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Table 2 Features of the 25 most abundant differentially accumulated representative RNA fragments

From: Small RNA fragments derived from multiple RNA classes – the missing element of multi-omics characteristics of the hepatitis C virus cell culture model

Sequence

Length

Parental RNA

RNA class

Fragment type

log2FC 72 hpia

log2FC 96 hpia

Relative abundance

72C

72I

96C

96I

CCCCCCACUGCUAAAUUUGACUG

23

hy4 Ro RNA

Y RNA

Ro60 binding region

2.00

3.01

4.03%

16.11%

5.51%

44.43%

UCCCACAUGGUCUAGCGGUUAGGAUUCCUGGUU

33

tRNA, TTC (Glu)

tRNA

tRF-5A

2.14

2.43

2.10%

9.25%

2.76%

14.90%

UCCCUGGUGGUCUAG

15

tRNA, CTC (Glu)

tRNA

tRF-5D

3.04

1.41

0.27%

2.25%

0.86%

2.29%

UACGACUCUUAGCGGUGGAUCACUCGGC

28

ambiguous mapping (intergenic / rRNA)

other

n/ab

2.38

1.95

0.20%

1.03%

0.30%

1.16%

GCCCGGCUAGCUCAGUCGGUAGAGCAUGGGACUCUUAAUCCCAGGGUCGUGGGUU

55

tRNA, CTT (Lys)

tRNA

tRF-5T

1.03

2.40

0.48%

0.98%

0.44%

2.34%

GUUAAGAUGGCAGAGCCCGGUAAUCGCAUAAAACUUAAAACU

42

tRNA, TAA (Leu)

tRNA

tRF-5A

0.93

2.54

0.50%

0.96%

0.54%

3.13%

UUGGUCGUGGUUGUAGUCCGUGCGAGAA

28

tRNA, TTC (Glu)

tRNA

tRF-Δ5A-Δ3AA

1.36

4.32

0.34%

0.86%

0.26%

5.24%

GUUCGCGCUUUCCCCUG

17

U1 spliceosomal RNA

snRNA

no functional region

0.61

3.56

0.54%

0.83%

0.21%

2.46%

CGGCCACUGAUUAUCGAGGCGAUUCUGAUCUG

32

scaRNA, HBII-382/scaRNA2

scaRNA

no functional region

0.80

2.62

0.46%

0.80%

0.57%

3.52%

CCCCACUGCUAAAUUUGACUG

21

hy4 Ro RNA

Y RNA

Ro60 binding region

2.63

3.70

0.12%

0.72%

0.25%

3.18%

ACUCGACUGCAUAAUUUGUGGUAGUGGGG

29

U1 spliceosomal RNA

snRNA

Sm binding

5.22

7.82

0.02%

0.58%

0.03%

7.43%

UAGGAUGGGGUGUGAUAGGUGGCACGGAGAA

31

ambiguous mapping (intergenic / tRNA)

other

n/a

1.38

3.55

0.21%

0.54%

0.17%

2.05%

CACAAAUGAUGAAUAACAAAGGGACU

26

C/D box snoRNA, SNORD82/U82

snoRNA

box C

2.40

3.49

0.10%

0.53%

0.15%

1.72%

UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACC

39

tRNA, TTC (Glu)

tRNA

tRF-5A

1.62

2.60

0.17%

0.51%

0.22%

1.35%

GGUUAGCACUCUGGACUC

18

tRNA,CTG (Gln)

tRNA

tRF-Δ5D-Δ3A

3.02

2.46

0.06%

0.49%

0.11%

0.63%

UCGUACGACUCUUAGCGGUGGAUCACUCGGC

31

ambiguous mapping (intergenic / rRNA)

other

n/a

1.98

2.37

0.12%

0.46%

0.14%

0.74%

AAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACU

35

U1 spliceosomal RNA

snRNA

Sm binding

5.70

9.02

0.01%

0.40%

0.01%

5.00%

GUUAAGAUGGCAGAGCCC

18

tRNA, TAA (Leu)

tRNA

tRF-5D

2.07

2.31

0.09%

0.38%

0.22%

1.07%

GGUAAAAUGGCUGAGUGAAGCAUUGGACU

29

tRNA, GTA (Tyr)

tRNA

tRF-5A

1.33

2.65

0.14%

0.36%

0.17%

1.05%

ACUUUAGCUCUAGAAUUACUCUGAGACCU

29

C/D box snoRNA, SNORD45/U45

snoRNA

box D, guide sequence 2

2.00

5.05

0.09%

0.35%

0.06%

2.14%

CUACGGGGAUGAUUUUACGAAC

22

C/D box snoRNA, SNORD26/U26

snoRNA

box C

3.05

2.40

0.04%

0.35%

0.11%

0.58%

UCACCCGGCCCGGACACG

18

piRNA

other

n/a

5.07

8.18

0.01%

0.34%

0.01%

4.13%

AAUGUGGGAAACUCGACUGCAUAAUUUGUGGUAGUGGGGGACU

43

U1 spliceosomal RNA

snRNA

Sm binding

8.36

9.93

0.00%

0.34%

0.00%

3.09%

AUUGGAAGACACUCUGCGACAGUG

24

H/ACA box snoRNA, ACA7/SNORA7/SNORA7A

snoRNA

box ACA, guide sequence 4

0.97

3.22

0.17%

0.33%

0.18%

1.64%

CACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACGG

38

U2 spliceosomal RNA

snRNA

no functional region

2.62

5.47

0.05%

0.31%

0.04%

1.78%

  1. adifferentially accumulated (log2FC ≥ 2 or ≤ −2 and FDR < 0.05; relative abundance sorted by 72I) are marked with boldtype
  2. bnot applicable