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

Database: DkikGB2 Primary Table: tRNAscanSE2Details Data last updated: 2019-07-06
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2.tRNAscanSE2Details.bb
Item Count: 412
Format description: tRNAs identified by tRNAscan-SE 2.0

field	example	description
`chrom`	AFFH02000063	Reference sequence chromosome or scaffold
`chromStart`	248	Start position in chromosome
`chromEnd`	322	End position in chromosome
`name`	tRNA-Pro-CGG-AFFH02000063-1	Short Name of item
`score`	1000	Score from 0-1000
`strand`	+	+ or -
`thickStart`	248	Start of where display should be thick (start codon)
`thickEnd`	322	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`	74	Comma separated list of block sizes
`chromStarts`	0	Start positions relative to chromStart
`tRNAType`	Pro	tRNA type
`antiCodon`	CGG	Anticodon
`trnaScore`	59.4	Infernal Score
`hmmScore`	23.40	Primary structure-only (HMM) score
`str2Score`	36.00	Secondary structure-only score
`isotypeCM`	His	Isotype covariance model
`isotypeScore`	48.7	Isotype score
`notes`	IPD:-20.20,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
AFFH02000063	248	322	tRNA-Pro-CGG-AFFH02000063-1	1000	+	248	322	0,0,0	1	74	0	Pro	CGG	59.4	23.40	36.00	His	48.7	IPD:-20.20,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