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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]  
 
Lancelet
Branchiostoma belcheri
 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 intestine
   V.anguillarum-infected intestine
Gene id: Bb_066660F 
Gene name: CASP2
Chromosome: Sc0000026(+)
Gene locus: Sc0000026:457132-460191
Gene description: Caspase-2
Notes:

Transcript id: Bb_066660F 
Transcript name: CASP2
Transcript locus: Sc0000026(+):457132-460191

Start codon: 457132
Stop codon: 460189
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
459719, 460305, 460696
polyA signals: AATAAA, ATTAAA, none

 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).
 

Bb_066660F; CASP2, Caspase-2
 
 
 
 
Sc0000026:(+)
CASP2
  
 Transcript   
 457132   
 Transcript   
 457132   
3(28.6%)
 
signal:AATAAA
 pA:459719    
 Codon   
 460189   
 Transcript   
 460191   
2(14.3%)
 
signal:ATTAAA
 pA:460305    
7(57.1%)
 
signal:none
 pA:460696    
    Start Start in intron StopCodon End in down_1kb in down_1kb
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
3
2
7
          Normal intestine          
0
0
0
 V.anguillarum-infected intestine 
 
 
 
PolyA sites produced by APA in Vibrio anguillarum-infected intestine and normal control. Vibrio anguillarum (V.anguillarum), a severe pathogen of marine fish. Mean reads: 6.



   
Gene id: Bb_066660F 
Gene name: CASP2
Chromosome: Sc0000026(+)
Gene locus: Sc0000026:457132-460191
Gene description: Caspase-2
Notes:

Transcript id: Bb_066660F 
Transcript name: CASP2
Transcript locus: Sc0000026(+):457132-460191

Start codon: 457132
Stop codon: 460189
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
459719, 460305, 460696
polyA signals: AATAAA, ATTAAA, none

 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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