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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]  
 
Mouse
Mus musculus
 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
  13.5 dpf
   15.5 dpf
   18.5 dpf
   0 dpp
   6 dpp
   22 dpp
   45 dpp
   90 dpp
Gene id: uc009dsc.2 
Gene name: Cdca3
Chromosome: chr6(+)
Gene locus: chr6:124780193-124783719
Gene description: cell division cycle-associated protein 3
Notes:

Transcript id: uc009dsc.2 
Transcript name: Cdca3
Transcript locus: chr6(+):124780193-124783719

Start codon: 124780549
Stop codon: 124783156
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
124780019, 124783293, 124783393, 124783545, 124783718
polyA signals: AATGAA, multi, none, CATAAA, none

 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).
 

uc009dsc.2; Cdca3, cell division cycle-associated protein 3
 
 
 
 
chr6:(+)
Cdca3
  
2(0%)
 
signal:AATGAA
 pA:124780019    
 Transcript   
 124780193   
 Codon   
 124780549   
 Codon   
 124783156   
4491(82.6%)
 
signal:multi
 pA:124783293    
5(0.1%)
 
signal:none
 pA:124783393    
483(8.9%)
 
signal:CATAAA
 pA:124783545    
456(8.4%)
 
signal:none
 pA:124783718    
 Transcript   
 124783719   
    in up_1kb Start StartCodon StopCodon in 3'UTR in 3'UTR in 3'UTR in 3'UTR End
PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb
 
 
 
0
632
0
29
100
 13.5 dpf  
0
460
1
28
44
 15.5 dpf 
0
652
4
83
48
 18.5 dpf 
0
539
0
65
44
   0 dpp   
0
825
0
101
63
   6 dpp  
0
374
0
60
37
   22 dpp  
2
541
0
69
79
   45 dpp  
0
468
0
48
41
 90 dpp   
 
 
 
PolyA sites used during the thymic development of mouse (Mus.musculus) from 13.5 dpf to 90 dpp. hpf, hours post fertilization. dpp, days post parturition. Reads bar break at 100 reads. Mean reads: 680.



   
Gene id: uc009dsc.2 
Gene name: Cdca3
Chromosome: chr6(+)
Gene locus: chr6:124780193-124783719
Gene description: cell division cycle-associated protein 3
Notes:

Transcript id: uc009dsc.2 
Transcript name: Cdca3
Transcript locus: chr6(+):124780193-124783719

Start codon: 124780549
Stop codon: 124783156
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
124780019, 124783293, 124783393, 124783545, 124783718
polyA signals: AATGAA, multi, none, CATAAA, none

 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 27, 2016. last modified
 
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