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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: ENSDARG00000058179 
Gene name: cxcr7b
Chromosome: chr6(-)
Gene locus: 6:15651809-15657695
Gene description: chemokine (C-X-C motif) receptor 7b [Source:ZFIN
Notes:

Transcript id: ENSDART00000063665 
Transcript name: cxcr7b-001
Transcript locus: chr6(-):15651810-15657695

Start codon: 15653603
Stop codon: 15652517
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
15657587, 15651881, 15651810
polyA signals: ATTAAA, 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).
 

ENSDARG00000058179; ENSDART00000063665; cxcr7b, chemokine (C-X-C motif) receptor 7b [Source:ZFIN;Acc:ZDB-GENE-031116-61]
 
 
 
 
chr6:(-)
cxcr7b
 Transcript   
 15651810   
 Transcript   
 15651810   
175(16.8%)
 
signal:AATAAA
 pA:15651881    
 Codon   
 15652517   
 Codon   
 15653603   
13(1.2%)
 
signal:ATTAAA
 pA:15657587    
 Transcript   
 15657695   
  
  End End in 3'UTR StopCodon StartCodon in 5'UTR Start  
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
1
1
0
       0 hpf       
119
20
4
       4 hpf       
75
17
9
       6 hpf       
121
41
0
       12 hpf      
159
19
0
   24 hpf (1 dpf)  
141
24
0
   48 hpf (2 dpf)  
164
46
0
   72 hpf (3 dpf)  
75
7
0
 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: 130.



   
Gene id: ENSDARG00000058179 
Gene name: cxcr7b
Chromosome: chr6(-)
Gene locus: 6:15651809-15657695
Gene description: chemokine (C-X-C motif) receptor 7b [Source:ZFIN
Notes:

Transcript id: ENSDART00000063665 
Transcript name: cxcr7b-001
Transcript locus: chr6(-):15651810-15657695

Start codon: 15653603
Stop codon: 15652517
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
15657587, 15651881, 15651810
polyA signals: ATTAAA, 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 19, 2019. Last updated  
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