Search by piRNA Name

Enter piRNABank or NCBI accession numbers to retrieve piRNA information. Human piRNAs have names ranging from "hsa_piR_000001" to "hsa_piR_023439". Similarly, mouse piRNAs are named as "mmu_piR_000001" to "mmu_piR_039986", rat piRNAs have been assigned "rno_piR_000001" to "rno_piR_038549" and drosophila piRNAs have assigned "dme_piR_000001" to dme_piR_022336". The result page will show the piRNA Accession, chromsome in which the piRNA is located, genomic start and end positions, sequence and its length in a tabular form. The sequence can be viewed (and/or) saved in FASTA format.


Search by Gene name/symbol

Select organism name and enter either gene name or gene symbol to view all piRNAs overlapping specific gene(s). The result page lists the genes matching the given gene name/symbol. Select one or more genes to view the overlapping piRNAs.


Search by Chromosome

Select only organism name to get list of all piRNAs in the selected organism. The result page will show a table of chromsomes and the number of piRNAs in each chromosome, each of which is hyperlinked to display the individual piRNA entry in that chromosome.

Alternatively, select organism name and chromosome number to get the number of piRNAs in the selected chromosome. The piRNA name is linked with the corresponding entry in piRNABank. Accession number and chromosomal position is externally linked with NCBI Nucleotide sequence database and Ensembl genome browser respectively.

piRNAs in specific regions on a selected chromosome can also be viewed by entering the range (start and end positions) of the region.


Search piRNA Clusters

Select only organism and click on "Show all clusters" to view all piRNA clusters in that organism. The cluster id, chromosome number, position and length of cluster alongwith the number of piRNAs and their strand orientation have been tabulated in the result page. The cluster position is hyperlinked to display the individual piRNAs in that cluster.

The organism name and the chromosome number can be chosen to view piRNA clusters. Genomic start and end position can also be specified to obtain cluster information in that particular range of the chromosome.

Select organism, chromosome number and also enter the piRNA density to view clusters having the specified number of piRNAs. User can enter the minimum number of piRNAs to be searched on "ALL" the chromosomes or on a specific chromosome in the selected organism. The range of piRNA density can also be selected from the drop-down, instead of entering the number of piRNAs, which will list the piRNA clusters with densities falling within the selected range.

Search by homology

Enter a sequence (either in FASTA format or the sequence only) to search against the piRNA database. Choose either String Search or BLASTN search options.
String search can be used for searching short motifs or sequences against the piRNA database.
BLASTN search can be used to find exact matches with existing piRNAs. Enter E-value and the maximum number of hits to perform the BLAST search. By default, ungapped alignments with a default E-value threshold of 10 and a maximum of 100 hits will be reported.

View piRNA Map

Select the organism name, chromosome number and genomic position to view the piRNAs, repeats and exons in the specific region of the chromosome on the genomic scale. The map is best viewed for shorter stretches on the chromosome (say upto 100kbases).