Schema for TransDecoder Transcripts - Transcripts and Coding Regions Predicted by TransDecoder

Database: DbusGB1 Primary Table: transdecoder Row Count: 18,487 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DbusGB1_stringtie.2.1_m.1105	`varchar(255)`	values
`chrom`	CP012523	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	33892	`int(10) unsigned`	range
`txEnd`	46049	`int(10) unsigned`	range
`cdsStart`	34561	`int(10) unsigned`	range
`cdsEnd`	44353	`int(10) unsigned`	range
`exonCount`	5	`int(10) unsigned`	range
`exonStarts`	33892,38845,42334,42770,43722,	`longblob`
`exonEnds`	37830,40134,42707,43181,46049,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DbusGB1_stringtie.2.1_m.1105	CP012523	-	33892	46049	34561	44353	5	33892,38845,42334,42770,43722,	37830,40134,42707,43181,46049,
585	DbusGB1_stringtie.10.1_m.3343	CP012523	+	91460	101321	91620	93601	15	91460,91729,94667,95078,95540,96801,96977,97181,97784,98112,98413,99028,99637,100286,101165,	91665,94605,94887,95477,95801,96900,97118,97725,97996,98283,98554,99577,100224,101101,101321,
585	DbusGB1_stringtie.10.1_m.3342	CP012523	+	91460	101321	94410	101280	15	91460,91729,94667,95078,95540,96801,96977,97181,97784,98112,98413,99028,99637,100286,101165,	91665,94605,94887,95477,95801,96900,97118,97725,97996,98283,98554,99577,100224,101101,101321,
585	DbusGB1_stringtie.1.1_m.290	CP012523	+	102771	105283	102773	103322	4	102771,102965,103826,104626,	102893,103775,104571,105283,
585	DbusGB1_stringtie.1.1_m.289	CP012523	+	102771	105283	103658	104189	4	102771,102965,103826,104626,	102893,103775,104571,105283,
585	DbusGB1_stringtie.1.1_m.288	CP012523	+	102771	105283	104421	105025	4	102771,102965,103826,104626,	102893,103775,104571,105283,
585	DbusGB1_stringtie.1.2_m.291	CP012523	+	102775	105283	103658	105025	3	102775,102965,104626,	102893,103775,105283,
585	DbusGB1_stringtie.1.2_m.292	CP012523	+	102775	105283	102776	103322	3	102775,102965,104626,	102893,103775,105283,
585	DbusGB1_stringtie.4.1_m.2001	CP012523	+	105539	112071	105611	109828	3	105539,105809,106540,	105639,106489,112071,
585	DbusGB1_stringtie.5.1_m.2410	CP012523	+	112203	113237	112398	112989	3	112203,112530,112896,	112456,112841,113237,

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 BioProject accession number PRJNA274996. 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. Zhou Q, Bachtrog D. Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila. PLoS Genet. 2015 Jun 26;11(6):e1005331.

Description