tRFtarget 2.0

Explore transfer RNA-derived Fragment targets

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Number of tRFs covered by tRFtarget

Human tRFs: 270 (13~48 nts)

  • tRF-1: 32
  • tRF-3: 62
    • tRF-3a: 32
    • tRF-3b: 30
  • tRF-5: 63
    • tRF-5a: 22
    • tRF-5b: 23
    • tRF-5c: 18
  • tsRNA: 113
tRF Length Boxplot

Mouse tRFs: 164 (14~34 nts)

  • tRF-1: 30
  • tRF-3: 92
    • tRF-3a: 45
    • tRF-3b: 47
  • tRF-5: 42
    • tRF-5a: 22
    • tRF-5b: 19
    • tRF-5c: 1

Mouse tRF Length Boxplot

Drosophila tRFs: 86 (16~29 nts)

  • tRF-1: 21
  • tRF-3: 43
  • tRF-5: 22
Drosophila tRF Length Boxplot

C. elegans tRFs: 47 (17~26 nts)

  • tRF-3: 30
  • tRF-5: 17

Elegans tRF Length Boxplot

S. pombe tRFs: 104 (14~31 nts)

  • tRF-1: 11
  • tRF-3: 44
  • tRF-5: 49
Pombe tRF Length Boxplot

R. sphaeroides tRFs: 87 (13~32 nts)

  • tRF-3: 40
  • tRF-5: 47

Sphaeroides tRF Length Boxplot

Xenopus tropicalis tRFs: 51 (13~36 nts)

  • tRF-1: 18
  • tRF-3: 13
  • tRF-5: 20
Xenopus tRF Length Boxplot

Zebrafish tRFs: 127 (17~28 nts)

  • tRF-1: 36
  • tRF-3: 35
  • tRF-5: 56
Zebrafish tRF Length Boxplot

Number of genes and transcripts covered by tRFtarget

Human

  • protein-coding transcripts: 100,291 (8~109,224 nts)
  • genes: 20,355
  • each gene has about 5 transcript isoforms on average

Mouse

  • protein-coding transcripts: 67,125 (9~123,179 nts)
  • genes: 22,385
  • each gene has about 3 transcript isoforms on average

Drosophila

  • protein-coding transcripts: 30,588 (152~71,382 nts)
  • genes: 13,947
  • each gene has about 2 transcript isoforms on average

C. elegans

  • protein-coding transcripts: 33,552 (30~45,950 nts)
  • genes: 20,191
  • each gene has about 2 transcript isoforms on average

S. pombe

  • protein-coding transcripts: 5,146 (75~15,022 nts)
  • genes: 5,145
  • each gene has about 1 transcript

R. sphaeroides

  • protein-coding transcripts: 3,111 (81~8,286 nts)
  • genes: 3,111
  • each gene has about 1 transcript

Xenopus tropicalis

  • protein-coding transcripts: 54,848 (18~26,729 nts)
  • genes: 19,983
  • each gene has about 3 transcript isoforms on average

Zebrafish

  • protein-coding transcripts: 51,259 (10~88,553 nts)
  • genes: 30,149
  • each gene has about 2 transcript isoforms on average

Number of binding interactions included in tRFtarget

Human

  • RNAhybrid predictions: 96,579,825 (3.57 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 56,704,483 (2.09 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.58 interactions for 1 tRF and 1 transcript on average):
    • 15,772,606 predictions from RNAhybrid (16.33%)
    • 15,772,606 predictions from IntaRNA (27.82%)

Mouse

  • RNAhybrid predictions: 37,414,246 (3.40 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 22,660,525 (2.06 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.57 interactions for 1 tRF and 1 transcript on average):
    • 6,247,913 predictions from RNAhybrid (16.70%)
    • 6,247,913 predictions from IntaRNA (27.57%)

Drosophila

  • RNAhybrid predictions: 8,986,901 (3.42 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 5,835,485 (2.22 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.58 interactions for 1 tRF and 1 transcript on average):
    • 1,535,375 predictions from RNAhybrid (17.08%)
    • 1,535,375 predictions from IntaRNA (26.31%)

C. elegans

  • RNAhybrid predictions: 4,495,315 (2.85 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 3,190,362 (2.02 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.67 interactions for 1 tRF and 1 transcript on average):
    • 1,062,987 predictions from RNAhybrid (23.65%)
    • 1,062,987 predictions from IntaRNA (33.32%)

S. pombe

  • RNAhybrid predictions: 1,916,852 (3.58 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 1,188,223 (2.22 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.56 interactions for 1 tRF and 1 transcript on average):
    • 301,556 predictions from RNAhybrid (15.73%)
    • 301,556 predictions from IntaRNA (25.38%)

R. sphaeroides

  • RNAhybrid predictions: 869,821 (3.21 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 563,500 (2.08 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.58 interactions for 1 tRF and 1 transcript on average):
    • 157,715 predictions from RNAhybrid (18.13%)
    • 157,715 predictions from IntaRNA (27.99%)

Xenopus tropicalis

  • RNAhybrid predictions: 10,151,269 (3.63 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 6,298,323 (2.25 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.87 interactions for 1 tRF and 1 transcript on average):
    • 2,445,761 predictions from RNAhybrid (24.09%)
    • 2,445,761 predictions from IntaRNA (38.83%)

Zebrafish

  • RNAhybrid predictions: 23,688,750 (3.64 interactions for 1 tRF and 1 transcript on average)
  • IntaRNA predictions: 13,701,030 (2.10 interactions for 1 tRF and 1 transcript on average)
  • Consensus predictions (0.67 interactions for 1 tRF and 1 transcript on average):
    • 4,372,146 predictions from RNAhybrid (18.46%)
    • 4,372,146 predictions from IntaRNA (31.91%)

Distribution of free energy of binding interactions

Human

  • RNAhybrid: -71.6~-15.0; median -24.1 kcal/mol
  • IntaRNA: -47.9~0.0; median -9.2 kcal/mol
Free Energy Boxplot

Mouse

  • RNAhybrid: -56.0~-15.0; median -25.0 kcal/mol
  • IntaRNA: -37.8~0.0; median -9.8 kcal/mol
Mouse Free Energy Boxplot

Drosophila

  • RNAhybrid: -58.2~-15.0; median -24.6 kcal/mol
  • IntaRNA: -40.9~0.0; median -9.2 kcal/mol
Drosophila Free Energy Boxplot

C. elegans

  • RNAhybrid: -43.5~-15.0; median -22.2 kcal/mol
  • IntaRNA: -31.7~0.0; median -9.1 kcal/mol
Elegans Free Energy Boxplot

S. pombe

  • RNAhybrid: -55.6~-15.0; median -24.2 kcal/mol
  • IntaRNA: -45.5~0.0; median -8.0 kcal/mol
Pombe Free Energy Boxplot

R. sphaeroides

  • RNAhybrid: -55.8~-15.0; median -25.5 kcal/mol
  • IntaRNA: -40.2~0.0; median -9.9 kcal/mol
Sphaeroides Free Energy Boxplot

Xenopus tropicalis

  • RNAhybrid: -58.8~-15.0; median -21.6 kcal/mol
  • IntaRNA: -31.6~0.0; median -9.6 kcal/mol
Xenopus Free Energy Boxplot

Zebrafish

  • RNAhybrid: -54.0~-15.0; median -23.6 kcal/mol
  • IntaRNA: -37.1~0.0; median -9.8 kcal/mol
Zebrafish Free Energy Boxplot

Distribution of maximum complementary length of binding interactions

Human

  • RNAhybrid: 6~31; median 7 nts
  • IntaRNA: 6~30; median 7 nts
Length Boxplot

Mouse

  • RNAhybrid: 6~25; median 7 nts
  • IntaRNA: 6~24; median 7 nts
Mouse Length Boxplot

Drosophila

  • RNAhybrid: 6~27; median 7 nts
  • IntaRNA: 6~27; median 7 nts
Drosophila Length Boxplot

C. elegans

  • RNAhybrid: 6~20; median 7 nts
  • IntaRNA: 6~22; median 7 nts
Elegans Length Boxplot

S. pombe

  • RNAhybrid: 6~30; median 7 nts
  • IntaRNA: 6~30; median 7 nts
Pombe Length Boxplot

R. sphaeroides

  • RNAhybrid: 6~22; median 7 nts
  • IntaRNA: 6~22; median 7 nts
Sphaeroides Length Boxplot

Xenopus tropicalis

  • RNAhybrid: 6~22; median 7 nts
  • IntaRNA: 6~22; median 7 nts
Xenopus Length Boxplot

Zebrafish

  • RNAhybrid: 6~22; median 7 nts
  • IntaRNA: 6~23; median 7 nts
Zebrafish Length Boxplot