Schema for tRNA Genes - Transfer RNA Genes Identified by tRNAscan-SE 2.0

Database: DtakGB2 Primary Table: tRNAscanSE2Details Data last updated: 2019-07-06
Big Bed File: /gbdb/DtakGB2/bbi/DtakGB2.tRNAscanSE2Details.bb
Item Count: 613
Format description: tRNAs identified by tRNAscan-SE 2.0

field	example	description
`chrom`	AFFI02000009	Reference sequence chromosome or scaffold
`chromStart`	32512	Start position in chromosome
`chromEnd`	32583	End position in chromosome
`name`	tRNA-Sup-CTA-AFFI02000009-1	Short Name of item
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`thickStart`	32512	Start of where display should be thick (start codon)
`thickEnd`	32583	End of where display should be thick (stop codon)
`reserved`	0,0,0	Used as itemRgb as of 2004-11-22
`blockCount`	1	Number of blocks
`blockSizes`	71	Comma separated list of block sizes
`chromStarts`	0	Start positions relative to chromStart
`tRNAType`	Sup	tRNA type
`antiCodon`	CTA	Anticodon
`trnaScore`	31.2	Infernal Score
`hmmScore`	53.50	Primary structure-only (HMM) score
`str2Score`	-22.30	Secondary structure-only score
`isotypeCM`	Met	Isotype covariance model
`isotypeScore`	30.7	Isotype score
`notes`	pseudo,IPD:-30.70	EukHighConfidenceFilter notes

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts	tRNAType	antiCodon	trnaScore	hmmScore	str2Score	isotypeCM	isotypeScore	notes
AFFI02000009	32512	32583	tRNA-Sup-CTA-AFFI02000009-1	1000	-	32512	32583	0,0,0	1	71	0	Sup	CTA	31.2	53.50	-22.30	Met	30.7	pseudo,IPD:-30.70

tRNA Genes (tRNAscanSE2Details) Track Description


	Description This track shows the locations of tRNA genes predicted by tRNAscan-SE 2.0. References Chan PP, Lowe TM. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019;1962:1-14.

Description

References