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(N|0 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:10.1186/1471-2164-11-453

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