Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
61 hits were found for UAAACCCCAAAGAAAAACC (35 guide strand hits and 26 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_015384 | NIPBL | 2476 | 2494 | g | A | A | A | C | C | C | C | A | A | A | G | c | A | A | A | A | g | g | 79 | 4 | 11 | false | <90% | 8648 | |||
NM_133433 | NIPBL | 2476 | 2494 | g | A | A | A | C | C | C | C | A | A | A | G | c | A | A | A | A | g | g | 79 | 4 | 11 | false | <90% | 9717 | |||
NM_033044 | MACF1 | 2027 | 2045 | a | A | A | A | C | C | C | C | A | A | A | G | c | A | A | A | A | a | g | 79 | 4 | 11 | false | <90% | 19271 | |||
NM_024867 | FLJ23577 | 3968 | 3986 | c | A | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | u | C | 75 | 3 | 14 | c | false | <90% | 5651 | ||
NM_016578 | RSF1 | 3613 | 3631 | a | A | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | a | u | 70 | 4 | 14 | c | false | <90% | 5138 | ||
NM_001032395 | GPR126 | 2591 | 2609 | a | g | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | C | u | 62 | 4 | 15 | bc | false | <90% | 6818 | ||
NM_001032394 | GPR126 | 2591 | 2609 | a | g | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | C | u | 62 | 4 | 15 | bc | false | <90% | 6864 | ||
NM_198569 | GPR126 | 2675 | 2693 | a | g | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | C | u | 62 | 4 | 15 | bc | false | <90% | 6902 | ||
NM_020455 | GPR126 | 2675 | 2693 | a | g | g | A | C | C | C | C | A | A | A | G | A | A | A | A | A | C | u | 62 | 4 | 15 | bc | false | <90% | 6948 | ||
NM_053054 | CATSPER1 | 2607 | 2625 | U | A | A | A | C | C | C | C | A | A | A | a | A | A | A | A | A | a | a | 58 | 3 | 11 | false | <90% | 2630 | |||
NM_004697 | PRPF4 | 2593 | 2611 | g | u | u | A | C | C | C | C | A | A | A | G | c | A | A | A | A | C | C | 56 | 4 | 9 | false | <90% | 2756 | |||
NM_020927 | KIAA1576 | 3761 | 3779 | a | A | A | A | C | C | C | C | A | A | A | a | A | A | A | A | A | a | a | 56 | 4 | 10 | false | <90% | 3784 | |||
NM_053056 | CCND1 | 4281 | 4299 | a | A | A | A | C | C | C | C | A | A | A | a | A | A | A | A | A | a | a | 56 | 4 | 10 | false | <90% | 4304 | |||
NM_001115 | ADCY8 | 5983 | 6001 | a | A | A | A | C | C | C | C | A | A | A | a | A | A | A | A | A | a | a | 56 | 4 | 10 | false | <90% | 6005 | |||
XM_930192 | LOC647166 | 901 | 919 | g | c | A | A | C | C | C | C | A | A | A | G | A | A | A | u | A | C | u | 55 | 4 | 13 | c | false | <90% | 1461 | ||
XM_941669 | LOC652259 | 1036 | 1054 | g | c | A | A | C | C | C | C | A | A | A | G | A | A | A | u | A | C | u | 55 | 4 | 13 | c | false | <90% | 1596 | ||
NM_152660 | FAM76A | 649 | 667 | g | A | A | A | u | C | C | C | A | A | A | G | A | A | A | A | A | g | u | 38 | 4 | 12 | c | false | <90% | 2161 | ||
XR_019020 | LOC645621 | 68 | 86 | g | A | A | A | C | C | C | C | u | A | A | G | A | A | A | A | A | g | C | 35 | 3 | 8 | c | false | <90% | 880 | ||
XR_015548 | LOC729449 | 68 | 86 | g | A | A | A | C | C | C | C | u | A | A | G | A | A | A | A | A | g | C | 35 | 3 | 8 | c | false | <90% | 934 | ||
NM_144664 | FAM76B | 952 | 970 | g | A | A | A | C | u | C | C | A | A | A | G | A | A | A | A | A | g | C | 32 | 3 | 11 | c | false | <90% | 3958 | ||
XM_941347 | LOC645790 | 710 | 728 | g | A | A | A | C | a | C | C | A | A | A | G | A | A | A | A | A | C | a | 29 | 3 | 12 | bc | false | <90% | 1658 | ||
XM_930464 | LOC645790 | 710 | 728 | g | A | A | A | C | a | C | C | A | A | A | G | A | A | A | A | A | C | a | 29 | 3 | 12 | bc | false | <90% | 1658 | ||
NR_003255 | TSIX | 9610 | 9628 | a | A | A | A | C | C | C | C | A | A | u | G | A | A | A | A | A | a | a | 29 | 4 | 9 | c | false | <90% | 36861 | ||
XM_001126246 | LOC730469 | 541 | 559 | g | A | A | A | C | C | a | C | A | A | A | G | A | A | A | A | A | a | a | 24 | 4 | 10 | c | false | <90% | 681 | ||
XM_001133483 | LOC729451 | 541 | 559 | g | A | A | A | C | C | a | C | A | A | A | G | A | A | A | A | A | a | a | 24 | 4 | 10 | c | false | <90% | 681 | ||
NM_002393 | MDM4 | 1868 | 1886 | U | g | A | A | C | C | C | a | A | A | A | G | A | A | A | A | A | C | u | 21 | 3 | 10 | bc | false | <90% | 2554 | ||
NM_004538 | NAP1L3 | 886 | 904 | a | A | A | A | C | C | C | u | A | A | A | G | A | A | A | A | c | C | C | 12 | 3 | 8 | c | false | <90% | 2687 | ||
NM_006269 | RP1 | 4182 | 4200 | U | A | A | A | C | u | C | C | A | A | A | G | A | A | A | A | c | a | C | 10 | 3 | 10 | c | false | <90% | 7100 | ||
NM_003897 | IER3 | 538 | 556 | a | A | A | A | C | C | a | C | A | A | A | G | A | A | A | c | A | C | C | 5 | 3 | 8 | c | false | <90% | 1254 | ||
NM_178858 | SFXN2 | 2264 | 2282 | U | A | A | A | C | a | C | C | A | A | A | G | A | A | A | g | A | C | u | 5 | 3 | 9 | c | false | <90% | 2599 | ||
NM_213603 | ZNF789 | 1052 | 1070 | U | u | c | A | C | a | C | C | A | A | A | G | A | A | A | A | A | C | C | 5 | 3 | 13 | bc | false | <90% | 1654 | ||
NM_018557 | LRP1B | 7 | 25 | a | g | A | A | C | C | C | C | A | g | A | G | A | A | A | A | A | C | g | -1 | 4 | 8 | bc | false | <90% | 16557 | ||
NM_020317 | C1orf63 | 956 | 974 | g | A | A | A | u | C | C | C | A | A | u | G | A | A | A | A | A | C | C | -14 | 3 | 8 | c | false | <90% | 1482 | ||
NM_080390 | TCEAL2 | 627 | 645 | g | A | A | A | g | C | C | a | A | A | A | G | A | A | A | A | A | C | C | -15 | 3 | 11 | bc | false | <90% | 1123 | ||
NM_002084 | GPX3 | 1270 | 1288 | U | A | A | A | C | C | C | a | A | A | g | G | A | A | A | A | A | C | C | -23 | 2 | 8 | c | false | <90% | 1779 |
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_133642 | LARGE | 3392 | 3410 | u | G | U | U | U | U | U | C | U | U | U | G | G | G | G | g | U | U | u | 66 | 3 | 14 | c | false | <90% | 4131 | ||
NM_004737 | LARGE | 3455 | 3473 | u | G | U | U | U | U | U | C | U | U | U | G | G | G | G | g | U | U | u | 66 | 3 | 14 | c | false | <90% | 4194 | ||
NM_020884 | MYH7B | 6200 | 6218 | u | u | c | U | U | U | U | C | U | U | U | G | G | G | G | U | U | c | A | 64 | 4 | 14 | c | false | <90% | 6289 | ||
NM_001004712 | OR4K14 | 89 | 107 | u | a | U | U | U | U | U | C | U | U | U | G | G | G | G | U | c | U | A | 63 | 3 | 14 | ac | false | <90% | 933 | ||
NM_022756 | C1orf149 | 1095 | 1113 | u | u | a | U | U | U | U | C | U | U | U | G | G | G | G | U | U | U | u | 62 | 4 | 15 | bc | false | <90% | 2166 | ||
NM_033542 | SYS1 | 1646 | 1664 | G | a | U | U | U | U | U | C | U | U | U | G | G | G | G | U | g | g | A | 62 | 3 | 14 | ac | false | <90% | 2823 | ||
NM_001042555 | FRS2 | 2880 | 2898 | u | u | U | U | U | U | U | C | U | U | U | G | G | u | G | U | U | U | g | 62 | 4 | 11 | c | false | <90% | 6875 | ||
NM_006654 | FRS2 | 2887 | 2905 | u | u | U | U | U | U | U | C | U | U | U | G | G | u | G | U | U | U | g | 62 | 4 | 11 | c | false | <90% | 6882 | ||
XM_941693 | GPR178 | 1152 | 1170 | G | G | U | U | U | U | U | C | U | U | U | G | u | G | G | U | g | c | u | 58 | 4 | 12 | false | <90% | 5586 | |||
XM_376550 | GPR178 | 1152 | 1170 | G | G | U | U | U | U | U | C | U | U | U | G | u | G | G | U | g | c | u | 58 | 4 | 12 | false | <90% | 5590 | |||
NM_004626 | WNT11 | 1704 | 1722 | G | c | U | U | U | U | U | C | U | U | U | G | G | G | G | U | g | g | c | 57 | 4 | 14 | ac | false | <90% | 1927 | ||
NM_024329 | EFHD2 | 2223 | 2241 | u | u | U | U | U | U | U | C | U | U | U | G | G | G | c | U | U | U | u | 56 | 4 | 12 | c | false | <90% | 2387 | ||
NM_198847 | FAM111A | 1791 | 1809 | a | a | U | U | U | U | U | C | U | U | U | G | G | G | G | c | U | U | c | 55 | 4 | 13 | c | false | <90% | 3623 | ||
NM_022074 | FAM111A | 1830 | 1848 | a | a | U | U | U | U | U | C | U | U | U | G | G | G | G | c | U | U | c | 55 | 4 | 13 | c | false | <90% | 3662 | ||
NM_001008222 | ZDHHC9 | 1572 | 1590 | u | G | U | U | U | U | U | C | U | U | U | G | G | u | c | U | U | U | A | 53 | 3 | 12 | c | false | <90% | 2913 | ||
NM_016032 | ZDHHC9 | 1608 | 1626 | u | G | U | U | U | U | U | C | U | U | U | G | G | u | c | U | U | U | A | 53 | 3 | 12 | c | false | <90% | 2949 | ||
NM_000615 | NCAM1 | 3877 | 3895 | u | G | U | g | U | U | U | C | U | U | U | G | G | G | G | g | U | U | A | 35 | 3 | 11 | c | false | <90% | 5951 | ||
NM_181351 | NCAM1 | 3907 | 3925 | u | G | U | g | U | U | U | C | U | U | U | G | G | G | G | g | U | U | A | 35 | 3 | 11 | c | false | <90% | 5981 | ||
NM_014734 | KIAA0247 | 3427 | 3445 | a | c | U | U | U | U | U | g | U | U | U | G | G | G | G | U | U | U | A | 24 | 3 | 11 | bc | false | <90% | 5402 | ||
NM_018070 | SSBP3 | 1721 | 1739 | G | u | U | U | U | U | U | g | U | U | U | G | G | G | G | U | U | U | u | 21 | 3 | 10 | bc | false | <90% | 2014 | ||
NM_145716 | SSBP3 | 1781 | 1799 | G | u | U | U | U | U | U | g | U | U | U | G | G | G | G | U | U | U | u | 21 | 3 | 10 | bc | false | <90% | 2074 | ||
NM_001009955 | SSBP3 | 1813 | 1831 | G | u | U | U | U | U | U | g | U | U | U | G | G | G | G | U | U | U | u | 21 | 3 | 10 | bc | false | <90% | 2106 | ||
NM_006767 | LZTR1 | 494 | 512 | u | G | U | U | U | g | U | C | U | U | U | G | G | G | G | g | U | U | A | 8 | 3 | 9 | c | false | <90% | 4332 | ||
NM_003028 | SHB | 4849 | 4867 | G | G | U | U | U | U | U | g | U | U | U | u | G | G | G | U | U | U | g | 0 | 3 | 7 | false | <90% | 6021 | |||
NM_014563 | TRAPPC2 | 1799 | 1817 | G | G | U | U | g | a | U | C | U | U | U | G | G | G | G | U | U | U | u | -19 | 3 | 12 | bc | false | <90% | 2691 | ||
NM_001011658 | TRAPPC2 | 1941 | 1959 | G | G | U | U | g | a | U | C | U | U | U | G | G | G | G | U | U | U | u | -19 | 3 | 12 | bc | false | <90% | 2833 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1408
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