Database Browser

Browse the Database of cleavage sites.

About

Welcome to the S. pombe cleavage site and polyadenylation signal Database. We have analysed RNA-seq data from different cell cycle stages. Polyadenylated reads were extracted and mapped back to the genome to yield cleavage sites. 50 nt regions before the cleavage sites were scanned for dominant motifs, these were ranked according to their p-values bases on the cumulative binomial distribution of motif occurrence before the cleavage site. For more detailed methods one can refer to our publication (submitted, details to appear soon). There are two datasets considered for cycling cells: one strand-specific (reads of length 51 nt) and non strand-specific (reads of length 30nt). All other datasets are strand-specific. The non strand-specific dataset aligned less specifically to the genome.

If you are interested in a particular gene from a particular dataset, please follow the link to an ensemble session. It displays all predicted cleavage sites (labelled “DATASET” “STRAND” Poly(A) site “STRAND-SPECIFICITY OF DATASET”) and the corresponding predicted signals (length 6) in the 3' UTRs (labelled “DATASET” “STRAND” Poly(A) signals “STRAND-SPECIFICITY OF DATASET”). The displayed value for each signal is the inverse of its rank – so the higher its absolute value, the more significant the signal. We included the data from J. Mata (2013), which was here analysed with our methodology (see Materials and Methods of Schlackow et al. (2013). The usage tracks are meant to give an idea of cleavage site usage between datasets. The values are scaled for each dataset according to final number of finally used poly(A) reads. Note that to compare strength of cleavage site usage, one should not compare within one dataset between different cleavage sites, but rather the same cleavage site between different datasets.

In Downloads (tab below) you can find an Excel file with all cleavage sites and predicted Poly(A) signals for each analysed dataset.

Browse the data on the ensemblfungi website: here. On the page go to Configure this page -> Polyadenylation Sites. Select the desired datasets.

Download the data here.