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EURASIP Journal on Bioinformatics and Systems Biology

Table 2 Number of target candidate genes against shRNA constructed using random oligonucleotides

From: shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library

  Number of aligned genes with mismatches
Sequences of shRNA-coding DNA 0a 1a 2a 3a
GGTAGCTCGTTAATTTAAT 0 0 1 3
GAATTCCGCGGTACGGGGG 0 0 0 6
GAATGCAGCAGGAGGGAGG 0 1 8 278
GAACTGGACGCAGGCCTAT 0 0 2 53
GACTAGTCTACTTCCTTAG 0 0 0 31
GCGATCTCTACCACCTGGC 0 0 4 79
GCGTAATCGGGCGAATAAC 0 0 0 0
GATAGTGCACGTTGAAACA 0 0 1 38
GTAGGGGGACCTAGAACAT 0 0 2 20
GACAAACCCTGCCTAGTTA 0 0 0 17
GGATCCGAGTGCACCTAAA 0 0 0 28
GAAGTAATGCGCTCGATCC 0 0 1 13
GCCACGTATGGCCGTACTG 0 0 0 10
GCACAATGTAAAAAGAATA 0 2 5 131
GAGCCAGTAAAAGAATATC 0 1 4 55
GTGCACTACTCGCAGTGGG 0 0 2 34
GTTCCTAGACTTCAAATAA 0 0 2 53
GACCTACCCATGTAGCAAG 0 0 0 43
GAGAAGGCGTCTCCGGAGA 0 0 4 82
GAGGAATGATATGGCCTTG 0 0 1 54
GGGGCAGTGGCAGGTGATC 0 1 7 140
GACCAGGGACACATTAGAT 0 0 1 37
GATCTAAATATGGCAGGCA 0 0 0 44
GAAGACAGACACGGAGATC 0 0 7 112
GTCAGCCAGCAAAGAAGTG 0 0 7 115
GTGGACTAGTATCGATATA 0 0 1 10
GTGAACCAAGTTACTAGCT 0 0 0 39
GGCCCGGTTAGGAACACTT 0 0 0 7
GGCCAAGAAGATACACTAG 0 0 1 65
GGACAGGGCAACAATGTGG 0 0 1 44
GGAAGATATGCTCATTCGC 0 0 0 24
GGAAGTGGTAAGGACTCCA 0 0 3 65
GGAGTCAGTACAGATACGA 0 0 1 22
GCGTTAATTAATCAACATC 0 0 0 12
GGCGTGATCGTATGCACCA 0 0 0 13
GAGAAGTCCAGATCTTTCC 0 0 5 95
GGACCCTGTCCCTAGAAGT 0 0 2 72
GAAAACTGTCAGACCCGAG 0 0 1 46
GCATTCCAAAGAAAAGAAT 0 0 7 167
GTCACATATCCTGGACACG 0 0 1 36
GTGTATAGTGCAAGACAAT 0 0 0 48
GTGAGAACGTTGGAGAGCC 0 0 1 59
GTTTTGATCGGAGAATCCA 0 0 1 31
GCAAACATCCAGAAAGTAA 0 0 1 93
GTCCAGGGGTTGGGGATCG 0 0 1 34
GGGCGTAGGTCAAAGCATG 0 0 0 17
GGGCGGGGTAAAGAAACCA 0 0 0 17
  1. Alignment between shRNA and human RefSeq was performed under conditions in which the indicated number of mismatches was allowed
  2. aRepresents number of mismatched nucleotides
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