Automatic recommendation
Not OK - siRNA is not specific
80 hits were found for CCUCAAAGAAAAACCAAAG (45 guide strand hits and 35 sense strand hits.)
Hits to Guide strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
NR_003506 | PLGLA1 | 14137 | 14155 | u | C | U | C | A | A | A | G | A | A | A | A | A | C | C | A | A | A | a | 93 | 2 | 17 | abc | false | <90% | 22167 | ||
NM_000856 | GUCY1A3 | 698 | 716 | C | C | U | C | A | A | A | G | A | A | A | A | A | C | C | A | g | u | c | 68 | 3 | 16 | ac | false | <90% | 3012 | ||
NM_018682 | MLL5 | 1769 | 1787 | C | C | U | C | A | A | A | G | A | A | A | A | c | C | C | A | g | A | G | 66 | 2 | 12 | false | <90% | 6725 | |||
NM_182931 | MLL5 | 1917 | 1935 | C | C | U | C | A | A | A | G | A | A | A | A | c | C | C | A | g | A | G | 66 | 2 | 12 | false | <90% | 6873 | |||
NM_016118 | NUB1 | 617 | 635 | a | C | U | C | A | A | A | G | A | A | A | A | A | C | a | A | A | u | u | 65 | 4 | 13 | c | false | <90% | 3112 | ||
XM_378517 | MGC15885 | 1164 | 1182 | u | C | U | C | A | A | A | G | A | A | A | c | A | C | C | A | A | A | G | 64 | 2 | 10 | false | <90% | 2698 | |||
XM_944564 | MGC15885 | 1164 | 1182 | u | C | U | C | A | A | A | G | A | A | A | c | A | C | C | A | A | A | G | 64 | 2 | 10 | false | <90% | 2698 | |||
XR_016171 | LOC347097 | 2393 | 2411 | a | g | U | C | A | A | A | G | A | A | A | A | A | C | C | g | A | A | G | 60 | 3 | 13 | c | false | <90% | 2860 | ||
XR_018087 | LOC347097 | 2401 | 2419 | a | g | U | C | A | A | A | G | A | A | A | A | A | C | C | g | A | A | G | 60 | 3 | 13 | c | false | <90% | 2868 | ||
NM_001080976 | DSE | 2608 | 2626 | a | g | U | C | A | A | A | G | A | A | A | A | A | C | C | g | A | A | G | 60 | 3 | 13 | c | false | <90% | 4043 | ||
NM_013352 | DSE | 2642 | 2660 | a | g | U | C | A | A | A | G | A | A | A | A | A | C | C | g | A | A | G | 60 | 3 | 13 | c | false | <90% | 4077 | ||
NM_001304 | CPD | 6252 | 6270 | C | C | U | g | A | A | A | G | A | A | A | A | A | C | C | A | A | A | u | 58 | 2 | 14 | bc | false | <90% | 8025 | ||
NM_002334 | LRP4 | 6935 | 6953 | u | u | U | C | A | A | A | G | A | A | A | A | A | C | C | A | g | A | a | 58 | 4 | 14 | ac | false | <90% | 8076 | ||
NM_020357 | PCNP | 1214 | 1232 | C | u | U | C | A | A | A | G | A | A | A | A | A | C | C | A | u | u | u | 57 | 4 | 14 | ac | false | <90% | 2250 | ||
NM_030641 | APOL6 | 5382 | 5400 | g | C | U | C | A | A | A | G | A | A | A | A | A | u | a | A | A | A | G | 53 | 3 | 12 | c | false | <90% | 10156 | ||
NM_019600 | KIAA1370 | 2606 | 2624 | C | C | U | C | A | A | A | G | A | A | A | A | A | C | a | c | A | A | u | 44 | 3 | 14 | c | false | <90% | 3863 | ||
XR_015789 | LOC146177 | 1905 | 1923 | C | C | c | g | A | A | A | G | A | A | A | A | A | C | C | A | A | A | G | 43 | 2 | 15 | bc | false | <90% | 4216 | ||
XR_015198 | LOC146177 | 1905 | 1923 | C | C | c | g | A | A | A | G | A | A | A | A | A | C | C | A | A | A | G | 43 | 2 | 15 | bc | false | <90% | 4216 | ||
NM_001083625 | ANKRD12 | 3185 | 3203 | C | C | U | u | A | A | A | G | A | A | A | A | A | a | C | A | A | A | a | 38 | 3 | 9 | c | false | <90% | 10459 | ||
NM_015208 | ANKRD12 | 3254 | 3272 | C | C | U | u | A | A | A | G | A | A | A | A | A | a | C | A | A | A | a | 38 | 3 | 9 | c | false | <90% | 10528 | ||
NM_007190 | SEC23IP | 2925 | 2943 | u | C | U | C | c | A | A | G | A | A | A | A | A | C | C | A | A | u | a | 38 | 4 | 12 | c | false | <90% | 4243 | ||
NM_003596 | TPST1 | 1404 | 1422 | u | C | U | u | A | A | A | G | A | A | A | A | A | C | C | A | c | A | G | 37 | 3 | 12 | c | false | <90% | 2033 | ||
NM_194451 | LIAS | 1054 | 1072 | g | C | U | a | A | A | A | G | A | A | A | A | A | C | a | A | A | A | G | 36 | 3 | 10 | c | false | <90% | 1631 | ||
NM_006859 | LIAS | 1166 | 1184 | g | C | U | a | A | A | A | G | A | A | A | A | A | C | a | A | A | A | G | 36 | 3 | 10 | c | false | <90% | 1743 | ||
NM_002913 | RFC1 | 1319 | 1337 | C | u | c | C | A | A | A | G | A | A | A | u | A | C | C | A | A | A | G | 35 | 3 | 8 | false | <90% | 4925 | |||
NM_001001675 | ZNF818 | 2229 | 2247 | C | C | U | C | A | A | A | a | A | A | A | A | A | C | C | A | A | A | c | 32 | 2 | 10 | bc | false | <90% | 2376 | ||
NM_002740 | PRKCI | 2882 | 2900 | u | C | U | C | A | A | A | c | A | A | A | A | A | C | C | A | A | A | u | 30 | 3 | 10 | bc | false | <90% | 4884 | ||
NM_020449 | THOC2 | 3919 | 3937 | u | g | g | u | A | A | A | G | A | A | A | A | A | C | C | A | A | A | G | 30 | 4 | 15 | bc | false | <90% | 5618 | ||
NM_001081550 | THOC2 | 3926 | 3944 | u | g | g | u | A | A | A | G | A | A | A | A | A | C | C | A | A | A | G | 30 | 4 | 15 | bc | false | <90% | 5625 | ||
NM_144643 | SCLT1 | 2113 | 2131 | g | C | U | C | A | A | A | a | A | A | A | A | g | C | C | A | A | A | G | 25 | 3 | 6 | false | <90% | 2816 | |||
NM_018451 | CENPJ | 1351 | 1369 | a | a | U | C | A | A | A | G | c | A | A | A | A | C | C | A | A | A | a | 21 | 4 | 9 | bc | false | <90% | 5187 | ||
NM_199246 | CCNG1 | 2154 | 2172 | a | C | a | C | A | A | u | G | A | A | A | A | A | C | C | A | A | A | G | 12 | 3 | 12 | bc | false | <90% | 2384 | ||
NM_004060 | CCNG1 | 2254 | 2272 | a | C | a | C | A | A | u | G | A | A | A | A | A | C | C | A | A | A | G | 12 | 3 | 12 | bc | false | <90% | 2484 | ||
NM_001039703 | NBPF10 | 1551 | 1569 | C | C | a | C | A | u | A | G | A | A | A | A | A | C | C | A | A | A | a | 12 | 3 | 12 | bc | false | <90% | 2701 | ||
XM_001133092 | LOC728912 | 2500 | 2518 | C | C | a | C | A | u | A | G | A | A | A | A | A | C | C | A | A | A | a | 12 | 3 | 12 | bc | false | <90% | 2950 | ||
XM_001133097 | LOC728912 | 2500 | 2518 | C | C | a | C | A | u | A | G | A | A | A | A | A | C | C | A | A | A | a | 12 | 3 | 12 | bc | false | <90% | 3194 | ||
NM_183372 | NBPF11 | 1918 | 1936 | C | C | a | C | A | u | A | G | A | A | A | A | A | C | C | A | A | A | a | 12 | 3 | 12 | bc | false | <90% | 4902 | ||
NM_022070 | ABC1 | 971 | 989 | a | u | c | C | A | A | A | G | u | A | A | A | A | C | C | A | A | A | G | 6 | 4 | 10 | bc | false | <90% | 3935 | ||
NM_015640 | SERBP1 | 2333 | 2351 | u | C | U | a | A | A | A | c | A | A | A | A | A | C | C | A | A | A | G | 0 | 3 | 11 | bc | false | <90% | 6701 | ||
NM_001018069 | SERBP1 | 2351 | 2369 | u | C | U | a | A | A | A | c | A | A | A | A | A | C | C | A | A | A | G | 0 | 3 | 11 | bc | false | <90% | 6719 | ||
NM_001018068 | SERBP1 | 2378 | 2396 | u | C | U | a | A | A | A | c | A | A | A | A | A | C | C | A | A | A | G | 0 | 3 | 11 | bc | false | <90% | 6746 | ||
NM_001018067 | SERBP1 | 2396 | 2414 | u | C | U | a | A | A | A | c | A | A | A | A | A | C | C | A | A | A | G | 0 | 3 | 11 | bc | false | <90% | 6764 | ||
NM_057096 | CYP3A43 | 883 | 901 | C | C | U | C | A | A | A | G | A | u | A | A | A | C | a | A | A | A | G | -7 | 2 | 9 | c | false | <90% | 2001 | ||
NM_057095 | CYP3A43 | 883 | 901 | C | C | U | C | A | A | A | G | A | u | A | A | A | C | a | A | A | A | G | -7 | 2 | 9 | c | false | <90% | 2164 | ||
NM_022820 | CYP3A43 | 883 | 901 | C | C | U | C | A | A | A | G | A | u | A | A | A | C | a | A | A | A | G | -7 | 2 | 9 | c | false | <90% | 2167 |
Hits to Sense strand
Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
NM_005822 | DSCR1L1 | 2620 | 2638 | u | U | U | U | G | G | U | U | U | U | U | C | a | U | U | G | A | u | G | 84 | 3 | 11 | false | <90% | 3318 | |||
NM_145013 | C11orf45 | 1748 | 1766 | u | U | U | U | G | G | U | U | U | U | U | C | U | U | U | G | c | a | G | 71 | 3 | 15 | ac | false | <90% | 3648 | ||
NM_152356 | ZNF491 | 2000 | 2018 | g | U | U | U | G | G | U | U | U | U | U | C | U | U | U | a | A | G | u | 66 | 3 | 14 | c | false | <90% | 2823 | ||
NM_021809 | TGIF2 | 1767 | 1785 | g | U | U | U | G | G | U | U | U | U | U | C | U | U | U | u | A | a | u | 64 | 4 | 14 | c | false | <90% | 3406 | ||
NM_015296 | DOCK9 | 2937 | 2955 | u | c | a | U | G | G | U | U | U | U | U | C | U | U | U | G | A | u | G | 64 | 4 | 14 | c | false | <90% | 7522 | ||
NM_001009899 | KIAA2018 | 6597 | 6615 | u | U | U | U | G | G | U | U | U | U | U | C | U | U | U | u | A | u | u | 64 | 4 | 14 | c | false | <90% | 13708 | ||
NM_001034845 | GALNT17 | 3873 | 3891 | u | U | U | U | G | G | U | U | U | U | U | g | U | U | U | G | A | a | G | 61 | 3 | 10 | false | <90% | 3937 | |||
NR_003255 | TSIX | 35107 | 35125 | a | U | U | U | G | G | U | U | U | U | U | g | U | U | U | G | A | u | u | 56 | 4 | 10 | false | <90% | 36861 | |||
NM_020642 | C11orf17 | 873 | 891 | g | g | U | U | G | G | U | U | U | U | U | u | U | U | U | G | A | G | a | 47 | 4 | 9 | false | <90% | 1308 | |||
NM_182901 | C11orf17 | 992 | 1010 | g | g | U | U | G | G | U | U | U | U | U | u | U | U | U | G | A | G | a | 47 | 4 | 9 | false | <90% | 1427 | |||
NM_001079846 | CREBBP | 7614 | 7632 | C | U | U | U | G | G | U | U | U | U | U | u | U | U | U | G | g | c | G | 40 | 3 | 11 | false | <90% | 10083 | |||
NM_004380 | CREBBP | 7728 | 7746 | C | U | U | U | G | G | U | U | U | U | U | u | U | U | U | G | g | c | G | 40 | 3 | 11 | false | <90% | 10197 | |||
XM_001129552 | LOC729173 | 2003 | 2021 | C | U | U | U | G | G | U | U | U | U | U | g | U | U | U | G | u | u | u | 35 | 4 | 11 | false | <90% | 2188 | |||
NM_001079818 | ITGA6 | 972 | 990 | C | U | U | a | G | G | U | U | U | U | U | C | U | U | U | G | g | a | c | 32 | 4 | 12 | c | false | <90% | 5680 | ||
NM_000210 | ITGA6 | 972 | 990 | C | U | U | a | G | G | U | U | U | U | U | C | U | U | U | G | g | a | c | 32 | 4 | 12 | c | false | <90% | 5810 | ||
NM_021627 | SENP2 | 614 | 632 | C | U | U | U | G | G | U | U | U | U | a | C | U | U | U | G | A | a | c | 31 | 3 | 10 | c | false | <90% | 3207 | ||
NM_001040147 | SERPINB7 | 1819 | 1837 | u | U | U | U | G | G | U | c | U | U | U | C | U | U | U | G | A | u | a | 28 | 4 | 9 | c | false | <90% | 1973 | ||
NM_003784 | SERPINB7 | 2080 | 2098 | u | U | U | U | G | G | U | c | U | U | U | C | U | U | U | G | A | u | a | 28 | 4 | 9 | c | false | <90% | 2235 | ||
NM_133642 | LARGE | 3389 | 3407 | g | U | U | U | u | G | U | U | U | U | U | C | U | U | U | G | g | G | G | 23 | 3 | 11 | c | false | <90% | 4131 | ||
NM_004737 | LARGE | 3452 | 3470 | g | U | U | U | u | G | U | U | U | U | U | C | U | U | U | G | g | G | G | 23 | 3 | 11 | c | false | <90% | 4194 | ||
NM_021615 | CHST6 | 1537 | 1555 | u | c | U | U | G | G | U | U | U | U | c | C | U | U | U | G | A | G | u | 20 | 4 | 8 | c | false | <90% | 6885 | ||
NM_015288 | PHF15 | 5906 | 5924 | C | U | U | U | G | G | U | U | g | U | U | C | U | U | U | a | A | G | G | 13 | 2 | 8 | c | false | <90% | 6463 | ||
NM_001077445 | PHF16 | 4208 | 4226 | C | U | g | U | G | c | U | U | U | U | U | C | U | U | U | G | A | G | u | 12 | 3 | 12 | bc | false | <90% | 4685 | ||
NM_014735 | PHF16 | 4455 | 4473 | C | U | g | U | G | c | U | U | U | U | U | C | U | U | U | G | A | G | u | 12 | 3 | 12 | bc | false | <90% | 4932 | ||
NM_024315 | C7orf23 | 740 | 758 | C | U | U | U | G | c | U | U | U | U | U | C | U | U | U | a | A | G | G | 10 | 2 | 9 | c | false | <90% | 1083 | ||
NM_014309 | RBM9 | 3640 | 3658 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6948 | ||
NM_001082579 | RBM9 | 3646 | 3664 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6954 | ||
NM_001082577 | RBM9 | 3649 | 3667 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6957 | ||
NM_001082578 | RBM9 | 3649 | 3667 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6957 | ||
NM_001082576 | RBM9 | 3677 | 3695 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6985 | ||
NM_001031695 | RBM9 | 3689 | 3707 | u | U | U | U | G | c | U | U | U | U | g | C | U | U | U | G | A | G | G | -26 | 3 | 8 | c | false | <90% | 6997 | ||
NM_182664 | RASSF5 | 1573 | 1591 | C | U | U | U | G | a | U | U | c | U | U | C | U | U | U | G | A | G | u | -28 | 3 | 9 | bc | false | <90% | 3521 | ||
NM_182665 | RASSF5 | 1583 | 1601 | C | U | U | U | G | a | U | U | c | U | U | C | U | U | U | G | A | G | u | -28 | 3 | 9 | bc | false | <90% | 3531 | ||
NM_182663 | RASSF5 | 1689 | 1707 | C | U | U | U | G | a | U | U | c | U | U | C | U | U | U | G | A | G | u | -28 | 3 | 9 | bc | false | <90% | 3637 | ||
NM_020964 | KIAA1632 | 9505 | 9523 | u | U | U | U | G | u | g | U | U | U | U | C | U | U | U | G | A | G | G | -31 | 3 | 12 | bc | false | <90% | 12715 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2687
View matched accessions
3 prime seed match details
Immunostimulatory motif search results
UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
No Immunostimulatory motif found (UGUGU).
GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).
Settings used for search
Scores were calculated using scoring scheme SS1
Using AVG scoring mode.
Hit scores
Parameter | Spec. Score cut-off | Colour | Comment |
Hit to same gene | Colour | Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit. | |
High scoring hit | ≥80 | Colour | Hits are very likely to cause an off-target effect |
Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
Cut-off | Colour |
Match | Colour |
Wobble base pairs (G-U) | Colour |
Critical bases (none) | Colour |
0.6 bits | Colour |
0.4 bits | Colour |
0.2 bits | Colour |
SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).
Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer