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. 2013 Apr 2;14:214. doi: 10.1186/1471-2164-14-214

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.