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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_133170F 
Gene name: Ssrp1
Chromosome: Sc0000088(+)
Gene locus: Sc0000088:78576-87585
Gene description: structure specific recognition protein 1
Notes:

Transcript id: Bb_133170F 
Transcript name: Ssrp1
Transcript locus: Sc0000088(+):78576-87585

Start codon: 78576
Stop codon: 87583
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
85969, 86994, 88203
polyA signals: none, none, 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).
 

Bb_133170F; Ssrp1, structure specific recognition protein 1
 
 
 
 
Sc0000088:(+)
Ssrp1
  
 Transcript   
 78576   
 Transcript   
 78576   
2(0.6%)
 
signal:none
 pA:85969    
2(0.5%)
 
signal:none
 pA:86994    
 Codon   
 87583   
 Transcript   
 87585   
360(98.9%)
 
signal:AATAAA
 pA:88203    
    Start Start in exon in exon StopCodon End in down_1kb
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
2
200
          Normal intestine          
2
0
160
 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 182 reads. Mean reads: 182.



   
Gene id: Bb_133170F 
Gene name: Ssrp1
Chromosome: Sc0000088(+)
Gene locus: Sc0000088:78576-87585
Gene description: structure specific recognition protein 1
Notes:

Transcript id: Bb_133170F 
Transcript name: Ssrp1
Transcript locus: Sc0000088(+):78576-87585

Start codon: 78576
Stop codon: 87583
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
85969, 86994, 88203
polyA signals: none, none, 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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