Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
25 hits were found for GCAGACUCACAGAACUUCA (16 guide strand hits and 9 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_032785 | AGBL4 | 2785 | 2803 | c | C | u | G | A | C | U | C | A | C | A | G | A | A | C | U | U | u | c | 70 | 4 | 14 | c | false | <90% | 3938 | ||
NM_002842 | PTPRH | 207 | 225 | c | u | A | G | A | C | U | C | A | C | A | G | A | A | C | U | c | C | A | 63 | 3 | 14 | ac | false | <90% | 3895 | ||
NM_004654 | USP9Y | 7998 | 8016 | G | C | A | G | A | C | U | C | A | C | A | G | A | A | u | U | c | a | u | 44 | 4 | 14 | c | false | <90% | 10048 | ||
NM_014811 | KIAA0649 | 335 | 353 | c | u | g | G | A | C | U | C | A | C | A | G | A | A | u | U | U | C | A | 42 | 4 | 11 | c | false | <90% | 4959 | ||
XR_016604 | LOC391657 | 454 | 472 | c | u | g | G | A | C | U | C | A | C | A | G | A | A | C | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 2106 | ||
XR_019613 | LOC391657 | 454 | 472 | c | u | g | G | A | C | U | C | A | C | A | G | A | A | C | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 2106 | ||
NM_005700 | DPP3 | 624 | 642 | c | u | g | G | A | C | U | C | A | C | A | G | A | A | C | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 2694 | ||
NM_130443 | DPP3 | 627 | 645 | c | u | g | G | A | C | U | C | A | C | A | G | A | A | C | c | U | C | A | 40 | 4 | 12 | c | false | <90% | 2697 | ||
NM_178011 | LRRTM3 | 1164 | 1182 | u | C | A | G | A | C | U | C | A | a | A | G | A | A | C | U | U | C | A | 15 | 2 | 9 | bc | false | <90% | 5609 | ||
NM_153620 | HOXA1 | 389 | 407 | u | a | u | G | g | C | U | C | A | C | A | G | A | A | C | U | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2358 | ||
NM_005522 | HOXA1 | 389 | 407 | u | a | u | G | g | C | U | C | A | C | A | G | A | A | C | U | U | C | A | 15 | 4 | 14 | bc | false | <90% | 2561 | ||
NM_002842 | PTPRH | 474 | 492 | c | C | A | G | A | C | c | C | A | C | A | G | A | A | C | U | c | C | A | 8 | 3 | 9 | c | false | <90% | 3895 | ||
NM_002842 | PTPRH | 1008 | 1026 | c | C | A | G | A | C | c | C | A | C | A | G | A | A | C | U | c | C | A | 8 | 3 | 9 | c | false | <90% | 3895 | ||
XR_018081 | LOC642074 | 561 | 579 | G | C | A | G | A | C | g | C | A | C | A | G | A | A | C | c | U | C | u | 2 | 3 | 8 | c | false | <90% | 1207 | ||
NM_001018078 | FPGS | 1389 | 1407 | G | C | A | G | A | C | c | a | A | C | A | G | A | A | C | U | U | C | A | -28 | 2 | 11 | bc | false | <90% | 2475 | ||
NM_004957 | FPGS | 1401 | 1419 | G | C | A | G | A | C | c | a | A | C | A | G | A | A | C | U | U | C | A | -28 | 2 | 11 | bc | false | <90% | 2487 |
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_016349 | LOC442459 | 460 | 478 | U | G | A | A | G | U | U | C | U | G | U | G | g | G | U | C | U | G | u | 84 | 2 | 12 | false | <90% | 1855 | |||
XR_018440 | LOC442459 | 460 | 478 | U | G | A | A | G | U | U | C | U | G | U | G | g | G | U | C | U | G | u | 84 | 2 | 12 | false | <90% | 1855 | |||
XR_016467 | LOC127086 | 308 | 326 | U | G | A | A | G | U | g | C | U | G | U | G | A | G | U | C | U | G | u | 28 | 2 | 11 | bc | false | <90% | 1696 | ||
XR_018426 | LOC648627 | 308 | 326 | U | G | A | A | G | U | g | C | U | G | U | G | A | G | U | C | U | G | u | 28 | 2 | 11 | bc | false | <90% | 1696 | ||
NM_002468 | MYD88 | 753 | 771 | U | G | A | A | G | U | U | g | U | G | U | G | u | G | U | C | U | G | a | 22 | 3 | 7 | false | <90% | 2826 | |||
XR_018635 | LOC387703 | 447 | 465 | U | G | A | A | G | U | g | C | U | G | U | G | g | G | U | C | U | G | u | 18 | 3 | 6 | false | <90% | 1882 | |||
XR_016730 | LOC387703 | 447 | 465 | U | G | A | A | G | U | g | C | U | G | U | G | g | G | U | C | U | G | u | 18 | 3 | 6 | false | <90% | 1882 | |||
NM_001469 | XRCC6 | 502 | 520 | U | G | A | A | G | U | g | C | U | G | U | G | g | G | U | C | U | G | u | 18 | 3 | 6 | false | <90% | 2156 | |||
NM_177980 | CDH26 | 1821 | 1839 | U | G | g | A | G | g | U | C | U | G | U | G | A | G | U | C | U | G | C | 17 | 2 | 13 | bc | false | <90% | 3192 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1508
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