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Analysis of genomic poly(A) sites
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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
  brain
  lung
  thyroid
  spleen
  stomach
  kidney
  cervix
  heart
  lymphNode
  placenta
  uterus
  bladder
  breast
  prostate
  liver
  pancreas
  smallIntestine
  thymus
  adipose
  skeletalMuscle
  ovary
  testicle
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.
138413053, 138412865, 138412260, 138411981, 138411927, 138411843, 138409644
polyA signals: ATTAAA, none, AATAAA, none, AATAAA, ATTAAA, 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   
124(1.1%)
 
signal:AATAAA
 pA:138409644    
5(0%)
 
signal:ATTAAA
 pA:138411843    
10752(91.1%)
 
signal:AATAAA
 pA:138411927    
6(0.1%)
 
signal:none
 pA:138411981    
14(0.1%)
 
signal:AATAAA
 pA:138412260    
5(0%)
 
signal:none
 pA:138412865    
892(7.6%)
 
signal:ATTAAA
 pA:138413053    
 Codon   
 138413179   
 Codon   
 138428475   
 Transcript   
 138428660   
  
  End in 3'UTR in 3'UTR in 3'UTR 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
 
 
 
0
0
54
0
0
0
4
     brain      
11
0
306
0
1
0
96
      lung      
2
0
279
0
0
0
14
    thyroid     
0
0
10
0
0
0
0
     spleen     
15
0
392
0
0
0
4
    stomach     
9
0
151
0
0
0
15
     kidney     
14
0
2051
3
2
4
117
     cervix     
4
0
217
0
0
0
26
     heart      
5
0
43
0
0
0
23
   lymphNode    
8
0
960
0
4
0
222
    placenta    
5
0
318
0
0
0
14
     uterus     
4
0
1496
0
0
0
79
    bladder     
4
5
850
3
1
0
30
     breast     
4
0
868
0
1
1
30
    prostate    
10
0
350
0
0
0
50
     liver      
2
0
141
0
1
0
2
    pancreas    
11
0
810
0
2
0
73
 smallIntestine 
0
0
344
0
0
0
25
     thymus     
8
0
792
0
2
0
49
    adipose     
0
0
46
0
0
0
3
 skeletalMuscle 
1
0
204
0
0
0
12
     ovary      
7
0
70
0
0
0
4
   testicle     
 
 
 
PolyA sites used in human (Homo spaiens) normal 22 tissues. White man, Reads bar break at 100 reads. Mean reads: 536.



   
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.
138413053, 138412865, 138412260, 138411981, 138411927, 138411843, 138409644
polyA signals: ATTAAA, none, AATAAA, none, AATAAA, ATTAAA, 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  
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