Welcome to PtncRNAdb
PtncRNAdb is the database of Transfer RNA-derived non-coding RNAs (e.g. tncRNAs) identified in a total of 2434 single-end small RNA-seq libraries from 6 plants, viz., Arabidopsis thaliana, Cicer arietinum, Zea mays, Oryza sativa, Medicago truncatula, and Solanum lycopersicum by using tncRNA-Tookit (Zahra et. al., 2021).
tncRNAs includes well-known shorter tRNA-derived RNA fragments (∼12 to 30 nucleotides) popularly termed as tRFs or tDRs, and longer tRNA halves or tRHs (∼30 to 40 nt).
Major Features:
Resource:
tncRNA-Toolkit was used for the identification and classification of tncRNAs (http://nipgr.ac.in/tncRNA and https://github.com/skbinfo/tncRNA-Toolkit).
tncRNA entries:
tncRNA entries: Different tncRNA classes viz. tRF-5, tRF-3, tRF-1, leader-tRF, 5'tRH, and 3'tRH with details of sequence, tncRNA type, length, coordinates, amino acid & anticodon type, modifications, alignment, structure, tncRNA targets, network of targets, SRA accessions, samples, and tissues are available at this database.
DE tncRNAs:
PtncRNAdb holds information related to DE tncRNAs as well as their targets. Network analysis and enrichment option are also provided for each condition.
BLAST:
The User can perform BLASTN against PtncRNAdb data. It is very useful for searching tncRNA sequences by finding regions of local similarity between sequences.
Key findings:
We identified six major tncRNA classes with a size between 14 to 50 nt by exploiting 2,434 samples from six different angiosperms.
1. tRNA nucleoside modifications may drive tncRNAs production.
2. tncRNAs target transcripts are involved in plant growth, development, and metabolism.
3. tncRNAs majorly bind to CDS region of targets and involved in regulating gene expression.
© Developed by Dr. Shailesh Laboratory | National Institute of Plant Genome Research (NIPGR), New Delhi, India | DBT