Plant tRF Database


Transfer RNA-derived fragments or tRFs is a novel class of small non-coding RNAs with length ranging from 15-28 nucleotides and have been detected in evolutionarily divergent organisms. The role of tRFs as regulators of gene expression has been established in different organisms and their differential expression is observed under various stress conditions. Recently, their exploration is gaining momentum in plants as well. Some plant tRFs have been proven to be over-expressed during abiotic and biotic stresses.

PtRFdb is the database developed exclusively for plants' tRFs by performing the analysis of small RNA sequencing data from 10 well-annotated diverse plant species. A total of 1,344 sequencing datasets of 10 plant species have been analyzed for the prediction of different tRF types (i.e. tRF-5, tRF-3, and tRF-1). This database harbors different types of information related to the tRFs and is believed to be beneficial to molecular biologists in facilitating future survey and characterization of tRFs across the plant kingdom.

Arabidopsis thaliana
(2,923 tRFs)
Brachypodium distachyon
(847 tRFs)
Glycine max
(1,348 tRFs)
Medicago truncatula
(631 tRFs)
Oryza sativa
(168 tRFs)

Physcomitrella patens
(508 tRFs)
Populus trichocarpa
(195 tRFs)
Sorghum bicolor
(433 tRFs)
Vitis vinifera
(893 tRFs)
Zea mays
(701 tRFs)

Cite this database: Gupta, N., Singh, A., Zahra, S. and Kumar S. PtRFdb: a database for plant transfer RNA-derived fragments. Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay063. PMID: 29939244