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Table 3 Compilation of known ADAR substrates with respect to how they are captured by the pipe.

From: A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

substrate

A-G mismatchera

name

Entrez gene

Codon change

Mm

Hs

stemPrediction b

stemConservation c

Adar2

Adarb1

intron

n/a

n/a

yes

no

Bc10

Blcap

Y/C

yes

yes

yes

no

 

Cyfip2

K/E

yes

yes

yes

no

 

Flna

Q/R

no

yes

yes

no

 

Ednrb

Q/R

n/ad

Noe

yes

no

Bc10

Blcap

Y/C

yes

yes

yes

no

GluR-B

Gria2

Q/R

yes

yes

yes

yes

  

R/G

yes

yes

yes

yes

GluR-C

Gria3

R/G

no

yes

yes

yes

GluR-D

Gria4

R/G

yes

yes

yes

yes

GluR-5

Grik1

Q/R

no

yes

yes

no

GluR-6

Grik2

Q/R

no

no

yes

no

  

Y/C

no

no

yes

yes

  

I/V

no

no

yes

yes

5-ht2c

Htr2c

I/V_1

no

no

yes

yes

  

I/V_2

no

no

yes

yes

  

N/S

no

no

yes

yes

 

Igfbp7

R/G

yes

yes

yes

no

  

K/R

yes

yes

yes

no

 

Kcna1

I/V

yes

yes

yes

yes

  1. aStates whether an A-G mismatch has been found in mouse (Mm) and human (Hs).
  2. bStates whether Stemprediction has assigned any stem overlapping an edited position, regardless of the stem ranking (or if it is the correct one).
  3. cStates whether the stem according to column 4 has a conservation score ≥ 75.
  4. dTo our knowledge this site has not been annotated in mouse which is also emphasized by low sequence similarity between the 2 species.
  5. eA-G mismatcher does not detect the annotated site but finds 2 additional A-G mismatches in the vicinity, inferring an I/M and a D/G codon change, respectively.
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BMC Bioinformatics

ISSN: 1471-2105

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