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Updated: Apr 21, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

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Published on: February 18, 2022

tRFdb: a database for transfer RNA fragments.

Pankaj Kumar¹, Suresh B Mudunuri², Jordan Anaya¹

¹Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.

Nucleic Acids Research

|November 14, 2014

Summary

This summary is machine-generated.

The first database of transfer RNA fragments (tRFs), tRFdb, catalogs 12,877 tRFs across eight species. This resource reveals tRF-1s are highly upregulated in B-cell malignancies.

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Published on: July 10, 2019

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Transfer RNA (tRNA) fragments (tRFs) are small RNA molecules with emerging roles in gene regulation.
The characterization and comprehensive cataloging of tRFs are crucial for understanding their biological functions.
Existing resources for tRFs are limited, hindering systematic research.

Purpose of the Study:

To develop and present tRFdb, the first comprehensive database of transfer RNA fragments (tRFs).
To provide a searchable platform for tRF sequences, read counts, and genomic origins across multiple species.
To demonstrate the utility of tRFdb through a case study on tRFs in B-cell malignancies.

Main Methods:

Analysis of over 100 small RNA libraries.
Creation of a database (tRFdb) containing sequences and read counts for three classes of tRFs.
Inclusion of data for eight species: R. sphaeroides, S. pombe, D. melanogaster, C. elegans, Xenopus, zebra fish, mouse, and human.
Implementation of search functionalities by tRF ID, sequence, and organism.

Main Results:

tRFdb currently houses 12,877 tRFs.
The database provides genome coordinates, parental tRNA information, and read counts across various small RNA libraries.
A case study demonstrated that tRF-1s are significantly upregulated in B-cell malignancies, highlighting a potential diagnostic or prognostic marker.

Conclusions:

tRFdb is a valuable resource for researchers studying transfer RNA fragments.
The database facilitates the exploration of tRFs' roles in different species and biological contexts.
The findings suggest specific tRFs, like tRF-1s, may serve as biomarkers for diseases such as B-cell malignancies.