Table 5 Characterization of small RNAs with high homology to repetitive sequences
smallRNA ID | Length (nt) | Blast hits (E < 10-4) | Potential target repeat | Description | Median reads per million (RPM) ± S.D of the longest isoform | |||
|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Â | Â | Pacific Ocean male | Pacific Ocean female | Japan Sea male | Japan Sea female |
iso_smRNA1 | 29 | scaffolds(7) | LSU-rRNA_Mfr | rRNA | 72.6 (17.5) | 56.9 (43.6) | 58.9 (11.4) | 22.6 (9.8) |
iso_smRNA2 | 27 | LG1(12) | tRNAGlyGGC_CB | tRNA | 64.2 (20.9) | 51.9 (71.8) | 56.9 (101.1) | 25.5 (13.7) |
iso_smRNA3 | 30 | LG1(12), LG12(1) | tRNAGlyGGC_CB | tRNA | 52.6 (7.5) | 34.4 (143.5) | 91.1 (32.1) | 18.1 (8.7) |
iso_smRNA4 | 30 | LG1(12), LG12(1) | tRNAGlyGGC_CB | tRNA | 308.0 (161.0) | 131.8 (611.1) | 729.2 (366.5) | 179.7 (105.6) |
iso_smRNA5 | 29 | LG1(2), LG7(2), LG8(3), LG10(1), LG11(7), LG15(1), LG16(1), LG17(1), scaffolds(86) | Gypsy-14_DAn-I | LTR retrotransposon | 304.6 (162.0) | 120.7 (572.5) | 51.5 (266.1) | 22.0 (30.8) |
iso_smRNA6 | 26 | LG3(1), LG7(1), LG11(2), LG12(1), LG17(5), LG18(1), LG19(1), LG20(1) | SINE2-1_EC | Non-LTR Retrotransposon | 79.0 (29.0) | 67.7 (28.7) | 83.7 (30.3) | 62.3 (23.4) |
iso_smRNA7 | 29 | LG3(54), LG5(1), LG9(1), LG11(2), LG12(1), LG13(1), LG17(1), LG19(1), LG20(32), scaffolds(30) | tRNA-Val-GTA | tRNA | 86.9 (22.0) | 57.2 (123.0) | 25.7 (16.6) | 12.7 (10.8) |
iso_smRNA8 | 29 | LG5(1), LG9(1), LG11(2), LG12(1), LG13(1), LG17(1) | DNA-TTAA-5_NV | DNA transposon | 219.9 (50.9) | 138.8 (312.8) | 53.7 (47.9) | 41.5 (23.3) |
iso_smRNA9 | 29 | LG8(1), LG9(1), LG11(1), LG12(1), LG13(1), LG16(1), scaffolds(5) | SINE2-8_SP | Non-LTR Retrotransposon | 72.0 (10.9) | 58.4 (61.2) | 15.2 (17.9) | 9.9 (12.2) |
iso_smRNA10 | 30 | LG7(6), LG18(10), scaffolds(44) | tRNA-Val-GTA | tRNA | 309.1 (78.0) | 150.1 (701.4) | 581.7 (417.1) | 153.0 (99.2) |
iso_smRNA11 | 29 | LG1(1), LG4(1), LG7(1), LG12(1), scaffold(1) | LTR10A2_SS | ERV1-type endogenous retrovirus | 292.2 (76.3) | 177.0 (434.9) | 364.8 (124.6) | 155.6 (74.5) |
iso_smRNA12 | 30 | LG3(1), LG7(1), LG11(2), LG12(1), LG17(5), LG18(1), LG19(1), LG20(1) | SINE2-1_EC | Non-LTR Retrotransposon | 94.4 (21.8) | 29.9 (90.1) | 51.3 (19.5) | 19.9 (7.5) |
iso_smRNA13 | 30 | LG3(1), LG7(1), LG11(2), LG12(1), LG17(5), LG18(1), LG19(1), LG20(1) | SINE2-1_EC | Non-LTR Retrotransposon | 135.5 (47.2) | 43.5 (124.1) | 101.0 (54.8) | 35.9 (12.3) |
iso_smRNA14 | 28 | LG7(7), LG12(1) | tRNA-Asp-GAY | tRNA | 86.0 (16.3) | 68.4 (51.3) | 140.7 (166.9) | 74.8 (25.0) |
iso_smRNA15 | 26 | scaffolds(10) | LSU-rRNA_Mfr | rRNA | 142.1 (40.6) | 122.1 (42.0) | 193.3 (64.9) | 69.9 (27.3) |
iso_smRNA16 | 28 | scaffolds(10) | LSU-rRNA_Mfr | rRNA | 140.7 (52.4) | 170.6 (82.9) | 140.1 (29.1) | 74.3 (26.3) |
iso_smRNA17 | 26 | LG12(1) | LTR41_SS | ERV1-type endogenous retrovirus | 76.8 (3.3) | 57.2 (20.0) | 64.1 (35.9) | 41.0 (5.8) |