Schema for tRNA Genes - Transfer RNA Genes Identified with tRNAscan-SE
  Database: mm9    Primary Table: tRNAs    Row Count: 433   Data last updated: 2012-02-02
Format description: transfer RNA genes
fieldexampleSQL type info description
bin 848smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values chromosome
chromStart 34491656int(10) unsigned range Start position in chromosome
chromEnd 34491728int(10) unsigned range End position in chromosome
name chr1.tRNA1547-GluTTCvarchar(255) values transfer RNA gene name
score 1000int(10) unsigned range Score from 900-1000. 1000 is best
strand -char(1) values Value should be + or -
aa Gluvarchar(255) values Amino acid for the tRNA
ac TTCvarchar(255) values Anticodon for the tRNA
intron No canonical tRNA intronsvarchar(255) values Coordinates for intron
trnaScore 75float range tRNAScanSE score
genomeUrl http://gtrnadb.ucsc.edu/Mmusc/varchar(255) values GtRNAdb genome summary URL
trnaUrl http://gtrnadb.ucsc.edu/Mmu...varchar(255) values GtRNAdb tRNA alignment URL

Sample Rows
 
binchromchromStartchromEndnamescorestrandaaacintrontrnaScoregenomeUrltrnaUrl
848chr13449165634491728chr1.tRNA1547-GluTTC1000-GluTTCNo canonical tRNA introns75http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1547-GluTTC
1156chr17486332074863391chr1.tRNA1392-GlyGCC1000-GlyGCCNo canonical tRNA introns74.71http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1392-GlyGCC
1182chr17829436978294441chr1.tRNA284-ProAGG1000+ProAGGNo canonical tRNA introns48.57http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna284-ProAGG
1445chr1112801323112801396chr1.tRNA1268-LysCTT1000-LysCTTNo canonical tRNA introns58.94http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1268-LysCTT
1614chr1134930538134930611chr1.tRNA485-LysTTT1000+LysTTTNo canonical tRNA introns83.8http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna485-LysTTT
1614chr1134930903134930976chr1.tRNA1184-LysTTT1000-LysTTTNo canonical tRNA introns83.8http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1184-LysTTT
1769chr1155305793155305866chr1.tRNA583-IleTAT1000+IleTATNo canonical tRNA introns59.1http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna583-IleTAT
1863chr1167571764167571836chr1.tRNA672-ProAGG1000+ProAGGNo canonical tRNA introns75.92http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna672-ProAGG
1863chr1167572401167572473chr1.tRNA1022-ProCGG1000-ProCGGNo canonical tRNA introns76.52http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1022-ProCGG
1904chr1172964072172964146chr1.tRNA1006-AsnGTT1000-AsnGTTNo canonical tRNA introns82.24http://gtrnadb.ucsc.edu/Mmusc/http://gtrnadb.ucsc.edu/Mmusc/Mmusc-align.html#Mus_musculus_chr1.trna1006-AsnGTT

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

tRNA Genes (tRNAs) Track Description
 

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.

Please note that tRNA genes marked as "Pseudo" are low scoring predictions that are mostly pseudogenes or tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary structure and the provided images of the predicted secondary structures may appear rotated.

Credits

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

Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri.

References

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

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. PMID: 18984615; PMC: PMC2686519

Eddy SR, Durbin R. RNA sequence analysis using covariance models. Nucleic Acids Res. 1994 Jun 11;22(11):2079-88. PMID: 8029015; PMC: PMC308124

Fichant GA, Burks C. Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol. 1991 Aug 5;220(3):659-71. PMID: 1870126

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. PMID: 9023104; PMC: PMC146525

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. PMID: 8165140; PMC: PMC523650