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

Database: DmirGB2 Primary Table: transdecoder Row Count: 20,875 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DmirGB2_stringtie.1.1_m.3624	`varchar(255)`	values
`chrom`	CM001516	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	1959	`int(10) unsigned`	range
`txEnd`	4867	`int(10) unsigned`	range
`cdsStart`	1961	`int(10) unsigned`	range
`cdsEnd`	4865	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	1959,4547,	`longblob`
`exonEnds`	2087,4867,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DmirGB2_stringtie.1.1_m.3624	CM001516	-	1959	4867	1961	4865	2	1959,4547,	2087,4867,
585	DmirGB2_stringtie.3.1_m.5686	CM001516	+	14995	18087	16242	16656	4	14995,15381,15810,16218,	15315,15759,16158,18087,
585	DmirGB2_stringtie.3.1_m.5683	CM001516	+	14995	18087	16973	18026	4	14995,15381,15810,16218,	15315,15759,16158,18087,
585	DmirGB2_stringtie.3.1_m.5687	CM001516	+	14995	18087	16490	16790	4	14995,15381,15810,16218,	15315,15759,16158,18087,
585	DmirGB2_stringtie.3.1_m.5684	CM001516	+	14995	18087	15164	15968	4	14995,15381,15810,16218,	15315,15759,16158,18087,
585	DmirGB2_stringtie.6.1_m.4432	CM001516	+	18424	21939	19790	21013	4	18424,18747,19130,20817,	18689,19050,20737,21939,
585	DmirGB2_stringtie.6.1_m.4435	CM001516	+	18424	21939	18571	18971	4	18424,18747,19130,20817,	18689,19050,20737,21939,
585	DmirGB2_stringtie.6.1_m.4433	CM001516	+	18424	21939	18931	19803	4	18424,18747,19130,20817,	18689,19050,20737,21939,
585	DmirGB2_stringtie.7.1_m.7173	CM001516	+	22270	30400	23489	29360	8	22270,24179,24309,24698,25969,26350,26512,29252,	24113,24243,24596,25901,26296,26439,28247,30400,
585	DmirGB2_stringtie.8.1_m.7063	CM001516	-	30577	31388	30578	31387	2	30577,31094,	31017,31388,

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 SRP009365. 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. Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science. 2012 Jul 20;337(6092):341-5.

Description