tRFtarget 2.0

Explore transfer RNA-derived Fragment targets

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Number of tRFs in tRFtarget

Organism Source Total
Homo sapiens 157 from tRFdb 1,944
113 from tsRNA study
78 from tsRBase
518 from tsRFun
583 from MINTbase v2.0 (04/04/2019)
17 from tRFexplorer (2019-05)
475 from tatDB
3 from OncotRF
Mus musculus 164 from tRFdb 170
6 from tsRBase
Caenorhabditis elegans 47 from tRFdb 47
Danio rerio 127 from tRFdb 127
Drosophila melanogaster 86 from tRFdb 90
4 from tsRBase
Rattus norvegicus 4 from tsRBase 4
Rhodobacter sphaeroides 77 from tRFdb 77
Schizosaccharomyces pombe 104 from tRFdb 104
Xenopus tropicalis 51 from tRFdb 51
Total 2,614

Number of target RNAs in tRFtarget

Organism #Protein-coding mRNAs #lncRNAs #rRNAs Total
Homo sapiens 110,980 412,754 6,720 530,454
Mus musculus 67,002 85,246 254 152,502
Caenorhabditis elegans 31,989 202 173 32,364
Danio rerio 67,002 85,246 254 152,502
Drosophila melanogaster 51,259 2,627 5,134 59,020
Rattus norvegicus 45,893 32,901 308 79,102
Rhodobacter sphaeroides 4,333 0 5 4,338
Schizosaccharomyces pombe 5,060 1 112 5,173
Xenopus tropicalis 49,787 2 459 50,248
Total 397,102 536,633 14,407 948,142

Number of target Genes in tRFtarget

Organism #Protein-coding Genes #lncRNA Genes #rRNA Genes Total
Homo sapiens 20,367 17,669 52 38,088
Mus musculus 22,322 11,102 170 33,594
Caenorhabditis elegans 19,981 193 19 20,193
Danio rerio 30,149 1,837 1,192 33,178
Drosophila melanogaster 13,986 2,369 106 16,461
Rattus norvegicus 23,096 2,456 212 25,764
Rhodobacter sphaeroides 4,333 0 5 4,338
Schizosaccharomyces pombe 4,333 0 0 4,333
Xenopus tropicalis 22,102 1 535 22,638
Total 161,387 35,627 2,332 199,346

Number of Predicted Binding Sites in tRFtarget

Organism #RNAhybrid #IntaRNA #Consensus (pairs)
Homo sapiens 3,377,427,836 2,416,199,928 542,988,333
Mus musculus 83,530,931 60,329,700 13,270,931
Caenorhabditis elegans 4,325,292 3,433,891 935,985
Danio rerio 25,605,277 18,787,232 4,452,811
Drosophila melanogaster 10,652,355 8,042,938 1,654,959
Rattus norvegicus 1,266,339 901,919 157,927
Rhodobacter sphaeroides 1,068,277 793,883 183,870
Schizosaccharomyces pombe 1,926,438 1,189,886 270,548
Xenopus tropicalis 9,404,617 7,590,218 2,081,926
Total 3,515,207,362 2,517,269,595 565,997,290

Number of Curated Gene-level Evidences

400 tRF target gene related publications have been manually curated, and total 232 gene-level evidence entries from 57 publications are extracted.