Table 2. Sanger validation of selected C>U recoding RNA editing sites identified in 293T/A3G cells.
| Genea | Chromosomal positionb | Reference: cDNA and amino acid changec | RNA editing level (RNA- Seq)d | RNA editing level (Sanger)e | Size of putative loop (N.’C)/size of flanking palindromef |
|---|---|---|---|---|---|
| ACIN1 | 14: 23063490 | NM_001164816:exon6:c.C676T:p.Q226X | 0.22 | 0.23 | 4/5 |
| CDC6 | 17: 40291480 | NM_001254:exon4:c.C472T:p.Q158X | 0.08 | 0.14 | 3/6 |
| CHMP4B | 20: 33850995 | NM_176812:exon3:c.C412T:p.Q138X | 0.07 | 0.09 | 4/5 |
| CLASP1 | 2: 121469844 | NM_001142273:exon9:c.C829T:p.R277W | 0.26 | 0.45 | 3 or 4/2 |
| GOLGA5#1 | 14: 92809464 | NM_005113:exon4:c.C937T:p.Q313X | 0.09 | 0.19 | 4/4 |
| GOLGA5#2 | 14: 92837408 | NM_005113:exon12:c.C2074T:p.R692X | 0.10 | 0.13 | 3/3 |
| ITFG1 | 16: 47155742 | NM_030790:exon18:c.C1816T:p.R606W | 0.16 | 0.38 | 3/2 |
| KIAA1715 | 2: 175939613 | NM_030650:exon10:c.C751T:p.R251X | 0.26 | 0.34 | 4/5 |
| MAPK1 | 22: 21788373 | NM_002745:exon6:c.C740T:p.P247L | 0.13 | 0.11 | 4/3 |
| MED1 | 17: 39410258 | NM_004774:exon17:c.C1963T:p.Q655X | 0.27 | 0.38 | 4/6 |
| NFAT5 | 16: 69693268 | NM_006599:exon12:c.C3389T:p.S1130L | 0.12 | 0.12 | 4/2 |
| NFRKB | 11: 129873843 | NM_006165:exon20:c.C2527T:p.Q843X | 0.07 | 0.09 | 7/5 |
| NMT1 | 17: 45061373 | NM_021079:exon1:c.C44T:p.P15L | 0.23 | 0.19 | 4/6(i + 1) |
| NVL | 1: 224289696 | NM_001243146:exon11:c.C796T:p.Q266X | 0.06 | 0.09 | 4/4 |
| PRPSAP2 | 17: 18928928 | NM_001243936:exon9:c.C802T:p.R268W | 0.25 | 0.35 | 4/4 |
| RBM14 | 11: 66626504 | NM_006328:exon3:c.C1846T:p.R616C | 0.22 | 0.26 | 4/2 |
| RFX7 | 15: 56096472 | NM_022841:exon9:c.C1256T:p.P419L | 0.29 | 0.29 | 4/3 |
| SCD | 10: 100352431 | NM_005063:exon3:c.C376T:p.R126C | 0.24 | 0.33 | 4/4 |
| SGPL1 | 10: 70854801 | NM_003901:exon5:c.C355T:p.Q119X | 0.05 | 0.11 | 4/4(i + 1) |
| SUCLA2 | 13: 47973266 | NM_003850:exon5:c.C661T:p.Q221X | 0.13 | 0.17 | 4/6 |
| TM7SF3 | 12: 26974149 | NM_016551:exon12:c.C1529T:p.P510L | 0.30 | 0.39 | 4/2 |
aGenes selected from bioinformatic analysis for verification.
bBased on the UCSC hg19 genome assembly.
cNCBI reference sequences and the editing related changes at cDNA and protein levels.
dEditing levels in RNA-Seq are averages estimated by Tophat and Subread alignment softwares.
eEditing levels in 293T/A3G cells are calculated from Sanger traces via SequencherTM software (2 or 3 replicates).
fIndicates size of putative loop where the edited C is at the most 3′-end of it, and the size of immediately flanking inverted repeats (i + 1 indicates interruption in complementarity by 1 unpaired nucleotide).