGAGGAGCTTATAACATGATGACCAAACTCTCAAAGGAGCAATTAG</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">AAAGAGGGGTTATAACTGCTTCAGCTGGAAATCATGCACAAGGTGTTGCATTAGGTGCTC</font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">AGAGACTTAAATGTACTGCTACGATT</font>gtcatgcctgttaccacaccagagatcaaggtaa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttagttctctcctgttaatttatccttcatgttcgattcatgtgaatctagttgatcggg</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">cactgagttttactaaaaaatgaagactttcggaacttgggagctttaacatgctgtaac</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">atttgtgtagttataagacttttgaaacttatagtcttagtgggtgtttggacataagaa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttgtaaagttccaagaaaagtgaaaaaaaattcaagtgaaaatggtatttgaaaattaga</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gttgtgtttggacatgaatataattttaggttgtttttgaagttttgtgagtgatctgac</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">acaaattttgaaaaaacaactttttggagtttttcaaattttcgaaaaattccaaaatgc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">atcttcaagtgaaaattggaaattatatgaccaaacgctgatttcgggaaaaaaattcga</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aaaaatgtgaaaattttcttatgtccaaacgggctcttaaatgcgtcataacgtttgtgt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ggttataaaagtctctcatctgaatagggtcacacaactaaaacagagagaacaaaataa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttcactaaaaaaaaattggaactagctacaaacttcgtcgcaagtctcgctaaatcgctc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gtagctaatagaatttctagataatttgtttagcttgtagcatgaaatttttctatttag</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">caacagaagtagtctgtcgctaattcctatttttttagtagaaagtattgtgaaattatt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tgtttttctaaaggaccattttctttacaaatgaacagattgaagcagttaagaacttgg</font></div><div><font class="Apple-style-span" face="Courier">atggtaatgtagttctacag<font class="Apple-style-span" color="#ff0000">GGTGACACATTTGATGAAGCTCAAGCACATGCTTTAAAGT</font></font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">TGGCTGAAGATGAAG</font>gtctcacattcatcccgcctttcgatcacatcttaaagatataca</font></div><div><font class="Apple-style-span" face="Courier">tgcagtatttctgcctgtag<font class="Apple-style-span" color="#ff0000">GAGGAGGAGGTTTAATAGCTGGTGTTGCTGCATATTTCAA</font></font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">AAGGGTTGCTCCTCATACAAAGATTATAGGAGTTGAGCCATTTGGTGCAAGTTCAATGAC</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">ACAGTCTTTGTACCACGGAATGAGAGTAAAGTTAGAACAAGTTGATAATTTTGCAGATGG</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">C</font><font class="Apple-style-span" face="Courier">gtagctgttgcactag</font><font class="Apple-style-span" face="Courier" color="#ff0000">TTAGTTGGTGAAGAAACTTTCCGTCTTTGCAAAGATTTAATAG</font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">ACGGAATGGTCTTAGTCAGTAACGATGCTATTAGTGCAGCAGTAAAG</font>gttagcacgcacc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">atctcctaatggtttcagatatgatccgtccaaccagccaaaattggttagaataggacg</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ggttgaactatcaacccaatcaatcacagcccaaataacatttatgtgggtatatgactc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gcccatttattaactcaaccaattttggtccattcaaattcaggctaacccgtccacgtt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tgacattcatactttagatgtggattaaagtaactttcttaaatttccctctggttttga</font></div><div><font class="Apple-style-span" face="Courier">catgtactagtttgtgtttgtgtgtgttttgttctttttttcaatag<font class="Apple-style-span" color="#ff0000">GATGTGTACGACA</font></font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">AAGGAAGGAACATATTAGAGACATCAGGTGCACTCGCCATAGCTGGAGCTGAAGCATACT</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">GCAAATACTATGACATAAAGGGCGAAAACGTTGTAGCAATTGCTAGTGGAGCCAATATGG</font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">ACATCAGCAAACTAAAATTAGTCGTCGATTTAGCAGATATTGGTGGACAGAGGGAAGCTC</font></div><div><font class="Apple-style-span" face="Courier"><font class="Apple-style-span" color="#ff0000">TGCTGGCTACTTTTATGCCAGAAGAACCAGGAAGCTTCAAAAAATTCTGCGAACTT</font>gtgc</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gttacttagagcacttaacaagcattttagccagagtttaagttatatacatcgtcgtca</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gtgtaagaaacttttataccgtcttgatggagtaaaaatttgttacactgacgtgtacat</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">aacttaaaacttttttagttactatatgatactttctgtctaagaaactgaaatattgac</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">ttgaattactggtgggacctatgattattaccgaattcaagtacagatataactctggaa</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">gaaaacaagctctagttctgtacaggtaattaaagttctattcatttttagaggggatgt</font></div><div style="color: rgb(0, 0, 0); "><font class="Apple-style-span" face="Courier">tggcttctcattttagatttgctttattagttgttaggaaaaaagaaattacttattaca</font></div><div><font class="Apple-style-span" face="Courier">ttcaatttttag<font class="Apple-style-span" color="#ff0000">ATTTTCTGTCAATTCATATTTCCTGAGAAGCCTGGAGCTTTAAGGAAG</font></font></div><div><font class="Apple-style-span" face="Courier" color="#ff0000">TTCTTAGATGCTTTCAGCCCTCGATGGAATATAAGTTTGTTCCATTATCGTGAACAG</font></div></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; ">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; ">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; "><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Barry Moore <<a href="mailto:bmoore@genetics.utah.edu">bmoore@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, 20 June, 2013 9:29 PM<br><span style="font-weight:bold">To: </span> Jingjing Jin <<a href="mailto:jjin01@mail.rockefeller.edu">jjin01@mail.rockefeller.edu</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] maker exon result<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><div dir="auto"><div>To clarify things a bit Jin. Not every exon will have a start and/or stop codon only the fist coding exon will have a start and the last coding exon will have a stop. In the GFF3 format a coding exon is a feature of type 'CDS' (column 3) so only look
at CDS features not at 'exon' features. For CDSs you must then concatenate the sequence I'd each CDS line for a given transcript (and reverse compliment the sequence if it is on the minus strand). The resulting sequence will usually (but not always) have start
and stop codons at the beginning and end. </div><div><br></div><div>B</div><div><br></div><div>Barry Moore
<div>Research Scientist</div><div>Dept. Human Genetics</div><div>University of Utah</div></div><div><br>
On Jun 20, 2013, at 6:18 PM, "Jingjing Jin" <<a href="mailto:jjin01@mail.rockefeller.edu">jjin01@mail.rockefeller.edu</a>> wrote:<br><br></div><blockquote type="cite"><div><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 [<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>]<br><b>Sent:</b> Thursday, June 20, 2013 7:06 PM<br><b>To:</b> Jingjing Jin; <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><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 [<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Jingjing Jin [<a href="mailto:jjin01@mail.rockefeller.edu">jjin01@mail.rockefeller.edu</a>]<br><b>Sent:</b> Thursday, June 20, 2013 2:22 PM<br><b>To:</b> <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><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><br></div></div></div></div></div></div></div></div></div></blockquote><blockquote type="cite"><div><span>_______________________________________________</span><br><span>maker-devel mailing list</span><br><span><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a></span><br><span><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></span><br></div></blockquote></div></div>
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