Table 5 

Nucleotide enrichment for several locations neighboring an editing sites 

neighbor 
helix 
interior 
pattern reported in [41] 


up18:A 
0.9468 
0.8720 
C = T > G 
up18:C 
1.0250 
1.0727 

up18:G 
0.9590 
1.0313 

up18:T 
1.0635 
1.0149 

up9:A 
0.9579 
0.7649 
G > A = T 
up9:C 
1.1032 
1.1904 

up9:G 
1.0449 
1.1040 

up9:T 
0.8916 
0.9270 

up1:A 
1.1147 
0.9294 
T = A > G 
up1:C 
0.9981 
1.1554 

up1:G 
0.3239 
0.2256 

up1:T 
2.2055 
1.7022 

dn7:A 
0.8456 
0.8678 
T > C > G = A 
dn7:C 
1.2455 
1.1647 

dn7:G 
0.9262 
0.9433 

dn7:T 
0.9932 
0.9908 

dn9:A 
1.0000 
0.9407 
U > A > G 
dn9:C 
0.9352 
1.0777 

dn9:G 
0.9574 
1.0675 

dn9:T 
1.1277 
0.9083 

dn10:A 
0.8874 
0.8125 
A = T > G = C 
dn10:C 
1.1173 
1.1853 

dn10:G 
1.1126 
1.1540 

dn10:T 
0.9114 
0.8079 

dn13:A 
0.8481 
0.8988 
T = A > G 
dn13:C 
0.9946 
1.0219 

dn13:G 
1.1912 
1.0726 

dn13:T 
1.0215 
1.0281 

dn15:A 
0.7704 
0.8653 
G > T > A = C 
dn15:C 
1.1095 
1.0859 

dn15:G 
1.1407 
1.0447 

dn15:T 
0.9629 
0.9884 



Nucleotide distributions at certain locations around editing sites, reported to exhibit nucleotide biases [41]. For each of the sites, we present the probability to have a given nucleotide N when the 0 location adenosine is edited, divided by the probability of that nucleotide regardless of whether the 0 adenosine is edited: P(N0 adenosine is edited)/P(N). Values > 1 indicate enrichment of N for edited sites, and < 1 indicate depletion. upX = X nucleotides upstream of site 0, dnX = X nucleotides downstream. The probabilities are given for editing sites in helices and interior loops separately, but are very similar for both. For comparison, we present the patterns reported in [41]. 

Kleinberger and Eisenberg BMC Genomics 2010 11:453 doi:10.1186/1471216411453 