Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
20 hits were found for GUCAUCAGACCAGCAACCC (9 guide strand hits and 11 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_001033554 | SPECC1 | 1056 | 1074 | a | U | u | A | U | C | A | G | A | C | C | A | G | C | A | A | C | a | a | 70 | 4 | 14 | c | false | <90% | 2536 | ||
| NM_152904 | SPECC1 | 1242 | 1260 | a | U | u | A | U | C | A | G | A | C | C | A | G | C | A | A | C | a | a | 70 | 4 | 14 | c | false | <90% | 2714 | ||
| NM_001033555 | SPECC1 | 1056 | 1074 | a | U | u | A | U | C | A | G | A | C | C | A | G | C | A | A | C | a | a | 70 | 4 | 14 | c | false | <90% | 3762 | ||
| NM_001033553 | SPECC1 | 1242 | 1260 | a | U | u | A | U | C | A | G | A | C | C | A | G | C | A | A | C | a | a | 70 | 4 | 14 | c | false | <90% | 3948 | ||
| NR_002832 | BDNFOS | 831 | 849 | c | U | C | u | U | C | A | G | A | C | C | A | G | C | A | A | C | C | g | 56 | 3 | 14 | bc | false | <90% | 2364 | ||
| NM_017554 | PARP14 | 325 | 343 | a | c | C | A | U | C | A | G | A | C | C | A | G | C | A | g | C | C | a | 55 | 4 | 13 | c | false | <90% | 6903 | ||
| NM_005826 | HNRPR | 1844 | 1862 | G | U | C | g | U | C | A | G | A | C | C | A | a | C | A | A | C | C | a | 47 | 3 | 8 | false | <90% | 2663 | |||
| NM_003281 | TNNI1 | 2275 | 2293 | G | U | u | A | U | C | A | G | A | g | C | A | G | C | A | A | C | C | C | -2 | 2 | 9 | bc | false | <90% | 6162 | ||
| NM_032221 | CHD6 | 5692 | 5710 | G | U | C | A | U | C | A | G | A | u | C | A | G | C | A | A | u | u | a | -13 | 4 | 9 | c | false | <90% | 10389 | ||
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_181504 | PIK3R1 | 4704 | 4722 | a | G | G | g | a | G | C | U | G | G | U | C | U | G | A | U | G | A | C | 9 | 3 | 14 | bc | false | <90% | 5663 | ||
| NM_181524 | PIK3R1 | 4864 | 4882 | a | G | G | g | a | G | C | U | G | G | U | C | U | G | A | U | G | A | C | 9 | 3 | 14 | bc | false | <90% | 5823 | ||
| NM_181523 | PIK3R1 | 5494 | 5512 | a | G | G | g | a | G | C | U | G | G | U | C | U | G | A | U | G | A | C | 9 | 3 | 14 | bc | false | <90% | 6453 | ||
| NM_148416 | ATXN2L | 1915 | 1933 | a | G | G | U | U | G | a | U | G | G | U | C | U | G | u | U | G | A | C | 6 | 3 | 7 | c | false | <90% | 3758 | ||
| NM_148415 | ATXN2L | 1915 | 1933 | a | G | G | U | U | G | a | U | G | G | U | C | U | G | u | U | G | A | C | 6 | 3 | 7 | c | false | <90% | 3781 | ||
| NM_145714 | ATXN2L | 1915 | 1933 | a | G | G | U | U | G | a | U | G | G | U | C | U | G | u | U | G | A | C | 6 | 3 | 7 | c | false | <90% | 3805 | ||
| NM_148414 | ATXN2L | 1915 | 1933 | a | G | G | U | U | G | a | U | G | G | U | C | U | G | u | U | G | A | C | 6 | 3 | 7 | c | false | <90% | 4000 | ||
| NM_007245 | ATXN2L | 1915 | 1933 | a | G | G | U | U | G | a | U | G | G | U | C | U | G | u | U | G | A | C | 6 | 3 | 7 | c | false | <90% | 4386 | ||
| XR_015342 | FLJ10661 | 1182 | 1200 | u | u | u | U | U | G | C | U | u | G | U | C | U | G | A | U | G | A | C | 6 | 4 | 10 | bc | false | <90% | 1681 | ||
| XR_015555 | FLJ10661 | 2073 | 2091 | u | u | u | U | U | G | C | U | u | G | U | C | U | G | A | U | G | A | C | 6 | 4 | 10 | bc | false | <90% | 2572 | ||
| NM_015113 | ZZEF1 | 1983 | 2001 | u | G | G | U | U | G | C | U | c | a | U | C | U | G | A | U | G | A | C | -44 | 3 | 9 | bc | false | <90% | 11412 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1634
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