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Analysis of genomic poly(A) sites
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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_073760F 
Gene name: ssr4
Chromosome: Sc0000031(+)
Gene locus: Sc0000031:1764674-1771073
Gene description: signal sequence receptor, delta
Notes:

Transcript id: Bb_073760F 
Transcript name: ssr4
Transcript locus: Sc0000031(+):1764674-1771073

Start codon: 1764674
Stop codon: 1771071
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
1770222, 1771090, 1771411, 1771566
polyA signals: none, AATAAA, none, 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_073760F; ssr4, signal sequence receptor, delta
 
 
 
 
Sc0000031:(+)
ssr4
  
 Transcript   
 1764674   
 Transcript   
 1764674   
1(0%)
 
signal:none
 pA:1770222    
 Codon   
 1771071   
 Transcript   
 1771073   
8040(99.3%)
 
signal:AATAAA
 pA:1771090    
3(0%)
 
signal:none
 pA:1771411    
56(0.7%)
 
signal:none
 pA:1771566    
    Start Start in intron StopCodon End in down_1kb 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
 
 
 
0
3014
0
39
          Normal intestine          
1
5026
3
17
 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. Reads bar break at 100 reads. Mean reads: 4050.



   
Gene id: Bb_073760F 
Gene name: ssr4
Chromosome: Sc0000031(+)
Gene locus: Sc0000031:1764674-1771073
Gene description: signal sequence receptor, delta
Notes:

Transcript id: Bb_073760F 
Transcript name: ssr4
Transcript locus: Sc0000031(+):1764674-1771073

Start codon: 1764674
Stop codon: 1771071
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
1770222, 1771090, 1771411, 1771566
polyA signals: none, AATAAA, none, 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 27, 2016. last modified
 
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