Table 3 Details of databases for piRNAs and functional predictions

piRBase

This database focuses on the comprehensive annotation of piRNA sequences and contains potential piRNA targets and disease-related piRNAs

21 organisms^a)

http://www.regulatoryrna.org/database/piRNA/

RNAdb 2.0

This database contains over 88,000 piRNA candidates that have been cloned and sequenced from mice, humans, and rats

Human, mouse and rat

http://research.imb.uq.edu.au/RNAdb/

piRNA Cluster Database

This database provides comprehensive data on piRNA clusters in multiple species, tissues, and developmental stages based on small RNA sequence data deposited in NCBI’s Sequence Read Archive (SRA)

51 organisms^b)

https://www.smallrnagroup.uni-mainz.de/piCdb/

piRNAdb

This database is a PIWI-interacting RNA sequence storage and search system that provides some other types of relevant information such as alignments, clusters, datasets, and targets of piRNAs

6 organisms^c)

https://www.pirnadb.org/

piRNABank

This database compiles all the possible clusters of piRNAs and depicts piRNAs along with the associated genomic elements such as genes and repeats on a genome-wide map

Human, mouse, rat, and Drosophila

http://pirnabank.ibab.ac.in/

piRNAQuest

This database provides annotation of piRNAs based on their genomic location in gene, intron, intergenic, CDS, UTR, repeat element, pseudogene, and syntenic regions. The database also contains information on all possible piRNA clusters along with significant motifs present within the piRNAs comprising a cluster

Human, mouse and rat

http://bicresources.jcbose.ac.in/zhumur/pirnaquest/

IsopiRBank

This database stores piRNA isoforms detected from small RNA sequencing data, performs detailed classification, and integrates annotation information as well as genome mapping results. Furthermore, target analysis and enrichment analysis revealing the piRNA isoform roles in certain biological processes are included

Human, mouse, Drosophila, and zebrafish

http://mcg.ustc.edu.cn/bsc/isopir/

piRNA-eQTL

This database demonstrates the effects of genetic variation on piRNA expression based on the Cancer Genome Atlas (TCGA) project and is a user-friendly database for the analysis of cis-piRNA eQTLs for 33 cancer types

Human

http://njmu-edu.cn:3838/piRNA-eQTL/

pirScan

This database allows C. elegans researchers to predict piRNA-targeting sites and to avoid the persistent germline silencing of transgenes that has rendered many constructs unusable

C. elegans or C. briggsae

http://cosbi4.ee.ncku.edu.tw/pirScan/

piRTarBase

This database allows researchers to explore piRNA-targeting sites and their regulatory effects on endogenous genes and identify predicted mRNA targets of specific piRNAs

C. elegans or C. briggsae

http://cosbi6.ee.ncku.edu.tw/piRTarBase/