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Analysis of genomic poly(A) sites
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 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: ENSDARG00000087474 
Gene name: ccr6a
Chromosome: chr20(+)
Gene locus: 20:30636454-30640427
Gene description: chemokine (C-C motif) receptor 6a [Source:ZFIN
Notes:

Transcript id: ENSDART00000122256 
Transcript name: ccr6a-001
Transcript locus: chr20(+):30636455-30640427

Start codon: 30639300
Stop codon: 30640425
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
30636076, 30640978, 30641318
polyA signals: 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).
 

ENSDARG00000087474; ENSDART00000122256; ccr6a, chemokine (C-C motif) receptor 6a [Source:ZFIN;Acc:ZDB-GENE-040625-126]
 
 
 
 
chr20:(+)
ccr6a
  
841(95.9%)
 
signal:AATAAA
 pA:30636076    
 Transcript   
 30636455   
 Codon   
 30639300   
 Codon   
 30640425   
 Transcript   
 30640427   
26(3%)
 
signal:AATAAA
 pA:30640978    
10(1.1%)
 
signal:AATAAA
 pA:30641318    
    in up_1kb Start StartCodon 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
 
 
 
102
19
7
       0 hpf       
88
2
0
       4 hpf       
87
1
0
       6 hpf       
105
2
1
       12 hpf      
120
0
0
   24 hpf (1 dpf)  
126
1
2
   48 hpf (2 dpf)  
112
0
0
   72 hpf (3 dpf)  
101
1
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. Mean reads: 110.



   
Gene id: ENSDARG00000087474 
Gene name: ccr6a
Chromosome: chr20(+)
Gene locus: 20:30636454-30640427
Gene description: chemokine (C-C motif) receptor 6a [Source:ZFIN
Notes:

Transcript id: ENSDART00000122256 
Transcript name: ccr6a-001
Transcript locus: chr20(+):30636455-30640427

Start codon: 30639300
Stop codon: 30640425
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
30636076, 30640978, 30641318
polyA signals: 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 19, 2019. Last updated  
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