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Analysis of genomic poly(A) sites
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 Searching APA sites in 3'UTR of a interesting gene  [Help]  
 
Human
Homo sapiens
 Database: for
 Dataset description: Detailed description on the searching dataset can be referred by unfolding more description in the dataset-list page 'APAS Search'.
 Tips for searching:
search using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases.
 Searching examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).
 
 
 1. Poly(A)-site map Poly(A)-site usage Heterogeneous cleavage-site selection [Help]   
   
  Pooled
  Normal intestinum rectum
   Tumorous intestinum rectum
Gene id: uc002rvx.3 
Gene name: EPCAM
Chromosome: chr2(+)
Gene locus: chr2:47596286-47614167
Gene description: Homo sapiens epithelial cell adhesion molecule (EPCAM), mRNA.
Notes:

Transcript id: uc002rvx.3 
Transcript name: EPCAM
Transcript locus: chr2(+):47596286-47614167

Start codon: 47596645
Stop codon: 47613750
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
47606550, 47613932, 47613980, 47614052, 47614156
polyA signals: ATTAAA, AATATA, none, multi, AATAAA

 Tips for marking poly(A) sites in the corresponding genome sequence:
All the heterogeneous cleavage sites clustered to a poly(A) site, are underlined and highlighted in light red, and their upstream poly(A) signals if exists, are highlighted in light green. Especially, the most-frequently used cleavage site defined as the reference poly(A) site in a cluster, is specially highlighted in dark red and underlined in bold. Also, the searched transcript locus is indicated, including the marked exons (light grey background with a brown font), introns and UTRs (light grey background with a green font).
 

uc002rvx.3; EPCAM, Homo sapiens epithelial cell adhesion molecule (EPCAM), mRNA.
 
 
 
 
chr2:(+)
EPCAM
  
 Transcript   
 47596286   
 Codon   
 47596645   
5(0%)
 
signal:ATTAAA
 pA:47606550    
 Codon   
 47613750   
185(1.8%)
 
signal:AATATA
 pA:47613932    
28(0.3%)
 
signal:none
 pA:47613980    
6750(66.7%)
 
signal:multi
 pA:47614052    
3147(31.1%)
 
signal:AATAAA
 pA:47614156    
 Transcript   
 47614167   
    Start StartCodon in intron StopCodon in 3'UTR in 3'UTR in 3'UTR in 3'UTR End
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
46
0
837
333
  Normal intestinum rectum   
5
139
28
5913
2814
 Tumorous intestinum rectum 
 
 
 
PolyA sites used in normal and tumorous tissues of intestinum rectum. Reads bar break at 100 reads. Mean reads: 5058.



   
Gene id: uc002rvx.3 
Gene name: EPCAM
Chromosome: chr2(+)
Gene locus: chr2:47596286-47614167
Gene description: Homo sapiens epithelial cell adhesion molecule (EPCAM), mRNA.
Notes:

Transcript id: uc002rvx.3 
Transcript name: EPCAM
Transcript locus: chr2(+):47596286-47614167

Start codon: 47596645
Stop codon: 47613750
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
47606550, 47613932, 47613980, 47614052, 47614156
polyA signals: ATTAAA, AATATA, none, multi, AATAAA

 Tips for marking poly(A) sites in the corresponding genome sequence:
 

Citation:
(Leiming You, et al. Nucleic Acids Res. 2015, 43: D59-D67) APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

 
May 19, 2019. Last updated  
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