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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: ENSDARG00000055100 
Gene name: cxcl12b
Chromosome: chr22(-)
Gene locus: 22:27551656-27567596
Gene description: chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1) [Source:ZFIN
Notes:

Transcript id: ENSDART00000077411 
Transcript name: cxcl12b-001
Transcript locus: chr22(-):27551657-27567596

Start codon: 27567540
Stop codon: 27554153
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
27551695
polyA signals: 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).
 

ENSDARG00000055100; ENSDART00000077411; cxcl12b, chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1) [Source:ZFIN;Acc:ZDB-GENE-030721-1]
 
 
 
 
chr22:(-)
cxcl12b
 Transcript   
 27551657   
276(100%)
 
signal:AATAAA
 pA:27551695    
 Codon   
 27554153   
 Codon   
 27567540   
 Transcript   
 27567596   
  
  End in 3'UTR StopCodon StartCodon Start  
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
       0 hpf       
1
       4 hpf       
16
       6 hpf       
107
       12 hpf      
61
   24 hpf (1 dpf)  
27
   48 hpf (2 dpf)  
47
   72 hpf (3 dpf)  
17
 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: 35.



   
Gene id: ENSDARG00000055100 
Gene name: cxcl12b
Chromosome: chr22(-)
Gene locus: 22:27551656-27567596
Gene description: chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1) [Source:ZFIN
Notes:

Transcript id: ENSDART00000077411 
Transcript name: cxcl12b-001
Transcript locus: chr22(-):27551657-27567596

Start codon: 27567540
Stop codon: 27554153
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
27551695
polyA signals: 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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