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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]  
 
Human
Homo sapiens
 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
Gene id: uc001xsc.2 
Gene name: TGFB3
Chromosome: chr14(-)
Gene locus: chr14:76424441-76448092
Gene description: Homo sapiens transforming growth factor, beta 3 (TGFB3), mRNA.
Notes:

Transcript id: uc001xsc.2 
Transcript name: TGFB3
Transcript locus: chr14(-):76424441-76448092

Start codon: 76447234
Stop codon: 76425530
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
76424500, 76424443
polyA signals: AATAAA, AGTAAA

 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).
 

uc001xsc.2; TGFB3, Homo sapiens transforming growth factor, beta 3 (TGFB3), mRNA.
 
 
 
 
chr14:(-)
TGFB3
 Transcript   
 76424441   
373(55.4%)
 
signal:AGTAAA
 pA:76424443    
300(44.6%)
 
signal:AATAAA
 pA:76424500    
 Codon   
 76425530   
 Codon   
 76447234   
 Transcript   
 76448092   
  
  End in 3'UTR 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
 
 
 
56
0
  
7
132
  
71
27
  
83
19
  
8
7
  
148
115
  
 
 
 
Mean reads: 112.



   
Gene id: uc001xsc.2 
Gene name: TGFB3
Chromosome: chr14(-)
Gene locus: chr14:76424441-76448092
Gene description: Homo sapiens transforming growth factor, beta 3 (TGFB3), mRNA.
Notes:

Transcript id: uc001xsc.2 
Transcript name: TGFB3
Transcript locus: chr14(-):76424441-76448092

Start codon: 76447234
Stop codon: 76425530
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
76424500, 76424443
polyA signals: AATAAA, AGTAAA

 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.

 
Jan 11, 2021. Last updated  
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