piRBase

piRBase is a manually curated database for PIWI-interacting RNAs (piRNAs), a type of small noncoding RNA with various regulatory functions. Since its initial launch in 2014, piRBase has become a comprehensive resource focused on assisting piRNA functional analysis and annotation.

Overview

The database integrates high-throughput sequencing data from multiple organisms and provides extensive information about piRNA sequences, genomic locations, functional annotations, and epigenetic features. As of version 3.0, piRBase has integrated hundreds of datasets from numerous organisms, with the collection containing over 173 million piRNA sequences.

Data Content

piRBase provides:

• piRNA Sequences: Comprehensive collection of piRNA sequences from multiple species in FASTA format
• Gold Standards: High-confidence piRNA sequences for model organisms
• Genomic Locations: Precise genome coordinates in BED format for various genome assemblies
• Functional Annotations: Information about piRNA functions and regulatory roles
• Epigenetic Features: Methylation and other epigenetic modifications associated with piRNAs
• Cross-species Data: piRNA information from over 50 species including humans, mice, rats, Drosophila, C. elegans, zebrafish, and many others

Species Coverage

The database includes piRNA data for:

• Model organisms: Human (hsa), mouse (mmu), rat (rno), Drosophila melanogaster (dme), C. elegans (cel), zebrafish (dre)
• Primates: Rhesus macaque, marmoset, crab-eating macaque
• Other mammals: Cow (bta), pig (ssc), horse (eca), rabbit (ocu), giant panda, tree shrew
• Birds: Chicken (gga)
• Invertebrates: Silkworm (bmo), multiple Caenorhabditis species, sea hare, sea anemone, various parasitic worms
• Other species: Multiple Drosophila species, mud crab, and more

Data Access

Data is available through multiple interfaces:

• Web Portal: Search and browse piRNA sequences by identifier or keyword
• Browse Interface: Explore piRNAs organized by species
• Function Interface: Analyze piRNA functional annotations
• Genome Browser: View piRNA genomic locations
• Epigenetics Interface: Explore methylation and epigenetic features
• Tools: Various analysis utilities
• Downloads: Complete datasets in FASTA and BED formats

Key Features

• Search piRNAs by identifier (e.g., piR-hsa-35391, piR-mmu-604679)
• Browse piRNAs by species
• Analyze piRNA functions and regulatory roles
• View genomic locations with integrated genome browser
• Explore epigenetic modifications
• Download sequences and coordinates for bioinformatics analysis
• Access gold standard high-confidence piRNA sets

Contact

piRBase is affiliated with the BIG Data Center (Beijing Institute of Genomics, Chinese Academy of Sciences).

Note: The piRBase website may experience intermittent availability. If you encounter access issues, please try again later.