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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: ENSDARG00000054846 
Gene name: XCR1(3of4)
Chromosome: chr23(-)
Gene locus: 23:40247742-40248642
Gene description: chemokine (C motif) receptor 1 [Source:HGNC Symbol
Notes:

Transcript id: ENSDART00000077122 
Transcript name: CU657980.1-201
Transcript locus: chr23(-):40247743-40248642

Start codon: 40248640
Stop codon:
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
40247620, 40247571, 40247524
polyA signals: none, TATAAA, AATACA

 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).
 

ENSDARG00000054846; ENSDART00000077122; XCR1(3of4), chemokine (C motif) receptor 1 [Source:HGNC Symbol;Acc:1625]
 
 
 
 
chr23:(-)
XCR1(3of4)
34(69.4%)
 
signal:AATACA
 pA:40247524    
8(16.3%)
 
signal:TATAAA
 pA:40247571    
7(14.3%)
 
signal:none
 pA:40247620    
 Transcript   
 40247743   
 Codon   
 40248640   
 Transcript   
 40248642   
  
  in down_1kb in down_1kb in down_1kb End StartCodon Start  
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
0
0
       0 hpf       
0
0
0
       4 hpf       
0
0
0
       6 hpf       
19
2
3
       12 hpf      
8
0
1
   24 hpf (1 dpf)  
0
1
0
   48 hpf (2 dpf)  
7
5
3
   72 hpf (3 dpf)  
0
0
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: 6.



   
Gene id: ENSDARG00000054846 
Gene name: XCR1(3of4)
Chromosome: chr23(-)
Gene locus: 23:40247742-40248642
Gene description: chemokine (C motif) receptor 1 [Source:HGNC Symbol
Notes:

Transcript id: ENSDART00000077122 
Transcript name: CU657980.1-201
Transcript locus: chr23(-):40247743-40248642

Start codon: 40248640
Stop codon:
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
40247620, 40247571, 40247524
polyA signals: none, TATAAA, AATACA

 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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