Table 1.
Exon-specific targets for HBII-85 C/D-box snoRNA genes
| SnoRNA | Common name of gene containing ASE target (protein RefSeq ID) |
The EID gene identifier; (exon containing target) |
Exon specificity | ASE sequence (5′->3′) |
Target sequence (5′->3′) |
mfe (kcal/mol) |
|---|---|---|---|---|---|---|
| HBII-85-1,2,6 | BAT1 (NP_004631.1) | 6563A; (ex #10) | +++ | CGUCAUUCUCAUCGGA | UCCGAUGAGAAUGAUG | −25.3 |
| HBII-85-1,2,6 | CDH23 (NP_071407.2) | 10252A; (ex #45) | +++ | GUCAUUCUCAUCGGAa | uUCUGAUGAGAAUGAC | −23.5 |
| HBII-85-3,8,9 | RASAL2 (NP_733793.1) | 1626A; (ex #8) | +− | GUUCUCAUCGGA | UCCGAUGAGAAC | −19.1 |
| HBII-85-3,8,9 | SH2BP1a (NP_055448.1) | 10875; (ex #25) | +− | GUUCUCAUCGGAa | uUCCGAUGAGAAC | −20.1 |
| HBII-85-3,8,9 | RGL3 (XP_290867) | 17313; (ex #9) | +− | GUUCUCAUCGGA | UCCGAUGAGAAC | −19.1 |
| HBII-85-3,8,9 | BAT1 (NP_004631.1) | 6563A; (ex #10) | + | GUCGUUCUCAUCGGA | UCCGAUGAGAAUGAU | −23 |
| HBII-85-5,7 | C8A (NP_000553.1) | 749; (ex #4) | +++ | GUCGUUCUCAUCAGA | UCUGAUGAGGACGAC | −24.1 |
| HBII-85-5,7 | CDH23 (NP_071407.2) | 10252A (ex #45) | +++ | GUCGUUCUCAUCAGAa | uUCUGAUGAGAAUGAC | −23.8 |
| HBII-85-12 | NCKAP1 (NP_038464.1) | 3161A; (ex #25) | +− | UGUCAUCCUCUUCAA | UUGAAGAGGAUGACA | −23.6 |
| HBII-85-12 | BAP1 (NP_004647.1) | 3929; (ex #13) | +− | CUGUCAUCCUCUUCAAa | uUUGGAGAGGAUGACAG | −26.5 |
| HBII-85-12 | NANS (NP_061819.2) | 9540; (ex #6) | +− | UGUCAUCCUCUUCAA | UUGAAGAGGAUGACA | −23.6 |
| HBII-85-13 | PPP1R8 (NP_054829.2) | 414A; (ex #5) | −+ | CAUCAUCCUCAUUGAa | uUCAGUGAGGAUGAUG | −24 |
| HBII-85-13 | RNF137b (NP_060543.5) | 10800; (ex #7) | −+ | CAUCAUCCUCAUUGA | UCAGUGAGGAUGAUG | −23 |
| HBII-85-13 | PITPNM2 (NP_065896.1) | 12794; (ex #5) | −+ | CAUCAUCCUCAUUGAa | uUCAAUGAGGAUGGUG | −23.4 |
| HBII-85-13 | DRF1c (NP_079380.1) | 16188B; (ex #5) | −+ | ACCAUCAUCCUCAUUGA | UCAGUGAGGAUGAUGGU | −28 |
| HBII-85-15 | LOC389550d (XP_371949.3) | 8076; (ex #1) | ++ | UCAUCCUCGUCGA | UCGACGAGGAUGA | −22.5 |
| HBII-85-15 | ERCC1 (NP_001974.1) | 17928A; (ex #1) | ++ | UCAUCCUCGUCGA | UCGACGAGGAUGA | −22.5 |
| HBII-85-15 | PPIL2 (NP_680481.1) | 19153A; (ex #12) | + | CAUCCUCGUCGA | UCGACGAGGAUG | −20.6 |
| HBII-85-19 | GTPBP3 (NP_598399.1) | 17468A; (ex #5) | +++ | UGUCAUCCUCGUCGAa | uUCGGCGAGGAUGACA | −27.3 |
| HBII-85-22 | NY-REN-41e (NP_542385.1) | 10957; (ex #1) | +++++ | UACCGUCGUCCUCGUCAAa | uUUGACGAGGACGACGGUG | −34.2 |
| HBII-85-22 | ANKRD11 (NP_037407.3) | 15508; (ex #9) | +++ | CGUCGUCCUCGUCAAa | uUUGAUGAGGACGACG | −26.4 |
| HBII-85-23 | NTRK2 (NP_006171.2) | 9438; (ex #3) | −+ | CGUCAUCUUCGUUGA | UCAACGAAGAUGAUG | −21.6 |
| HBII-52-type-I | HTR2C (NP_000859.1) | 20027; (ex #5) | +++++ | AUGCUCAAUAGGAUUACg | cGUAAUCCUAUUGAGCAU | −27.6 |
Column three shows the EID identifier for the gene containing the target, which is the necessary reference for obtaining the gene sequence from the Exon/Intron Database (Saxonov et al., 2000). Exon specificity (column 4) demonstrates the preference of an ASE toward guiding exons compared to introns: five pluses ‘+++++’ means super-specificity of the ASE toward exons (even when a 2–3 nt shorter ASE does not have targets among all human introns); ‘+++’ means that the ASE matches only exons and no introns; ‘+’ means that the ASE has approximately equal number of targets within exons and introns; ‘+−’ means that the ASE has 2–4 times more targets within introns than in exons; and ‘−+’ means that the ASE has 5–7 times more targets within introns than in exons. G–U non-Watson–Crick pairs between the ASE and its target in columns 5 and 6, respectively, are underlined and shown in red. If the match between the ASE and its target extends to the closest nucleotide adjacent to the D-box, then this nucleotide is shown in lowercase at the 3′-end of the ASE sequence.
Another common name for this gene is CTR9.
Another common name for this gene is TRIM68.
Another common name for this gene is DBF4B.
Another common name for this gene is LMOD2.
Another common name for this gene is CCDC34.