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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: ENSDARG00000037116 
Gene name: cxcl12a
Chromosome: chr13(+)
Gene locus: 13:31027968-31043317
Gene description: chemokine (C-X-C motif) ligand 12a (stromal cell-derived factor 1) [Source:ZFIN
Notes:

Transcript id: ENSDART00000053946 
Transcript name: cxcl12a-001
Transcript locus: chr13(+):31027969-31043317

Start codon: 31028066
Stop codon: 31040671
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
31040950, 31041075, 31041303, 31042052, 31042222, 31042612, 31043309, 31043625
polyA signals: AGTAAA, AATAAA, none, ATTAAA, AATACA, AATAAA, AATAAA, 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).
 

ENSDARG00000037116; ENSDART00000053946; cxcl12a, chemokine (C-X-C motif) ligand 12a (stromal cell-derived factor 1) [Source:ZFIN;Acc:ZDB-GENE-030318-1]
 
 
 
 
chr13:(+)
cxcl12a
  
 Transcript   
 31027969   
 Codon   
 31028066   
 Codon   
 31040671   
236(43.9%)
 
signal:AGTAAA
 pA:31040950    
6(1.1%)
 
signal:AATAAA
 pA:31041075    
6(1.1%)
 
signal:none
 pA:31041303    
95(17.7%)
 
signal:ATTAAA
 pA:31042052    
7(1.3%)
 
signal:AATACA
 pA:31042222    
5(0.9%)
 
signal:AATAAA
 pA:31042612    
167(31%)
 
signal:AATAAA
 pA:31043309    
 Transcript   
 31043317   
16(3%)
 
signal:AATAAA
 pA:31043625    
    Start StartCodon StopCodon in 3'UTR in 3'UTR in 3'UTR in 3'UTR in 3'UTR in 3'UTR in 3'UTR End in down_1kb
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
0
0
0
0
0
0
0
       0 hpf       
12
1
0
0
0
2
4
0
       4 hpf       
38
5
0
5
0
0
0
0
       6 hpf       
96
0
2
17
3
3
60
0
       12 hpf      
43
0
0
20
0
0
11
7
   24 hpf (1 dpf)  
15
0
0
13
0
0
22
7
   48 hpf (2 dpf)  
15
0
4
12
4
0
34
1
   72 hpf (3 dpf)  
17
0
0
28
0
0
36
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. Mean reads: 67.



   
Gene id: ENSDARG00000037116 
Gene name: cxcl12a
Chromosome: chr13(+)
Gene locus: 13:31027968-31043317
Gene description: chemokine (C-X-C motif) ligand 12a (stromal cell-derived factor 1) [Source:ZFIN
Notes:

Transcript id: ENSDART00000053946 
Transcript name: cxcl12a-001
Transcript locus: chr13(+):31027969-31043317

Start codon: 31028066
Stop codon: 31040671
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
31040950, 31041075, 31041303, 31042052, 31042222, 31042612, 31043309, 31043625
polyA signals: AGTAAA, AATAAA, none, ATTAAA, AATACA, AATAAA, AATAAA, 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 27, 2016. last modified
 
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