Schema for TransDecoder Transcripts - Transcripts and Coding Regions Predicted by TransDecoder
  Database: DyakCAF1    Primary Table: transdecoder    Row Count: 24,760   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
name DyakCAF1_stringtie.3.1_m.5811varchar(255) values
chrom chr2Lvarchar(255) values
strand -char(1) values
txStart 6687int(10) unsigned range
txEnd 16512int(10) unsigned range
cdsStart 8643int(10) unsigned range
cdsEnd 14684int(10) unsigned range
exonCount 9int(10) unsigned range
exonStarts 6687,8836,9279,9784,10693,1...longblob  
exonEnds 8773,8945,9722,10427,10799,...longblob  

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
585DyakCAF1_stringtie.3.1_m.5811chr2L-66871651286431468496687,8836,9279,9784,10693,10856,12106,14600,15864,8773,8945,9722,10427,10799,12048,12885,14761,16512,
585DyakCAF1_stringtie.3.2_m.5813chr2L-66871651290451468496687,8836,9279,9784,10693,10856,12106,14600,15864,8773,9068,9722,10427,10799,12048,12885,14761,16512,
585DyakCAF1_stringtie.5.1_m.9521chr2L-19963257442096225743719963,21194,21490,22503,23238,23487,24943,21130,21393,21928,22729,23432,23574,25744,
585DyakCAF1_stringtie.5.3_m.9518chr2L-20011257452096222523620011,21194,21490,22503,23487,24943,21130,21393,21928,23432,23574,25745,
585DyakCAF1_stringtie.5.2_m.9509chr2L-200114884220962477051220011,21194,21490,22503,23238,23487,28097,28211,32040,32502,47635,48763,21130,21393,21928,22729,23432,23574,28144,28695,32237,33059,47737,48842,
585DyakCAF1_stringtie.5.4_m.9513chr2L-200114884220962477051220011,21194,21490,22503,23238,23487,28097,28211,32040,32502,47635,48763,21130,21393,21928,22729,23432,23574,28144,28404,32237,33059,47737,48842,
585DyakCAF1_stringtie.5.3_m.9517chr2L-20011257452318825743620011,21194,21490,22503,23487,24943,21130,21393,21928,23432,23574,25745,
585DyakCAF1_stringtie.5.5_m.9507chr2L-210254879821025477051321025,21194,21490,22503,23238,23487,27371,28097,28211,32040,32502,47635,48763,21130,21393,21928,22729,23432,23574,27815,28144,28404,32237,33059,47737,48798,
585DyakCAF1_stringtie.6.1_m.11951chr2L+55212603025613959389455212,56413,56602,59103,56277,56545,59046,60302,
585DyakCAF1_stringtie.7.1_m.4221chr2L+60808655476119565401360808,64196,64380,61273,64312,65547,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TransDecoder Transcripts (transdecoder) Track Description
 

Description

This track shows the RNA-Seq transcripts assembled by StringTie. Coding regions within the transcript are identified by TransDecoder. The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the accession number SRP006203.

Methods

TransDecoder was run against the transcripts assembled by StringTie using default parameters. The open reading frames predicted by TransDecoder were searched against the Swiss-Prot database using NCBI blastp and against the Pfam database using HMMER. Open reading frames are kept if they satisfy the TransDecoder.Predict filtering criteria or if they show significant matches to either Swiss-Prot or Pfam.

References

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015 Mar;33(3):290-5.

Haas BJ et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013 Aug;8(8):1494-512.

Chen ZX et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 Jul;24(7):1209-23.