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
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)

The numbers in parentheses in the Blast hits indicate the number of hits on that linkage group.

Kitano et al.

Kitano et al. BMC Genomics 2013 14:214   doi:10.1186/1471-2164-14-214

Open Data