Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
27 hits were found for AGGUAUUUGAAUUUGCAUU (13 guide strand hits and 14 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_181042 | PBRM1 | 6383 | 6401 | c | u | G | g | A | U | U | U | G | A | A | U | U | U | G | C | A | U | c | 44 | 4 | 14 | bc | false | <90% | 7448 | ||
| NM_018165 | PBRM1 | 6443 | 6461 | c | u | G | g | A | U | U | U | G | A | A | U | U | U | G | C | A | U | c | 44 | 4 | 14 | bc | false | <90% | 7508 | ||
| NM_018313 | PBRM1 | 6480 | 6498 | c | u | G | g | A | U | U | U | G | A | A | U | U | U | G | C | A | U | c | 44 | 4 | 14 | bc | false | <90% | 7545 | ||
| NM_015937 | PIGT | 1978 | 1996 | u | G | G | c | A | U | U | U | G | A | A | U | U | U | G | a | A | U | U | 35 | 3 | 11 | c | false | <90% | 2228 | ||
| NR_002726 | HNRPA3P1 | 1837 | 1855 | g | G | G | U | A | U | U | U | a | A | A | U | U | a | G | C | A | U | U | 18 | 3 | 7 | c | false | <90% | 3043 | ||
| NM_194247 | HNRPA3 | 1909 | 1927 | g | G | G | U | A | U | U | U | a | A | A | U | U | a | G | C | A | U | U | 18 | 3 | 7 | c | false | <90% | 5808 | ||
| NM_014612 | FAM120A | 3780 | 3798 | u | u | a | U | A | U | U | U | G | A | u | U | U | U | G | C | A | U | U | 5 | 4 | 8 | c | false | <90% | 4957 | ||
| NM_032569 | N-PAC | 2484 | 2502 | u | a | G | U | A | U | U | U | G | g | A | U | U | U | G | C | A | U | U | 3 | 3 | 9 | bc | false | <90% | 3732 | ||
| NM_206937 | LIG4 | 3604 | 3622 | u | u | u | U | A | U | g | U | G | A | A | U | U | U | G | C | A | U | U | 0 | 4 | 12 | bc | false | <90% | 3994 | ||
| NM_002312 | LIG4 | 3725 | 3743 | u | u | u | U | A | U | g | U | G | A | A | U | U | U | G | C | A | U | U | 0 | 4 | 12 | bc | false | <90% | 4115 | ||
| NM_001080534 | UNC13C | 4966 | 4984 | g | a | u | U | A | U | a | U | G | A | A | U | U | U | G | C | A | U | U | 0 | 4 | 12 | bc | false | <90% | 8140 | ||
| XM_941380 | UNC13C | 4966 | 4984 | g | a | u | U | A | U | a | U | G | A | A | U | U | U | G | C | A | U | U | 0 | 4 | 12 | bc | false | <90% | 8145 | ||
| NM_001977 | ENPEP | 2842 | 2860 | A | G | G | U | A | U | U | U | G | g | A | U | U | U | G | C | u | c | a | -13 | 4 | 9 | c | false | <90% | 5004 | ||
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_138698 | LOC91431 | 438 | 456 | A | A | g | G | C | A | A | A | U | U | C | A | c | A | U | A | C | C | a | 65 | 3 | 9 | false | <90% | 3113 | |||
| XR_018256 | LOC643067 | 347 | 365 | A | A | U | u | C | A | A | A | U | U | C | A | A | A | U | A | C | a | c | 55 | 3 | 13 | c | false | <90% | 1184 | ||
| XR_016316 | LOC643067 | 347 | 365 | A | A | U | u | C | A | A | A | U | U | C | A | A | A | U | A | C | a | c | 55 | 3 | 13 | c | false | <90% | 1184 | ||
| NM_032132 | HORMAD1 | 452 | 470 | A | A | U | u | C | A | A | A | U | U | C | A | A | A | U | A | C | a | c | 55 | 3 | 13 | c | false | <90% | 1894 | ||
| NM_016578 | RSF1 | 2226 | 2244 | A | A | a | G | C | A | A | A | U | U | C | A | A | A | U | A | u | a | a | 49 | 4 | 13 | c | false | <90% | 5138 | ||
| XM_944502 | FLJ31033 | 4474 | 4492 | A | A | U | G | C | A | A | A | U | U | C | A | A | A | U | g | a | g | U | 47 | 3 | 15 | c | false | <90% | 5925 | ||
| XM_930969 | FLJ31033 | 4474 | 4492 | A | A | U | G | C | A | A | A | U | U | C | A | A | A | U | g | a | g | U | 47 | 3 | 15 | c | false | <90% | 5925 | ||
| XM_944501 | FLJ31033 | 5282 | 5300 | A | A | U | G | C | A | A | A | U | U | C | A | A | A | U | g | a | g | U | 47 | 3 | 15 | c | false | <90% | 6733 | ||
| XM_930988 | FLJ31033 | 5468 | 5486 | A | A | U | G | C | A | A | A | U | U | C | A | A | A | U | g | a | g | U | 47 | 3 | 15 | c | false | <90% | 6919 | ||
| NM_021073 | BMP5 | 348 | 366 | u | u | U | G | C | u | A | A | U | U | C | A | A | A | U | A | C | C | a | 18 | 4 | 12 | bc | false | <90% | 2207 | ||
| NM_005168 | RND3 | 1705 | 1723 | A | A | U | G | C | A | A | A | g | U | C | A | A | A | U | A | a | a | a | 8 | 4 | 8 | c | false | <90% | 2683 | ||
| NM_015718 | NOX3 | 300 | 318 | c | A | U | G | C | u | A | A | U | U | C | u | A | A | U | A | C | C | U | 0 | 3 | 7 | false | <90% | 2044 | |||
| NM_001029999 | MGC26718 | 882 | 900 | A | A | U | G | C | A | A | A | U | g | C | A | A | A | U | A | a | u | U | -8 | 3 | 9 | c | false | <90% | 2087 | ||
| NR_002723 | GABPAP | 117483 | 117501 | A | A | U | G | g | A | A | A | a | U | C | A | A | A | U | A | C | C | a | -16 | 3 | 9 | bc | false | <90% | 194142 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1890
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