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

Database: DereCAF1 Primary Table: tRNAscanSE2Details Data last updated: 2019-07-06
Big Bed File: /gbdb/DereCAF1/bbi/DereCAF1.tRNAscanSE2Details.bb
Item Count: 290
Format description: tRNAs identified by tRNAscan-SE 2.0

field	example	description
`chrom`	scaffold_3597	Reference sequence chromosome or scaffold
`chromStart`	9	Start position in chromosome
`chromEnd`	82	End position in chromosome
`name`	tRNA-Ile-GAT-scaffold_3597-2	Short Name of item
`score`	1000	Score from 0-1000
`strand`	-	+ or -
`thickStart`	9	Start of where display should be thick (start codon)
`thickEnd`	82	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`	73	Comma separated list of block sizes
`chromStarts`	0	Start positions relative to chromStart
`tRNAType`	Ile	tRNA type
`antiCodon`	GAT	Anticodon
`trnaScore`	35.9	Infernal Score
`hmmScore`	30.80	Primary structure-only (HMM) score
`str2Score`	5.10	Secondary structure-only score
`isotypeCM`	Lys	Isotype covariance model
`isotypeScore`	61.4	Isotype score
`notes`	IPD:-38.20,secondary filtered	EukHighConfidenceFilter notes

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts	tRNAType	antiCodon	trnaScore	hmmScore	str2Score	isotypeCM	isotypeScore	notes
scaffold_3597	9	82	tRNA-Ile-GAT-scaffold_3597-2	1000	-	9	82	0,0,0	1	73	0	Ile	GAT	35.9	30.80	5.10	Lys	61.4	IPD:-38.20,secondary filtered
scaffold_3597	727	800	tRNA-Ile-GAT-scaffold_3597-1	1000	-	727	800	0,0,0	1	73	0	Ile	GAT	35.9	30.80	5.10	Lys	61.4	IPD:-38.20,secondary filtered

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