Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
34 hits were found for GCACAGUUGUCACUGCUUC (11 guide strand hits and 23 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_052845 | MMAB | 1702 | 1720 | u | u | u | C | A | G | U | U | G | U | C | A | C | U | G | C | U | g | C | 64 | 4 | 14 | c | false | <90% | 4154 | ||
NM_144671 | FAM109A | 2568 | 2586 | G | a | A | C | A | G | U | U | G | U | C | A | C | U | G | C | c | c | C | 62 | 3 | 14 | ac | false | <90% | 3054 | ||
XM_001133349 | NOTCH2 | 3330 | 3348 | c | u | A | C | A | G | U | U | G | U | C | g | C | U | G | C | U | U | g | 47 | 4 | 9 | false | <90% | 10836 | |||
NM_024408 | NOTCH2 | 3997 | 4015 | c | u | A | C | A | G | U | U | G | U | C | g | C | U | G | C | U | U | g | 47 | 4 | 9 | false | <90% | 11433 | |||
NM_032115 | KCNK16 | 308 | 326 | G | C | A | C | A | G | U | U | G | U | C | A | C | U | a | C | c | a | u | 44 | 4 | 14 | c | false | <90% | 1226 | ||
NM_015353 | KCTD2 | 3467 | 3485 | G | C | A | C | A | G | U | U | G | U | a | A | C | U | G | C | U | c | u | 31 | 3 | 10 | c | false | <90% | 3714 | ||
NM_018046 | AGGF1 | 3489 | 3507 | G | C | A | C | A | G | g | U | G | U | C | A | C | U | G | C | U | c | u | 26 | 3 | 10 | c | false | <90% | 4480 | ||
NM_001037293 | PALM2 | 7100 | 7118 | G | C | A | C | A | G | U | U | G | g | C | A | u | U | G | C | U | U | g | 1 | 3 | 9 | false | <90% | 9261 | |||
NM_053016 | PALM2 | 7202 | 7220 | G | C | A | C | A | G | U | U | G | g | C | A | u | U | G | C | U | U | g | 1 | 3 | 9 | false | <90% | 9363 | |||
NM_024627 | C22orf29 | 5506 | 5524 | c | u | A | C | A | G | U | U | G | g | C | A | C | U | G | C | U | U | a | -1 | 4 | 8 | bc | false | <90% | 6693 | ||
NM_001002909 | GPATCH8 | 783 | 801 | G | C | A | C | A | G | g | U | G | c | C | A | C | U | G | C | U | U | C | -49 | 2 | 9 | bc | false | <90% | 6877 |
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_001010976 | LOC149950 | 425 | 443 | a | c | A | G | C | A | G | U | G | A | C | A | A | C | U | G | U | G | u | 81 | 3 | 16 | abc | false | <90% | 846 | ||
NM_194277 | FRMD7 | 515 | 533 | c | A | u | G | C | A | G | U | G | A | C | A | A | C | U | G | U | a | C | 75 | 3 | 14 | c | false | <90% | 3200 | ||
NM_138285 | NUP35 | 854 | 872 | a | A | A | G | C | A | G | U | G | A | C | A | g | a | U | G | U | G | C | 68 | 3 | 11 | false | <90% | 1649 | |||
XR_015821 | LOC728954 | 594 | 612 | a | A | A | G | C | A | G | U | G | A | C | A | A | C | U | G | a | a | g | 66 | 4 | 15 | ac | false | <90% | 1793 | ||
XR_015798 | LOC731252 | 594 | 612 | a | A | A | G | C | A | G | U | G | A | C | A | A | C | U | G | a | a | g | 66 | 4 | 15 | ac | false | <90% | 1793 | ||
NM_032802 | SPPL2A | 774 | 792 | a | A | A | G | C | A | G | U | G | A | C | A | A | C | U | G | a | a | g | 66 | 4 | 15 | ac | false | <90% | 2010 | ||
NM_000379 | XDH | 329 | 347 | G | u | u | G | C | A | G | U | G | A | C | A | A | C | U | G | U | G | g | 64 | 3 | 15 | bc | false | <90% | 5717 | ||
NM_001042669 | ARHGAP24 | 1874 | 1892 | G | u | A | G | C | A | G | U | G | A | C | A | A | C | a | G | U | G | a | 58 | 3 | 12 | c | false | <90% | 4195 | ||
NM_031305 | ARHGAP24 | 2253 | 2271 | G | u | A | G | C | A | G | U | G | A | C | A | A | C | a | G | U | G | a | 58 | 3 | 12 | c | false | <90% | 4574 | ||
NM_001025616 | ARHGAP24 | 2323 | 2341 | G | u | A | G | C | A | G | U | G | A | C | A | A | C | a | G | U | G | a | 58 | 3 | 12 | c | false | <90% | 4644 | ||
NM_001269 | RCC1 | 1404 | 1422 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2439 | |||
NM_001048195 | RCC1 | 1455 | 1473 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2490 | |||
NM_001048194 | RCC1 | 1497 | 1515 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2532 | |||
NM_001048199 | SNHG3-RCC1 | 1538 | 1556 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2573 | |||
NM_001048198 | SNHG3-RCC1 | 1677 | 1695 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2712 | |||
NM_001048197 | SNHG3-RCC1 | 1681 | 1699 | G | A | A | G | C | A | G | U | G | A | C | A | g | C | U | G | c | a | g | 58 | 4 | 12 | false | <90% | 2716 | |||
NM_015288 | PHF15 | 210 | 228 | u | c | A | G | C | A | G | U | G | A | C | A | A | C | U | c | U | G | a | 55 | 4 | 13 | c | false | <90% | 6463 | ||
NM_015328 | KIAA0828 | 599 | 617 | G | A | A | G | C | A | G | U | G | A | C | u | u | C | U | G | U | G | u | 50 | 3 | 11 | false | <90% | 5052 | |||
NM_005293 | GPR20 | 145 | 163 | a | c | c | G | C | A | G | U | G | A | C | A | A | C | a | G | U | G | C | 42 | 4 | 11 | c | false | <90% | 1528 | ||
NM_005010 | NRCAM | 3550 | 3568 | G | A | A | G | C | A | G | U | a | A | C | A | A | C | U | G | U | G | g | 34 | 2 | 9 | bc | false | <90% | 6296 | ||
NM_001037132 | NRCAM | 3598 | 3616 | G | A | A | G | C | A | G | U | a | A | C | A | A | C | U | G | U | G | g | 34 | 2 | 9 | bc | false | <90% | 6659 | ||
NM_012352 | OR1A2 | 805 | 823 | G | A | u | G | C | A | G | U | G | A | u | A | A | C | U | G | U | G | a | 14 | 3 | 7 | c | false | <90% | 930 | ||
NM_000413 | HSD17B1 | 268 | 286 | G | A | A | G | C | A | u | g | G | A | C | A | A | C | U | G | U | G | a | -33 | 3 | 10 | bc | false | <90% | 2230 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2018
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