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Analysis of genomic poly(A) sites
  Search For [ Example ] [ Tips ]
 Searching APA sites in 3'UTR of a interesting gene  [Help]  
 
Zebrafish
Danio rerio
 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
  0 hpf
   4 hpf
   6 hpf
   12 hpf
   24 hpf (1 dpf)
   48 hpf (2 dpf)
   72 hpf (3 dpf)
   120 hpf (5 dpf)
Gene id: ENSDARG00000041959 
Gene name: cxcr4b
Chromosome: chr9(+)
Gene locus: 9:10917684-10919710
Gene description: chemokine (C-X-C motif), receptor 4b [Source:ZFIN
Notes:

Transcript id: ENSDART00000061499 
Transcript name: cxcr4b-001
Transcript locus: chr9(+):10917685-10919710

Start codon: 10917774
Stop codon: 10919185
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
10919200, 10919608, 10919706
polyA signals: TATAAA, 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).
 

ENSDARG00000041959; ENSDART00000061499; cxcr4b, chemokine (C-X-C motif), receptor 4b [Source:ZFIN;Acc:ZDB-GENE-010614-1]
 
 
 
 
chr9:(+)
cxcr4b
  
 Transcript   
 10917685   
 Codon   
 10917774   
 Codon   
 10919185   
330(76.7%)
 
signal:TATAAA
 pA:10919200    
9(2.1%)
 
signal:ATTAAA
 pA:10919608    
91(21.2%)
 
signal:AATAAA
 pA:10919706    
 Transcript   
 10919710   
    Start StartCodon StopCodon in 3'UTR in 3'UTR in 3'UTR End
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
3
1
6
       0 hpf       
173
0
36
       4 hpf       
117
6
25
       6 hpf       
0
1
18
       12 hpf      
14
1
3
   24 hpf (1 dpf)  
22
0
1
   48 hpf (2 dpf)  
1
0
1
   72 hpf (3 dpf)  
0
0
1
 120 hpf (5 dpf) 
 
 
 
PolyA sites used in the embryonic development of zebrafish (Tubingen, Danio rerio) from 0 to 120 hpf. hpf, hours post fertilizaiton. dpf, days post fertilizaiton. Reads bar break at 150 reads. Mean reads: 54.



   
Gene id: ENSDARG00000041959 
Gene name: cxcr4b
Chromosome: chr9(+)
Gene locus: 9:10917684-10919710
Gene description: chemokine (C-X-C motif), receptor 4b [Source:ZFIN
Notes:

Transcript id: ENSDART00000061499 
Transcript name: cxcr4b-001
Transcript locus: chr9(+):10917685-10919710

Start codon: 10917774
Stop codon: 10919185
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
10919200, 10919608, 10919706
polyA signals: TATAAA, 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  
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