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GtRNAdb specifications

Information


Unique identifier OMICS_06107
Name GtRNAdb
Alternative name Genomic tRNA Database
Restrictions to use None
Data access Browse
Version 2.0
Maintained Yes

Publications for Genomic tRNA Database

GtRNAdb citations

 (138)
library_books

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

2018
BMC Genomics
PMCID: 5936030
PMID: 29728066
DOI: 10.1186/s12864-018-4726-6

[…] ads that are not mapped to the human genome are mapped to the human transcriptome, The library for the human transcriptome is built by concatenating miRNAs and hairpins from miRBase 21 [], tRNAs from gtRNAdb [], piRNAs from piRBase v1.0 [], protein-coding, non-coding and and other RNA sequences from ENSEMBL 75. The STAR alignment is performed end to end with a single mismatch allowed while mapping […]

library_books

Alterations in sperm DNA methylation, non coding RNA expression, and histone retention mediate vinclozolin induced epigenetic transgenerational inheritance of disease

2018
PMCID: 5920293
PMID: 29732173
DOI: 10.1093/eep/dvy010

[…] q data were annotated as follows: reads shorter than 15 nt were discarded by Cutadapt []. The remaining reads were matched to known rat sncRNA, consisting of mature miRNA (miRBase, release 21), tRNA (Genomic tRNA Database, rn5), piRNA (piRNABank), rRNA (ENSEMBL, release 76), and mitochondrial RNA (ENSEMBL, release 76) using AASRA pipeline with default parameters []. Read counts generated by AASRA […]

library_books

Association of Circulating Transfer RNA fragments with antibody response to Mycoplasma bovis in beef cattle

2018
PMCID: 5851088
PMID: 29534724
DOI: 10.1186/s12917-018-1418-z

[…] two mismatches. Those aligned to the genome were then mapped to a database containing different annotated genome features to determine their origin: genomic tRNA sequences were downloaded from http://gtrnadb.ucsc.edu/; mitochondrial tRNA, cDNA, and other non-coding RNA sequences were downloaded from ENSEMBL version 75. The Illumina reads that aligned to tRNA genes or their flanking sequences were […]

library_books

Alterations in sperm DNA methylation, non coding RNA and histone retention associate with DDT induced epigenetic transgenerational inheritance of disease

2018
PMCID: 5827984
PMID: 29482626
DOI: 10.1186/s13072-018-0178-0

[…] s shorter than 15nt were discarded by Cutadapt []. The remaining reads were matched to known rat sncRNA, consisting of mature miRNA (miRBase, release 21), precursor miRNA (miRBase, release 21), tRNA (Genomic tRNA Database, rn5), piRNA (piRBase), rRNA (Ensembl, release 76) and mitochondrial RNA (Ensembl, release 76) using AASRA pipeline with default parameters []. Read counts generated by AASRA wer […]

call_split

Data Mining of Small RNA Seq Suggests an Association Between Prostate Cancer and Altered Abundance of 5′ Transfer RNA Halves in Seminal Fluid and Prostatic Tissues

2018
PMCID: 5824904
PMID: 29497340
DOI: 10.1177/1179299X18759545
call_split See protocol

[…] 38 human genome with Bowtie v1.1.2. The alignment files were analyzed with Bedtools v2.25.044 to annotate and count reads mapped to noncoding RNA genes from Ensembl GRCh38 release 86, tRNA genes from Genomic tRNA Database,, and YRNA from the UCSC GENCODE v24 track. The obtained read counts were compared with find differences in the abundance of tRNA halves between noncancer and cancer seminal flui […]

library_books

A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

2018
Nat Commun
PMCID: 5802732
PMID: 29410408
DOI: 10.1038/s41467-017-02204-w

[…] re subjected to phylogenetic tree construction using the web server http://www.phylogeny.fr/ (bootstrap number = 100) and iTOL web server http://itol.embl.de/. tRNA gene sequences were retrieved from GtRNAdb and sequences having tRNAscan-SE score > 50 were used for analysis (http://gtrnadb.ucsc.edu/). The list of organisms whose genomes have been completely sequenced was obtained from KEGG GENOME […]

Citations

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GtRNAdb institution(s)
Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
GtRNAdb funding source(s)
National Human Genome Research Institute, National Institutes of Health [HG006753-02]

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