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_284020F 
Gene name: TLR2-1
Chromosome: Sc0000769(+)
Gene locus: Sc0000769:55784-57750
Gene description: Toll-like receptor 2 type-1
Notes:

Transcript id: Bb_284020F 
Transcript name: TLR2-1
Transcript locus: Sc0000769(+):55784-57750

Start codon: 55784
Stop codon: 57748
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
58252, 58386, 58677
polyA signals: none, AATACA, AAGAAA

 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_284020F; TLR2-1, Toll-like receptor 2 type-1
 
 
 
 
Sc0000769:(+)
TLR2-1
  
 Transcript   
 55784   
 Transcript   
 55784   
 Codon   
 57748   
 Transcript   
 57750   
3(26.9%)
 
signal:none
 pA:58252    
6(46.1%)
 
signal:AATACA
 pA:58386    
3(26.9%)
 
signal:AAGAAA
 pA:58677    
    Start Start 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
 
 
 
3
5
3
          Normal intestine          
0
1
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_284020F 
Gene name: TLR2-1
Chromosome: Sc0000769(+)
Gene locus: Sc0000769:55784-57750
Gene description: Toll-like receptor 2 type-1
Notes:

Transcript id: Bb_284020F 
Transcript name: TLR2-1
Transcript locus: Sc0000769(+):55784-57750

Start codon: 55784
Stop codon: 57748
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
58252, 58386, 58677
polyA signals: none, AATACA, AAGAAA

 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.

 
Jan 11, 2021. Last updated  
Copyright© Laboratory of Molecular Medicine, Sun Yat-Sen University, High Education Mega Center, Guangzhou 510006 China.