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

Database: DhydGB1 Primary Table: transdecoder Row Count: 19,393 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DhydGB1_stringtie.6.1_m.72	`varchar(255)`	values
`chrom`	NWQH01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	20925	`int(10) unsigned`	range
`txEnd`	31596	`int(10) unsigned`	range
`cdsStart`	22743	`int(10) unsigned`	range
`cdsEnd`	31596	`int(10) unsigned`	range
`exonCount`	10	`int(10) unsigned`	range
`exonStarts`	20925,22572,25271,25485,268...	`longblob`
`exonEnds`	21468,22779,25365,25634,271...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DhydGB1_stringtie.6.1_m.72	NWQH01000001	+	20925	31596	22743	31596	10	20925,22572,25271,25485,26820,27805,28045,28584,29834,31514,	21468,22779,25365,25634,27118,27988,28326,28735,30000,31596,
585	DhydGB1_stringtie.6.2_m.77	NWQH01000001	+	21074	31597	22743	31596	10	21074,22572,25271,25485,26820,27805,28045,28584,29834,31514,	21357,22779,25365,25634,27118,27988,28326,28735,30000,31597,
585	DhydGB1_stringtie.6.4_m.75	NWQH01000001	+	21121	31597	25304	31596	9	21121,25271,25485,26820,27805,28045,28584,29834,31514,	21468,25365,25634,26989,27988,28326,28735,30000,31597,
585	DhydGB1_stringtie.6.3_m.73	NWQH01000001	+	21121	31597	22743	31596	10	21121,22572,25271,25485,26820,27805,28045,28584,29834,31514,	21281,22779,25365,25634,26989,27988,28326,28735,30000,31597,
585	DhydGB1_stringtie.7.1_m.1057	NWQH01000001	+	31670	33032	31670	32312	2	31670,32213,	32153,33032,
585	DhydGB1_stringtie.5.2_m.607	NWQH01000001	-	37093	43974	38662	43892	5	37093,39239,40325,40605,43836,	39180,40217,40543,40758,43974,
585	DhydGB1_stringtie.5.2_m.608	NWQH01000001	-	37093	43974	38637	39069	5	37093,39239,40325,40605,43836,	39180,40217,40543,40758,43974,
585	DhydGB1_stringtie.5.1_m.605	NWQH01000001	-	37093	41490	38637	39069	5	37093,39239,40325,40605,40856,	39180,40217,40543,40758,41490,
585	DhydGB1_stringtie.5.1_m.604	NWQH01000001	-	37093	41490	38662	41104	5	37093,39239,40325,40605,40856,	39180,40217,40543,40758,41490,
585	DhydGB1_stringtie.3.1_m.273	NWQH01000001	+	46987	48144	47105	47959	2	46987,47178,	47119,48144,

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 PRJNA373926. 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. Zhao L, Begun DJ. Genomics of parallel adaptation at two timescales in Drosophila. PLoS Genet. 2017 Oct 2;13(10):e1007016.

Description