Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
73 hits were found for GGAAGAAAACGAUGAAAUA (60 guide strand hits and 13 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 | |||||||||||||
NM_002417 | MKI67 | 3196 | 3214 | a | a | A | A | G | A | A | A | A | C | G | A | U | G | A | A | A | a | g | 78 | 4 | 15 | ac | false | <90% | 12684 | ||
NM_013243 | SCG3 | 1134 | 1152 | G | G | g | A | G | A | A | A | A | C | G | A | U | G | A | A | A | c | A | 77 | 2 | 14 | c | false | <90% | 3371 | ||
XM_929149 | LOC646192 | 458 | 476 | c | c | A | A | G | A | A | A | A | C | G | A | g | G | A | A | A | U | u | 71 | 4 | 10 | false | <90% | 687 | |||
XM_936129 | LOC642051 | 458 | 476 | c | c | A | A | G | A | A | A | A | C | G | A | g | G | A | A | A | U | u | 71 | 4 | 10 | false | <90% | 687 | |||
XM_936090 | LOC642019 | 458 | 476 | c | c | A | A | G | A | A | A | A | C | G | A | g | G | A | A | A | U | u | 71 | 4 | 10 | false | <90% | 690 | |||
XM_940540 | LOC651388 | 458 | 476 | c | c | A | A | G | A | A | A | A | C | G | A | g | G | A | A | A | U | u | 71 | 4 | 10 | false | <90% | 690 | |||
NM_022115 | PRDM15 | 3033 | 3051 | G | G | A | A | G | A | A | A | A | C | G | A | U | G | A | c | A | a | u | 66 | 3 | 15 | c | false | <90% | 4710 | ||
NM_001040424 | PRDM15 | 2037 | 2055 | G | G | A | A | G | A | A | A | A | C | G | A | U | G | A | c | A | a | u | 66 | 3 | 15 | c | false | <90% | 6654 | ||
NM_000845 | GRM8 | 1631 | 1649 | G | G | A | A | G | A | A | A | A | C | G | g | U | G | A | A | A | g | g | 58 | 3 | 11 | false | <90% | 3321 | |||
NM_014774 | KIAA0494 | 1633 | 1651 | a | c | A | A | G | A | A | A | A | C | G | A | U | G | g | A | A | U | u | 56 | 4 | 12 | c | false | <90% | 5766 | ||
NM_001018104 | FAHD1 | 598 | 616 | u | a | A | A | G | A | A | A | A | C | G | A | U | G | A | g | A | U | c | 55 | 4 | 13 | c | false | <90% | 1666 | ||
NM_031208 | FAHD1 | 603 | 621 | u | a | A | A | G | A | A | A | A | C | G | A | U | G | A | g | A | U | c | 55 | 4 | 13 | c | false | <90% | 1705 | ||
NM_018077 | RBM28 | 805 | 823 | G | G | A | A | G | A | A | A | A | C | G | A | U | G | A | u | g | a | u | 42 | 4 | 15 | c | false | <90% | 2809 | ||
NM_000031 | ALAD | 1942 | 1960 | a | G | A | A | G | A | A | A | A | C | a | A | a | G | A | A | A | U | A | 26 | 3 | 9 | false | <90% | 3151 | |||
NM_001003945 | ALAD | 2108 | 2126 | a | G | A | A | G | A | A | A | A | C | a | A | a | G | A | A | A | U | A | 26 | 3 | 9 | false | <90% | 3317 | |||
NM_080591 | PTGS1 | 3317 | 3335 | a | u | A | A | G | g | A | A | A | C | G | A | U | G | A | A | A | U | A | 23 | 3 | 13 | bc | false | <90% | 4982 | ||
NM_000962 | PTGS1 | 3428 | 3446 | a | u | A | A | G | g | A | A | A | C | G | A | U | G | A | A | A | U | A | 23 | 3 | 13 | bc | false | <90% | 5093 | ||
NM_012120 | CD2AP | 1554 | 1572 | u | G | A | A | G | A | A | A | A | g | G | A | U | G | A | A | A | a | A | 12 | 3 | 8 | c | false | <90% | 5425 | ||
NM_014803 | ZNF518 | 1967 | 1985 | u | G | A | A | G | A | A | A | A | g | G | A | U | G | A | A | A | g | A | 12 | 3 | 8 | c | false | <90% | 8296 | ||
NM_001684 | ATP2B4 | 2194 | 2212 | u | G | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | g | A | 12 | 3 | 8 | c | false | <90% | 8733 | ||
NM_001001396 | ATP2B4 | 2194 | 2212 | u | G | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | g | A | 12 | 3 | 8 | c | false | <90% | 8911 | ||
NM_032507 | PGBD1 | 2404 | 2422 | a | G | A | A | G | A | A | A | A | C | a | A | U | G | A | g | A | U | A | 10 | 3 | 9 | c | false | <90% | 3082 | ||
NM_078630 | MSL3L1 | 376 | 394 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 2260 | ||
NM_006800 | MSL3L1 | 403 | 421 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 2305 | ||
NM_078629 | MSL3L1 | 459 | 477 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 2343 | ||
NM_003843 | SCEL | 273 | 291 | a | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 2381 | ||
NM_144777 | SCEL | 273 | 291 | a | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 2441 | ||
NM_078628 | MSL3L1 | 459 | 477 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | a | u | 7 | 4 | 8 | c | false | <90% | 3564 | ||
NM_152750 | FLJ23834 | 1749 | 1767 | u | G | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | a | g | 7 | 4 | 8 | c | false | <90% | 3810 | ||
NM_005645 | TAF13 | 88 | 106 | G | G | A | A | G | A | A | A | A | u | G | A | a | G | A | A | A | U | u | 1 | 3 | 9 | false | <90% | 577 | |||
NM_024416 | OGN | 409 | 427 | G | a | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | g | 0 | 3 | 8 | bc | false | <90% | 2705 | ||
NM_014057 | OGN | 490 | 508 | G | a | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | g | 0 | 3 | 8 | bc | false | <90% | 2786 | ||
NM_033014 | OGN | 772 | 790 | G | a | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | g | 0 | 3 | 8 | bc | false | <90% | 3068 | ||
NM_017868 | TTC12 | 1796 | 1814 | u | a | A | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | u | -1 | 4 | 8 | bc | false | <90% | 2330 | ||
NM_032440 | LCOR | 1736 | 1754 | c | a | A | A | G | A | A | A | A | a | G | A | U | G | A | A | A | U | u | -1 | 4 | 8 | bc | false | <90% | 4851 | ||
NM_014810 | CEP350 | 9514 | 9532 | G | G | c | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | u | -7 | 3 | 8 | bc | false | <90% | 13470 | ||
NM_001023571 | IQCB1 | 552 | 570 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | u | U | A | -8 | 3 | 8 | c | false | <90% | 1915 | ||
NM_001023570 | IQCB1 | 605 | 623 | u | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | u | U | A | -8 | 3 | 8 | c | false | <90% | 2392 | ||
NM_148894 | FAM44A | 8625 | 8643 | G | G | A | A | G | A | A | A | A | a | G | A | U | G | A | A | u | a | u | -13 | 4 | 9 | c | false | <90% | 10542 | ||
NM_144690 | ZNF582 | 2261 | 2279 | a | a | c | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | A | -15 | 4 | 9 | bc | false | <90% | 2297 | ||
NM_032119 | GPR98 | 771 | 789 | a | c | c | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | A | -15 | 4 | 9 | bc | false | <90% | 19333 | ||
NR_003149 | GPR98 | 771 | 789 | a | c | c | A | G | A | A | A | A | u | G | A | U | G | A | A | A | U | A | -15 | 4 | 9 | bc | false | <90% | 19250 | ||
NM_015035 | ZHX3 | 213 | 231 | G | G | A | A | a | A | A | A | A | C | a | A | U | G | A | A | A | U | u | -17 | 3 | 7 | c | false | <90% | 9991 | ||
NM_001025596 | CUGBP1 | 1968 | 1986 | u | G | A | A | G | u | A | A | A | C | a | A | U | G | A | A | A | U | A | -26 | 3 | 8 | c | false | <90% | 2024 | ||
NM_006560 | CUGBP1 | 2101 | 2119 | u | G | A | A | G | u | A | A | A | C | a | A | U | G | A | A | A | U | A | -26 | 3 | 8 | c | false | <90% | 2157 | ||
NM_198700 | CUGBP1 | 2150 | 2168 | u | G | A | A | G | u | A | A | A | C | a | A | U | G | A | A | A | U | A | -26 | 3 | 8 | c | false | <90% | 2206 | ||
NM_000813 | GABRB2 | 2575 | 2593 | c | G | A | A | G | A | u | A | A | C | c | A | U | G | A | A | A | U | A | -29 | 3 | 8 | c | false | <90% | 7295 | ||
NM_021911 | GABRB2 | 2689 | 2707 | c | G | A | A | G | A | u | A | A | C | c | A | U | G | A | A | A | U | A | -29 | 3 | 8 | c | false | <90% | 7409 | ||
XM_940948 | LOC651731 | 555 | 573 | G | G | A | A | G | A | g | A | u | C | G | A | U | G | A | A | A | U | u | -31 | 3 | 9 | bc | false | <90% | 741 | ||
XM_930256 | LOC647216 | 555 | 573 | G | G | A | A | G | A | g | A | u | C | G | A | U | G | A | A | A | U | u | -31 | 3 | 9 | bc | false | <90% | 741 | ||
NR_001558 | C20orf56 | 14104 | 14122 | G | G | A | A | c | A | A | A | A | a | G | A | U | G | A | A | A | U | g | -39 | 3 | 8 | bc | false | <90% | 18090 | ||
NM_001010990 | HERPUD1 | 1096 | 1114 | G | G | A | A | G | A | A | g | A | u | G | A | U | G | A | A | A | U | A | -44 | 2 | 9 | bc | false | <90% | 2123 | ||
NM_001010989 | HERPUD1 | 1168 | 1186 | G | G | A | A | G | A | A | g | A | u | G | A | U | G | A | A | A | U | A | -44 | 2 | 9 | bc | false | <90% | 2195 | ||
NM_014685 | HERPUD1 | 1171 | 1189 | G | G | A | A | G | A | A | g | A | u | G | A | U | G | A | A | A | U | A | -44 | 2 | 9 | bc | false | <90% | 2198 | ||
XM_926455 | LOC653198 | 98 | 116 | u | G | A | A | G | A | A | A | A | g | a | A | U | G | A | A | A | U | A | -46 | 3 | 8 | c | false | <90% | 660 | ||
XM_938879 | LOC653198 | 98 | 116 | u | G | A | A | G | A | A | A | A | g | a | A | U | G | A | A | A | U | A | -46 | 3 | 8 | c | false | <90% | 660 | ||
NM_014233 | UBTF | 531 | 549 | a | G | A | A | G | A | A | g | A | a | G | A | U | G | A | A | A | U | A | -46 | 3 | 9 | bc | false | <90% | 4603 | ||
NM_001076684 | UBTF | 643 | 661 | a | G | A | A | G | A | A | g | A | a | G | A | U | G | A | A | A | U | A | -46 | 3 | 9 | bc | false | <90% | 4604 | ||
NM_001076683 | UBTF | 674 | 692 | a | G | A | A | G | A | A | g | A | a | G | A | U | G | A | A | A | U | A | -46 | 3 | 9 | bc | false | <90% | 4635 | ||
NM_000465 | BARD1 | 2014 | 2032 | G | G | A | A | G | A | A | A | A | g | u | A | U | G | A | A | A | U | u | -49 | 3 | 9 | c | false | <90% | 2530 |
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 | |||||||||||||
XR_016411 | LOC121456 | 1770 | 1788 | c | c | U | U | U | C | A | U | C | G | U | g | U | U | C | U | U | C | a | 47 | 4 | 9 | false | <90% | 2678 | |||
XR_019143 | LOC651737 | 1866 | 1884 | c | c | U | U | U | C | A | U | C | G | U | g | U | U | C | U | U | C | a | 47 | 4 | 9 | false | <90% | 2774 | |||
NM_052837 | SCAMP3 | 870 | 888 | a | A | U | U | U | C | u | U | C | G | U | U | U | U | C | U | U | C | u | 26 | 3 | 11 | bc | false | <90% | 1525 | ||
NM_005698 | SCAMP3 | 948 | 966 | a | A | U | U | U | C | u | U | C | G | U | U | U | U | C | U | U | C | u | 26 | 3 | 11 | bc | false | <90% | 1614 | ||
NM_018046 | AGGF1 | 3064 | 3082 | U | c | U | U | U | C | A | U | u | G | U | U | U | U | C | U | U | C | u | 23 | 3 | 9 | bc | false | <90% | 4480 | ||
NM_138426 | GLCCI1 | 3614 | 3632 | a | c | U | U | U | C | A | U | u | G | U | U | U | U | C | U | U | C | a | 21 | 4 | 9 | bc | false | <90% | 4762 | ||
NR_002947 | TCAM1 | 2567 | 2585 | U | A | U | U | U | C | A | U | g | G | U | U | U | U | C | U | g | a | u | 8 | 4 | 8 | c | false | <90% | 3291 | ||
NM_005183 | CACNA1F | 2271 | 2289 | U | A | U | U | U | C | A | U | C | a | U | U | c | U | C | U | U | C | a | 1 | 3 | 9 | false | <90% | 6080 | |||
XR_016598 | LOC339843 | 2922 | 2940 | U | A | U | U | U | C | A | U | C | c | U | U | U | U | C | U | a | C | u | -11 | 3 | 9 | c | false | <90% | 3275 | ||
XR_018254 | LOC339843 | 2922 | 2940 | U | A | U | U | U | C | A | U | C | c | U | U | U | U | C | U | a | C | u | -11 | 3 | 9 | c | false | <90% | 3275 | ||
NM_002284 | KRT86 | 1758 | 1776 | g | g | a | U | U | C | A | U | C | u | U | U | U | U | C | U | U | C | C | -15 | 4 | 9 | bc | false | <90% | 2091 | ||
NM_023923 | PHACTR4 | 4481 | 4499 | U | A | U | U | U | C | A | U | a | G | a | U | U | U | C | U | U | C | u | -26 | 3 | 8 | c | false | <90% | 6208 | ||
NM_001048183 | PHACTR4 | 4498 | 4516 | U | A | U | U | U | C | A | U | a | G | a | U | U | U | C | U | U | C | u | -26 | 3 | 8 | c | false | <90% | 6225 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3934
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