Home APASdb Home APAS Search APAS Browse BLAST Download Contact Us Help Citation
Analysis of genomic poly(A) sites
  Search For [ Example ] [ Tips ]
 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_130940F 
Gene name: CASP2
Chromosome: Sc0000085(+)
Gene locus: Sc0000085:496479-500495
Gene description: Caspase-2
Notes:

Transcript id: Bb_130940F 
Transcript name: CASP2
Transcript locus: Sc0000085(+):496479-500495

Start codon: 496479
Stop codon: 500493
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
495486, 495645, 495858, 500570, 500928
polyA signals: none, none, AATAAA, ATTAAA, 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_130940F; CASP2, Caspase-2
 
 
 
 
Sc0000085:(+)
CASP2
  
8(1.1%)
 
signal:none
 pA:495486    
1(0.2%)
 
signal:none
 pA:495645    
557(70.4%)
 
signal:AATAAA
 pA:495858    
 Transcript   
 496479   
 Transcript   
 496479   
 Codon   
 500493   
 Transcript   
 500495   
7(0.9%)
 
signal:ATTAAA
 pA:500570    
217(27.4%)
 
signal:AATAAA
 pA:500928    
    in up_1kb in up_1kb in up_1kb Start Start 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
 
 
 
8
0
305
7
58
          Normal intestine          
0
1
252
1
159
 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: 396.



   
Gene id: Bb_130940F 
Gene name: CASP2
Chromosome: Sc0000085(+)
Gene locus: Sc0000085:496479-500495
Gene description: Caspase-2
Notes:

Transcript id: Bb_130940F 
Transcript name: CASP2
Transcript locus: Sc0000085(+):496479-500495

Start codon: 496479
Stop codon: 500493
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
495486, 495645, 495858, 500570, 500928
polyA signals: none, none, AATAAA, ATTAAA, 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  
Copyright© Laboratory of Molecular Medicine, Sun Yat-Sen University, High Education Mega Center, Guangzhou 510006 China.