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PITA catalogs of predicted microRNA targets


Files contain lists of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream (see text for details).

Versions History

Last version is available here for download.
  • PITA Catalog version 1 (23-Sept-07): Initial release
  • PITA Catalog version 2 (30-Sept-07): Fixed energy value signs (energies are now negative as should be)
  • PITA Catalog version 3 (17-Oct-07): Fixed targets scores
  • PITA Catalog version 4 (5-Nov-07): Catalogs are now based on RefSeq annotations in all species and contain genomic coordinates for each target. Target prediction is only done on annotated 3' UTR regions. Fly predictions updated to dm3 assembly.
  • PITA Catalog version 5 (20-Nov-07): The gene ID column may now contain more than one RefSeq ID in case the same target is found on different isoforms. In addition, the gene name (column 2) is now provided.
  • PITA Catalog version 6 (31-Aug-08): Based on miRBase r11.0 microRNAs and on latest genome versions (ce6, dm3, mm9 and hg18); "TOP" catalog is now restricted to full complementarity 7- and 8-mers; New "TOP targets" catalog.


PITA Sites catalog


For each organism, the top predictions (having a full match 7- or 8-mer seed and a conservation score of 0.9 or higher) or the complete list of predictions can be downloaded. Each line describes a single microRNA binding site. Files have 8 columns with the following format: ReSeq ID (column 1), Gene name (column 2), microRNA name (column 3), site position (column 4, given is the base in the 3' UTR where the microRNA 5' end is predicted to bind), seed type (column 5, describing the seed length, number of mismatches and number of G:U wobbles in that order), microRNA-target hybridization energy (ΔGduplex, column 6), energy required to make the target site accessible (ΔGopen, column 7), combined interaction energy (ΔΔG, column 8), site conservation (column 9), chromosome (column 10), unique PITA site name (column 11), seed start and end positions (columns 12 and 13), and strand (column 14).

    Worm Fly Mouse Human
no flankTop
All
3/15 flankTop
All


PITA Targets catalog


Each line describes the combined interaction of potentially many sites for a single microRNA on the same UTR, compiled from either the "TOP" of "ALL" site catalogs. Files have four columns with the following format: microRNA name (column 1), Gene ID (column 2), number of sites (column 3) and total combined energy (column 4).

    Worm Fly Mouse Human
no flankTop
All
3/15 flankTop
All