[maker-devel] maker exon result

Thu Jun 20 18:18:18 MDT 2013

For my understanding, the prediction gene model should be connect different exon together.

For each exon of a gene, I think it should have a start codon and stop codon. However, it may be wrong.

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.

Even for last 3 NT for last exon, it is also not a stop codon.

Is it reasonable?

Thanks!

Jingjing

________________________________
From: Daniel Ence [dence at genetics.utah.edu]
Sent: Thursday, June 20, 2013 7:06 PM
To: Jingjing Jin; maker-devel at yandell-lab.org
Subject: RE: maker exon result

Hi Jingjing,

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.

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.

I hope that I understood your question. Feel free to reply back on the mailing list if I didn't.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Jingjing Jin [jjin01 at mail.rockefeller.edu]
Sent: Thursday, June 20, 2013 2:22 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] maker exon result

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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