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

Database: DpseGB3 Primary Table: transdecoder Row Count: 23,914 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DpseGB3_stringtie.2.1_m.2785	`varchar(255)`	values
`chrom`	CH379058	`varchar(255)`	values
`strand`	-	`char(1)`	values
`txStart`	17031	`int(10) unsigned`	range
`txEnd`	22898	`int(10) unsigned`	range
`cdsStart`	17120	`int(10) unsigned`	range
`cdsEnd`	22628	`int(10) unsigned`	range
`exonCount`	2	`int(10) unsigned`	range
`exonStarts`	17031,22691,	`longblob`
`exonEnds`	22629,22898,	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DpseGB3_stringtie.2.1_m.2785	CH379058	-	17031	22898	17120	22628	2	17031,22691,	22629,22898,
585	DpseGB3_stringtie.2.2_m.2780	CH379058	-	17031	22930	17120	22628	2	17031,22691,	22649,22930,
585	DpseGB3_stringtie.4.1_m.1265	CH379058	+	57111	58521	57285	58327	4	57111,57379,57841,58214,	57325,57776,58152,58521,
585	DpseGB3_stringtie.1.2_m.557	CH379058	+	58580	65560	59479	61516	5	58580,58972,59383,65067,65382,	58899,59324,65001,65324,65560,
585	DpseGB3_stringtie.1.2_m.560	CH379058	+	58580	65560	58811	59477	5	58580,58972,59383,65067,65382,	58899,59324,65001,65324,65560,
585	DpseGB3_stringtie.5.1_m.2700	CH379058	-	67361	71136	70546	71053	5	67361,67736,67938,69521,70545,	67680,67857,68249,70488,71136,
585	DpseGB3_stringtie.6.1_m.1640	CH379058	+	68422	71136	68422	70371	3	68422,68601,69530,	68537,69475,71136,
73	DpseGB3_stringtie.7.1_m.786	CH379058	-	73179	148215	74330	146318	7	73179,74559,75375,75584,75859,146278,148046,	74417,74715,75522,75770,76029,146409,148215,
73	DpseGB3_stringtie.7.1_m.787	CH379058	-	73179	148215	74152	74636	7	73179,74559,75375,75584,75859,146278,148046,	74417,74715,75522,75770,76029,146409,148215,
585	DpseGB3_stringtie.7.2_m.780	CH379058	-	73364	79055	74152	74636	6	73364,74559,75375,75584,75859,78100,	74417,74715,75522,75770,76029,79055,

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.

Description