PtRFdb


29939244	PtRFdb: a database for plant transfer RNA-derived fragments. [PMID: 29939244] Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar Abstract Transfer RNA-derived fragments (tRFs) represent a novel class of small RNAs (sRNAs) generated through endonucleolytic cleavage of both mature and precursor transfer RNAs (tRNAs). These 14-28 nt length tRFs that have been extensively studied in animal kingdom are to be explored in plants. In this study, we introduce a database of plant tRFs named PtRFdb (www.nipgr.res.in/PtRFdb), for the scientific community. We analyzed a total of 1344 sRNA sequencing datasets of 10 different plant species and identified a total of 5607 unique tRFs (758 tRF-1, 2269 tRF-3 and 2580 tRF-5), represented by 487 765 entries. In PtRFdb, detailed and comprehensive information is available for each tRF entry. Apart from the core information consisting of the tRF type, anticodon, source organism, tissue, sequence and the genomic location; additional information like PubMed identifier (PMID), Sample accession number (GSM), sequence length and frequency relevant to the tRFs may be of high utility to the user. Two different types of search modules (Basic Search and Advanced Search), sequence similarity search (by BLAST) and Browse option with data download facility for each search is provided in this database. We believe that PtRFdb is a unique database of its kind and it will be beneficial in the validation and further characterization of plant tRFs.Database URL: http://www.nipgr.res.in/PtRFdb/. Database (Oxford). 2018:2018() \| 24 Citations (from Europe PMC, 2025-03-01)

PtRFdb: a database for plant transfer RNA-derived fragments. [PMID: 29939244]

Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar

Transfer RNA-derived fragments (tRFs) represent a novel class of small RNAs (sRNAs) generated through endonucleolytic cleavage of both mature and precursor transfer RNAs (tRNAs). These 14-28 nt length tRFs that have been extensively studied in animal kingdom are to be explored in plants. In this study, we introduce a database of plant tRFs named PtRFdb (www.nipgr.res.in/PtRFdb), for the scientific community. We analyzed a total of 1344 sRNA sequencing datasets of 10 different plant species and identified a total of 5607 unique tRFs (758 tRF-1, 2269 tRF-3 and 2580 tRF-5), represented by 487 765 entries. In PtRFdb, detailed and comprehensive information is available for each tRF entry. Apart from the core information consisting of the tRF type, anticodon, source organism, tissue, sequence and the genomic location; additional information like PubMed identifier (PMID), Sample accession number (GSM), sequence length and frequency relevant to the tRFs may be of high utility to the user. Two different types of search modules (Basic Search and Advanced Search), sequence similarity search (by BLAST) and Browse option with data download facility for each search is provided in this database. We believe that PtRFdb is a unique database of its kind and it will be beneficial in the validation and further characterization of plant tRFs.Database URL: http://www.nipgr.res.in/PtRFdb/.

Database (Oxford). 2018:2018() | 24 Citations (from Europe PMC, 2025-03-01)

URL:	http://www.nipgr.res.in/PtRFdb
Full name:	Plant transfer RNA-derived fragments
Description:	Database of plant Transfer RNA-derived fragments named PtRFdb, for the scientific community. contains a total of 1344 sRNA sequencing datasets of 10 different plant species and identified a total of 5607 unique tRFs (758 tRF-1, 2269 tRF-3 and 2580 tRF-5), represented by 487 765 entries.
Year founded:	2018
Last update:
Version:
Accessibility:	Unaccessible
Country/Region:	India

Data type:	RNA
Data object:	Plant
Database category:	Expression Gene genome and annotation
Major species:	Arabidopsis thaliana Brachypodium distachyon Glycine max Medicago truncatula Oryza sativa Zea mays Vitis vinifera Sorghum bicolor Populus trichocarpa
Keywords:	tRNA sRNA tRF Plant Transfer RNA-derived fragments small RNAs

University/Institution:	National Institute of Plant Genome Research
Address:	National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
City:	New Delhi
Province/State:
Country/Region:	India
Contact name (PI/Team):	Shailesh Kumar
Contact email (PI/Helpdesk):	shailesh@nipgr.ac.in

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Database Commons a catalog of worldwide biological databases