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.