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

Database: DperCAF1 Primary Table: transdecoder Row Count: 18,296 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DperCAF1_stringtie.1.1_m.2677	`varchar(255)`	values
`chrom`	super_0	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	31822	`int(10) unsigned`	range
`txEnd`	32631	`int(10) unsigned`	range
`cdsStart`	31823	`int(10) unsigned`	range
`cdsEnd`	32191	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	31822,32065,	`longblob`
`exonEnds`	32006,32631,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DperCAF1_stringtie.1.1_m.2677	super_0	+	31822	32631	31823	32191	2	31822,32065,	32006,32631,
585	DperCAF1_stringtie.7.1_m.3061	super_0	-	33628	79165	34774	39998	8	33628,34853,35301,38231,38485,39182,62986,78603,	34796,35204,37803,38427,39056,40021,63143,79165,
585	DperCAF1_stringtie.7.2_m.3088	super_0	-	33636	79165	34774	39998	8	33636,34853,35301,38231,38485,39182,62986,78603,	34796,35204,37836,38427,39056,40021,63143,79165,
585	DperCAF1_stringtie.7.3_m.3069	super_0	-	33636	79092	34774	39998	7	33636,34853,35301,38231,38485,62986,78603,	34796,35075,37803,38427,40021,63143,79092,
585	DperCAF1_stringtie.7.5_m.3077	super_0	-	33643	79113	34774	39998	7	33643,34853,35301,38231,38485,62986,78603,	34796,35075,37836,38427,40021,63143,79113,
585	DperCAF1_stringtie.7.4_m.3104	super_0	-	33643	46510	34774	42841	7	33643,34853,35301,38231,38485,42159,46177,	34796,35204,37803,38427,40021,43117,46510,
585	DperCAF1_stringtie.7.6_m.3096	super_0	-	33685	42722	34774	42721	6	33685,34853,35301,38231,38485,42159,	34796,35075,37803,38427,40021,42722,
585	DperCAF1_stringtie.7.7_m.3085	super_0	-	53661	79165	53819	54713	3	53661,62986,78603,	55338,63143,79165,
585	DperCAF1_stringtie.7.7_m.3086	super_0	-	53661	79165	54336	55119	3	53661,62986,78603,	55338,63143,79165,
585	DperCAF1_stringtie.9.1_m.4592	super_0	+	61755	62358	61756	62149	2	61755,61860,	61806,62358,

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 PRJNA388952. 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. The RNA-Seq data were produced by Dr. Brian Oliver's Developmental Genomics Lab at NIDDK, NIH.

Description