Retrieve the poly(A) sites in your gene/genomic region of interest.

1. Enter either

  • a genomic region (e.g., 1:1,000-2,000, chr2:1000-2000:+, chrII:60,000-100,000) or
  • a gene symbol (e.g., CPSF6, not case-sensitive) or
  • an Ensembl gene identifier (e.g., ENSG00000111605).

2. Select an organism from the drop-down list.

3. Hit the 'Search' button!


Column description

The result columns represent:

- Click to expand: ID, TPM, protocol, cell type and treatment information for all samples contributing to the selected cluster

ID/Site - ID of the poly(A) site cluster, consisting of chromosome:position:strand, where position is that of the representative (most often used) site of the cluster

Cluster - chromosome, start and end positions, and strand of poly(A) site cluster, respectively (1-based coordinates)

TPM - transcripts/tags per million, averaged across all contributing samples

Usage - poly(A) site cluster TPM value divided by sum of TPM values in selected region

Samples - percentage of samples that support the particular cluster

Protocols - number of different 3' end sequencing protocols that support the particular cluster

Type - two letter code for the cluster annotation (in order of decreasing priority: TE, terminal exon; EX, exonic; IN, intronic; DS, 1,000 nt downstream of an annotated terminal exon; AE, anti-sense to an exon; AI, anti-sense to an intron; AU, 1,000 nt upstream in anti-sense direction of a transcription start site; IG, intergenic)

Gene names - gene symbols for annotated genes overlapping with the cluster

Gene IDs - Ensembl gene IDs for annotated genes overlapping with the cluster

Signals - poly(A) signals in the region of -60 to +10 nucleotides around the representative site of the cluster with relative (e.g. @-28) and absolute position on the chromosome (e.g. @1001018)