Schema for tRNA Genes - Transfer RNA genes identified with tRNAscan-SE

Database: hg19 Primary Table: tRNAs Row Count: 625
Format description: transfer RNA genes

field	example	SQL type	info	description
`bin`	645	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	chromosome
`chromStart`	7990338	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	7990408	`int(10) unsigned`	range	End position in chromosome
`name`	chr1.tRNA137-Pseudo???	`varchar(255)`	values	transfer RNA gene name
`score`	1000	`int(10) unsigned`	range	Score from 900-1000. 1000 is best
`strand`	-	`char(1)`	values	Value should be + or -
`aa`	Pseudo	`varchar(255)`	values	Amino acid for the tRNA
`ac`	???	`varchar(255)`	values	Anticodon for the tRNA
`intron`	No canonical tRNA introns	`varchar(255)`	values	Coordinates for intron
`trnaScore`	35.54	`float`	range	tRNAScanSE score
`genomeUrl`	http://gtrnadb.ucsc.edu/Hsa...	`varchar(255)`	values	GtRNAdb genome summary URL
`trnaUrl`	http://gtrnadb.ucsc.edu/Hsa...	`varchar(255)`	values	GtRNAdb tRNA alignment URL

bin	chrom	chromStart	chromEnd	name	score	strand	aa	ac	intron	trnaScore	genomeUrl	trnaUrl
645	chr1	7990338	7990408	chr1.tRNA137-Pseudo???	1000	-	Pseudo	???	No canonical tRNA introns	35.54	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna137-Pseudo???
713	chr1	16847079	16847153	chr1.tRNA136-AsnGTT	1000	-	Asn	GTT	No canonical tRNA introns	77.65	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna136-AsnGTT
713	chr1	16858892	16858966	chr1.tRNA135-AsnGTT	1000	-	Asn	GTT	No canonical tRNA introns	48.81	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna135-AsnGTT
713	chr1	16861773	16861845	chr1.tRNA134-GluTTC	1000	-	Glu	TTC	No canonical tRNA introns	72.33	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna134-GluTTC
713	chr1	16872433	16872504	chr1.tRNA133-GlyCCC	1000	-	Gly	CCC	No canonical tRNA introns	78.31	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna133-GlyCCC
713	chr1	16874159	16874232	chr1.tRNA132-PseudoCAC	1000	-	Pseudo	CAC	No canonical tRNA introns	41.96	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna132-PseudoCAC
714	chr1	17004765	17004836	chr1.tRNA131-GlyCCC	1000	-	Gly	CCC	No canonical tRNA introns	69.75	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna131-GlyCCC
714	chr1	17006500	17006573	chr1.tRNA130-ValCAC	1000	-	Val	CAC	No canonical tRNA introns	52.98	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna130-ValCAC
715	chr1	17052060	17052133	chr1.tRNA1-PseudoCAC	1000	+	Pseudo	CAC	No canonical tRNA introns	30.83	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna1-PseudoCAC
715	chr1	17053779	17053850	chr1.tRNA2-GlyCCC	1000	+	Gly	CCC	No canonical tRNA introns	63.06	http://gtrnadb.ucsc.edu/Hsapi19/	http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-align.html#Homo_sapiens_chr1.trna2-GlyCCC

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Description

This track displays tRNA genes predicted by using tRNAscan-SE v.1.23.

tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. The program then filters these candidates with a covariance model-based search program COVE (Eddy) to obtain a highly specific set of primary sequence and secondary structure predictions that represent 99-100% of true tRNAs with a false positive rate of fewer than 1 per 15 gigabases.

Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at Genomic tRNA Database (GtRNAdb).

What does the tRNAscan-SE score mean? Anything with a score above 20 bits is likely to be derived from a tRNA, although this does not indicate whether the tRNA gene still encodes a functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation). Vertebrate tRNAs with scores of >60.0 (bits) are likely to encode functional tRNA genes, and those with scores below ~45 have sequence or structural features that indicate they probably are no longer involved in translation. tRNAs with scores between 45-60 bits are in the "grey" zone, and may or may not have all the required features to be functional. In these cases, tRNAs should be inspected carefully for loss of specific primary or secondary structure features (usually in alignments with other genes of the same isotype), in order to make a better educated guess. These rough score range guides are not exact, nor are they based on specific biochemical studies of atypical tRNA features, so please treat them accordingly.

Both tRNAscan-SE and GtRNAdb are maintained by the Lowe Lab at UCSC.

Credits

Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659-71.

Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S. Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucleic Acids Res. 1994 Apr 11;22(7):1247-56.

Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994 Jun 11;22(11):2079-88.

References

When making use of these data, please cite the following articles:

Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64.

Chan PP, Lowe TM. GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7.