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

Database: DobsGB1 Primary Table: transdecoder Row Count: 25,893 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`name`	DobsGB1_stringtie.4.1_m.413	`varchar(255)`	values
`chrom`	BDQP01000001	`varchar(255)`	values
`strand`	+	`char(1)`	values
`txStart`	11070	`int(10) unsigned`	range
`txEnd`	33102	`int(10) unsigned`	range
`cdsStart`	14012	`int(10) unsigned`	range
`cdsEnd`	32204	`int(10) unsigned`	range
`exonCount`	15	`int(10) unsigned`	range
`exonStarts`	11070,13525,18205,18970,232...	`longblob`
`exonEnds`	11352,14324,18323,19158,233...	`longblob`

Sample Rows

bin	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
585	DobsGB1_stringtie.4.1_m.413	BDQP01000001	+	11070	33102	14012	32204	15	11070,13525,18205,18970,23291,23671,25913,26185,26487,27912,28843,29149,30315,30773,31448,	11352,14324,18323,19158,23346,23987,26047,26361,26722,28683,29077,29245,30687,31387,33102,
585	DobsGB1_stringtie.3.1_m.81	BDQP01000001	-	42634	44487	42804	44219	4	42634,43483,43884,44134,	43414,43812,44039,44487,
585	DobsGB1_stringtie.1.1_m.1873	BDQP01000001	-	45826	47572	46003	47571	6	45826,46501,46772,46886,47177,47417,	46428,46695,46821,47100,47350,47572,
585	DobsGB1_stringtie.2.1_m.930	BDQP01000001	-	48096	54781	48683	54552	7	48096,49733,49970,50335,50566,51679,54535,	48706,49898,50265,50488,51616,51869,54781,
585	DobsGB1_stringtie.2.2_m.932	BDQP01000001	-	48096	54781	49657	54552	7	48096,49769,49970,50335,50566,51679,54535,	49692,49898,50265,50488,51616,51869,54781,
585	DobsGB1_stringtie.6.1_m.636	BDQP01000001	+	55326	77490	57234	76079	8	55326,55455,56024,56675,73000,73214,74019,75061,	55397,55967,56443,57270,73141,73955,74987,77490,
585	DobsGB1_stringtie.6.1_m.637	BDQP01000001	+	55326	77490	55387	56267	8	55326,55455,56024,56675,73000,73214,74019,75061,	55397,55967,56443,57270,73141,73955,74987,77490,
585	DobsGB1_stringtie.10.1_m.6	BDQP01000001	+	77900	81242	78088	80958	4	77900,78665,79350,79729,	78594,79283,79667,81242,
585	DobsGB1_stringtie.11.1_m.1355	BDQP01000001	-	79784	85861	81011	83963	12	79784,81340,82353,82732,83244,83591,83870,84469,84855,85127,85499,85712,	81287,82302,82670,83181,83534,83811,84407,84795,85067,85437,85647,85861,
585	DobsGB1_stringtie.11.1_m.1359	BDQP01000001	-	79784	85861	80100	81012	12	79784,81340,82353,82732,83244,83591,83870,84469,84855,85127,85499,85712,	81287,82302,82670,83181,83534,83811,84407,84795,85067,85437,85647,85861,

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 PRJDB4576. 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. Nozawa M, Onizuka K, Fujimi M, Ikeo K, Gojobori T. Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nat Commun. 2016 Nov 29;7:13659.

Description

Methods

References