Home APASdb Home APAS Search APAS Browse BLAST Download Contact Us Help Citation
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: ENSDARG00000007358 
Gene name: cxcr3.1
Chromosome: chr16(+)
Gene locus: 16:13603463-13609316
Gene description: chemokine (C-X-C motif) receptor 3.1 [Source:ZFIN
Notes:

Transcript id: ENSDART00000145754 
Transcript name: cxcr3.1-001
Transcript locus: chr16(+):13603464-13609316

Start codon: 13608011
Stop codon: 13604933
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
13462216, 13462675, 13510597, 13510989, 13530754, 13535291, 13588415, 13589617, 13589653, 13590133, 13596199
polyA signals: ATTAAA, AATAAA, AATAAA, AATAAA, CATAAA, AATAAA, TATAAA, ACTAAA, 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).
 

ENSDARG00000007358; ENSDART00000145754; cxcr3.1, chemokine (C-X-C motif) receptor 3.1 [Source:ZFIN;Acc:ZDB-GENE-060130-38]
 
 
 
 
chr16:(+)
cxcr3.1
  
13(3.6%)
 
signal:ATTAAA
 pA:13462216    
128(35.5%)
 
signal:AATAAA
 pA:13462675    
45(12.5%)
 
signal:AATAAA
 pA:13510597    
24(6.6%)
 
signal:AATAAA
 pA:13510989    
7(1.9%)
 
signal:CATAAA
 pA:13530754    
100(27.7%)
 
signal:AATAAA
 pA:13535291    
10(2.8%)
 
signal:TATAAA
 pA:13588415    
5(1.4%)
 
signal:ACTAAA
 pA:13589617    
7(1.9%)
 
signal:ATTAAA
 pA:13589653    
17(4.7%)
 
signal:AATAAA
 pA:13590133    
5(1.4%)
 
signal:AATAAA
 pA:13596199    
 Transcript   
 13603464   
 Codon   
 13604933   
 Codon   
 13608011   
 Transcript   
 13609316   
    in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb in out_1kb Start StopCodon StartCodon End
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
0
0
0
7
87
2
5
0
0
0
       0 hpf       
0
1
0
0
0
10
3
0
0
0
0
       4 hpf       
0
0
0
0
0
0
5
0
2
5
0
       6 hpf       
0
4
0
0
0
0
0
0
0
1
0
       12 hpf      
1
9
4
1
0
0
0
0
0
1
0
   24 hpf (1 dpf)  
0
5
8
11
0
3
0
0
3
1
0
   48 hpf (2 dpf)  
0
51
13
7
0
0
0
0
1
3
0
   72 hpf (3 dpf)  
12
58
20
5
0
0
0
0
1
6
5
 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: 45.



   
Gene id: ENSDARG00000007358 
Gene name: cxcr3.1
Chromosome: chr16(+)
Gene locus: 16:13603463-13609316
Gene description: chemokine (C-X-C motif) receptor 3.1 [Source:ZFIN
Notes:

Transcript id: ENSDART00000145754 
Transcript name: cxcr3.1-001
Transcript locus: chr16(+):13603464-13609316

Start codon: 13608011
Stop codon: 13604933
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
13462216, 13462675, 13510597, 13510989, 13530754, 13535291, 13588415, 13589617, 13589653, 13590133, 13596199
polyA signals: ATTAAA, AATAAA, AATAAA, AATAAA, CATAAA, AATAAA, TATAAA, ACTAAA, 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  
Copyright© Laboratory of Molecular Medicine, Sun Yat-Sen University, High Education Mega Center, Guangzhou 510006 China.