PolyA Cleavage Site & 3' UTR Database

Message(s)

Welcome to PACdb Public Release Version 1

[Sept 10, 2008] Our support Email address is back up after Exchange Server migration.

[Jan 15, 2007] New human data available (assembly 36). Human and mouse BLAST and genomic alignment functionality unavailable, will be updated soon. The data download page will be updated soon as well, for both human and mouse.

[Sept 15, 2005] PACdb paper published in Bioinformatics.

Overview

PACdb is a database of mRNA three prime (3') processing sites. These sites are also called polyadenylation cleavage sites (or PAC sites) because they are the location that the mRNA is cleaved and a 3' polyadenylate tail is added for most eukaryotic mRNAs. The location of these sites determines the length of the 3' untranslated region (3' UTR) of the mRNA transcript. ESTs (Expressed Sequence Tags) are used to identify putative 3'-processing sites, and these putative 3'-processing sites can then be used to retrieve 3' UTR length and sequence. PACdb is also an excellent resource to study alternative polyadenylation since it catalogs all putative 3'-processing sites across many organisms.

Currently in PACdb
Organism Name PAC site count (in PACdb) Genes with at least one PAC site
Mus musculus 450650 20852
Rattus norvegicus 92016 16345
Takifugu rubripes 2950 2111
Arabidopsis thaliana 112514 17557
Oryza sativa 48400 14693
Schizosaccharomyces pombe 1697 741
Saccharomyces cerevisiae 1187 826
Caenorhabditis elegans 47719 11259
Anopheles gambiae 7643 4115
Drosophila melanogaster 34003 10382
Danio rerio 53966 12847
Gallus gallus 28153 8724
Homo sapiens 959480 20529
Canis familiaris 29730 9286