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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
  MCF10A
   MCF7
   MB231
Gene id: uc003qht.2 
Gene name: PERP
Chromosome: chr6(-)
Gene locus: chr6:138409641-138428660
Gene description: Homo sapiens PERP, TP53 apoptosis effector (PERP), mRNA.
Notes:

Transcript id: uc003qht.2 
Transcript name: PERP
Transcript locus: chr6(-):138409641-138428660

Start codon: 138428475
Stop codon: 138413179
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
138413054, 138412261, 138411928, 138409645
polyA signals: ATTAAA, AATAAA, 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).
 

uc003qht.2; PERP, Homo sapiens PERP, TP53 apoptosis effector (PERP), mRNA.
 
 
 
 
chr6:(-)
PERP
 Transcript   
 138409641   
60(1.7%)
 
signal:AATAAA
 pA:138409645    
3288(90.9%)
 
signal:AATAAA
 pA:138411928    
5(0.1%)
 
signal:AATAAA
 pA:138412261    
264(7.3%)
 
signal:ATTAAA
 pA:138413054    
 Codon   
 138413179   
 Codon   
 138428475   
 Transcript   
 138428660   
  
  End in 3'UTR in 3'UTR 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
 
 
 
39
1075
0
128
 MCF10A  
5
586
0
85
   MCF7  
16
1627
5
51
 MB231 
 
 
 
PolyA sites produced by APA among human breast cancer and normal cells. MCF7 and MB231, two human breast cancer cell lines, and MCF10A, one cultured mammary epithelial cell line. Reads bar break at 100 reads. Mean reads: 1206.



   
Gene id: uc003qht.2 
Gene name: PERP
Chromosome: chr6(-)
Gene locus: chr6:138409641-138428660
Gene description: Homo sapiens PERP, TP53 apoptosis effector (PERP), mRNA.
Notes:

Transcript id: uc003qht.2 
Transcript name: PERP
Transcript locus: chr6(-):138409641-138428660

Start codon: 138428475
Stop codon: 138413179
Alternative polyA sites: Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
138413054, 138412261, 138411928, 138409645
polyA signals: ATTAAA, AATAAA, 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 27, 2016. last modified
 
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