Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for UGCUUCUUGGUUCAACUCC (6 guide strand hits and 15 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_000061 | BTK | 2155 | 2173 | a | G | C | U | U | C | U | U | G | G | U | U | C | u | A | C | U | u | C | 75 | 3 | 12 | c | false | <90% | 2591 | ||
| NM_016437 | TUBG2 | 1697 | 1715 | c | c | C | U | U | C | U | U | G | G | U | U | C | A | u | C | U | C | C | 61 | 3 | 12 | c | false | <90% | 1830 | ||
| NM_000573 | CR1 | 3918 | 3936 | g | a | C | U | U | C | U | U | G | G | g | U | C | A | A | C | U | C | C | 25 | 3 | 8 | c | false | <90% | 8629 | ||
| NM_000651 | CR1 | 5268 | 5286 | g | a | C | U | U | C | U | U | G | G | g | U | C | A | A | C | U | C | C | 25 | 3 | 8 | c | false | <90% | 9979 | ||
| NM_006328 | RBM14 | 1067 | 1085 | a | G | C | U | U | C | U | U | c | G | c | U | C | A | A | C | U | C | C | -23 | 3 | 8 | c | false | <90% | 2811 | ||
| NM_004279 | PMPCB | 1266 | 1284 | a | G | C | U | U | g | a | U | G | G | U | U | C | A | A | C | U | C | C | -31 | 3 | 12 | bc | false | <90% | 3939 | ||
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_004852 | ONECUT2 | 6097 | 6115 | c | u | A | G | U | U | G | A | A | C | C | A | g | G | A | A | G | C | A | 76 | 3 | 10 | false | <90% | 16142 | |||
| NM_144698 | ANKRD35 | 1523 | 1541 | G | G | A | G | U | U | G | A | A | C | C | A | g | G | A | g | G | C | A | 63 | 2 | 12 | false | <90% | 3363 | |||
| NM_006297 | XRCC1 | 850 | 868 | G | G | A | u | U | U | G | A | A | C | C | A | A | G | A | A | G | a | A | 60 | 2 | 13 | c | false | <90% | 2083 | ||
| NM_001002235 | SERPINA1 | 67 | 85 | u | G | A | G | c | U | G | A | A | C | C | A | A | G | A | A | G | g | A | 43 | 3 | 12 | c | false | <90% | 1588 | ||
| NM_001002236 | SERPINA1 | 67 | 85 | u | G | A | G | c | U | G | A | A | C | C | A | A | G | A | A | G | g | A | 43 | 3 | 12 | c | false | <90% | 1902 | ||
| NM_003615 | SLC4A7 | 3717 | 3735 | a | G | A | a | U | U | G | A | A | C | C | A | A | G | A | g | G | C | A | 35 | 3 | 11 | c | false | <90% | 7757 | ||
| NR_003265 | SDHALP2 | 11338 | 11356 | G | c | c | G | U | g | G | A | A | C | C | A | A | G | A | A | G | C | A | 5 | 3 | 13 | bc | false | <90% | 30843 | ||
| NR_003264 | SDHALP1 | 11311 | 11329 | G | c | u | G | U | g | G | A | A | C | C | A | A | G | A | A | G | C | A | 5 | 3 | 13 | bc | false | <90% | 30398 | ||
| NM_000575 | IL1A | 2121 | 2139 | G | c | A | G | U | U | G | A | A | a | C | A | A | G | A | A | G | C | c | 0 | 3 | 8 | bc | false | <90% | 2943 | ||
| NM_133378 | TTN | 26960 | 26978 | a | G | A | G | g | U | G | A | A | g | C | A | A | G | A | A | G | C | A | -36 | 3 | 9 | bc | false | <90% | 101519 | ||
| NM_178038 | ERC1 | 2125 | 2143 | G | G | A | G | a | U | G | A | A | g | C | A | A | G | A | A | G | C | u | -39 | 3 | 8 | bc | false | <90% | 6070 | ||
| NM_178039 | ERC1 | 2929 | 2947 | G | G | A | G | a | U | G | A | A | g | C | A | A | G | A | A | G | C | u | -39 | 3 | 8 | bc | false | <90% | 6809 | ||
| NM_178040 | ERC1 | 3013 | 3031 | G | G | A | G | a | U | G | A | A | g | C | A | A | G | A | A | G | C | u | -39 | 3 | 8 | bc | false | <90% | 6893 | ||
| NM_015064 | ERC1 | 2974 | 2992 | G | G | A | G | a | U | G | A | A | g | C | A | A | G | A | A | G | C | u | -39 | 3 | 8 | bc | false | <90% | 6919 | ||
| NM_178037 | ERC1 | 3106 | 3124 | G | G | A | G | a | U | G | A | A | g | C | A | A | G | A | A | G | C | u | -39 | 3 | 8 | bc | false | <90% | 7051 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3854
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