Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
22 hits were found for GCCUUAUUAUCUAUAGAAA (9 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_031950 | FGFBP2 | 999 | 1017 | u | a | C | U | U | A | U | U | A | U | C | U | g | U | A | G | A | A | g | 71 | 4 | 10 | false | <90% | 1199 | |||
| NM_002031 | FRK | 2690 | 2708 | G | a | g | U | U | A | U | U | A | U | C | U | A | U | g | G | A | A | A | 44 | 3 | 11 | c | false | <90% | 2864 | ||
| NM_017755 | NSUN2 | 2744 | 2762 | a | a | a | U | U | A | U | U | A | U | u | U | A | U | A | G | A | A | A | 5 | 4 | 8 | c | false | <90% | 3089 | ||
| XR_017966 | MGC16291 | 2159 | 2177 | a | a | u | U | U | A | a | U | A | U | C | U | A | U | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 2283 | ||
| XR_017865 | MGC16291 | 2159 | 2177 | a | a | u | U | U | A | a | U | A | U | C | U | A | U | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 2283 | ||
| NM_013269 | CLEC2D | 3134 | 3152 | a | a | u | U | U | A | a | U | A | U | C | U | A | U | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 5167 | ||
| NM_001004419 | CLEC2D | 3216 | 3234 | a | a | u | U | U | A | a | U | A | U | C | U | A | U | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 5249 | ||
| NM_001077261 | NCOR2 | 7097 | 7115 | G | C | C | U | U | A | U | g | A | c | C | U | A | U | A | G | A | A | g | -49 | 3 | 8 | bc | false | <90% | 8550 | ||
| NM_006312 | NCOR2 | 7145 | 7163 | G | C | C | U | U | A | U | g | A | c | C | U | A | U | A | G | A | A | g | -49 | 3 | 8 | bc | false | <90% | 8826 | ||
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_013431 | KLRC4 | 651 | 669 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | G | G | a | 70 | 2 | 14 | c | false | <90% | 928 | ||
| NM_007360 | KLRK1 | 106 | 124 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | G | G | a | 70 | 2 | 14 | c | false | <90% | 1770 | ||
| NM_003819 | PABPC4 | 1120 | 1138 | a | a | U | C | U | A | U | A | G | A | U | A | A | c | A | A | G | G | C | 67 | 3 | 11 | c | false | <90% | 3065 | ||
| NM_144659 | TCP10L | 906 | 924 | U | U | U | C | U | A | U | A | G | A | U | A | A | a | A | A | c | u | u | 49 | 4 | 13 | c | false | <90% | 984 | ||
| NM_002260 | KLRC2 | 465 | 483 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | a | G | a | 46 | 3 | 14 | c | false | <90% | 1223 | ||
| NM_213657 | KLRC1 | 567 | 585 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | a | G | a | 46 | 3 | 14 | c | false | <90% | 1332 | ||
| NM_007328 | KLRC1 | 574 | 592 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | a | G | a | 46 | 3 | 14 | c | false | <90% | 1339 | ||
| NM_213658 | KLRC1 | 621 | 639 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | a | G | a | 46 | 3 | 14 | c | false | <90% | 1386 | ||
| NM_002259 | KLRC1 | 628 | 646 | U | U | U | C | U | A | U | A | G | A | U | A | A | U | g | A | a | G | a | 46 | 3 | 14 | c | false | <90% | 1393 | ||
| NM_172160 | KCNAB1 | 1302 | 1320 | g | g | a | C | U | A | U | A | G | A | U | c | A | U | A | A | G | G | C | 33 | 4 | 8 | false | <90% | 3170 | |||
| NM_003471 | KCNAB1 | 1433 | 1451 | g | g | a | C | U | A | U | A | G | A | U | c | A | U | A | A | G | G | C | 33 | 4 | 8 | false | <90% | 3301 | |||
| NM_172159 | KCNAB1 | 2066 | 2084 | g | g | a | C | U | A | U | A | G | A | U | c | A | U | A | A | G | G | C | 33 | 4 | 8 | false | <90% | 4094 | |||
| NM_005671 | UBXD6 | 988 | 1006 | U | U | U | C | U | A | U | A | u | A | U | A | A | U | A | A | u | c | u | 8 | 4 | 8 | c | false | <90% | 1442 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1567
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