Automatic recommendation
Not OK - siRNA is not specific
20 hits were found for GAGCUUUGAGAUUGACAAA (12 guide strand hits and 8 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_005440 | RND2 | 245 | 263 | G | A | G | C | U | U | U | G | A | G | A | U | c | G | A | C | A | A | g | 84 | 2 | 12 | false | <90% | 4169 | |||
| NM_178824 | WDR49 | 1386 | 1404 | c | A | a | C | U | U | U | G | A | G | A | U | U | G | A | C | A | c | u | 70 | 4 | 14 | c | false | <90% | 2672 | ||
| NM_021083 | XK | 727 | 745 | G | A | G | C | U | U | U | G | A | G | A | U | U | G | c | C | A | c | u | 67 | 3 | 14 | c | false | <90% | 5089 | ||
| NM_006498 | LGALS2 | 370 | 388 | G | A | c | C | U | U | U | G | A | G | A | g | U | G | A | C | A | A | A | 46 | 2 | 8 | false | <90% | 543 | |||
| NM_014048 | MKL2 | 1780 | 1798 | c | u | c | C | U | U | U | G | A | G | A | a | U | G | A | C | A | A | A | 33 | 4 | 8 | false | <90% | 8680 | |||
| NM_145185 | MAP2K7 | 329 | 347 | G | A | G | C | a | U | U | G | A | G | A | U | U | G | A | C | c | A | g | 20 | 3 | 11 | c | false | <90% | 3386 | ||
| NM_017709 | FAM46C | 5657 | 5675 | a | A | G | C | U | U | U | G | A | G | u | U | U | G | A | g | A | A | A | 10 | 3 | 9 | c | false | <90% | 5720 | ||
| NM_201267 | NRP2 | 2681 | 2699 | c | A | G | C | U | U | U | G | A | G | g | a | U | G | A | C | A | A | A | 2 | 3 | 9 | false | <90% | 4148 | |||
| NM_018534 | NRP2 | 2681 | 2699 | c | A | G | C | U | U | U | G | A | G | g | a | U | G | A | C | A | A | A | 2 | 3 | 9 | false | <90% | 4163 | |||
| NM_201279 | NRP2 | 2681 | 2699 | c | A | G | C | U | U | U | G | A | G | g | a | U | G | A | C | A | A | A | 2 | 3 | 9 | false | <90% | 6605 | |||
| NM_003872 | NRP2 | 2681 | 2699 | c | A | G | C | U | U | U | G | A | G | g | a | U | G | A | C | A | A | A | 2 | 3 | 9 | false | <90% | 6656 | |||
| NM_201266 | NRP2 | 2681 | 2699 | c | A | G | C | U | U | U | G | A | G | g | a | U | G | A | C | A | A | A | 2 | 3 | 9 | false | <90% | 6671 | |||
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_012204 | GTF3C4 | 1283 | 1301 | c | c | U | G | U | C | A | A | U | C | U | C | A | A | A | G | C | a | g | 78 | 4 | 15 | ac | false | <90% | 3210 | ||
| NM_018941 | CLN8 | 682 | 700 | U | U | g | G | U | C | A | A | U | C | U | C | c | A | A | G | C | U | g | 65 | 3 | 9 | false | <90% | 4817 | |||
| NM_015702 | C2orf25 | 230 | 248 | g | U | U | G | U | C | A | A | U | C | c | C | A | A | A | G | C | c | u | 29 | 4 | 9 | c | false | <90% | 1416 | ||
| NM_006717 | SPIN1 | 3020 | 3038 | c | a | U | G | U | a | A | A | U | C | U | C | A | A | A | G | C | U | g | 18 | 4 | 12 | bc | false | <90% | 4535 | ||
| NM_206595 | ESRRG | 1260 | 1278 | U | U | U | G | U | C | A | c | c | C | U | C | A | A | A | G | C | U | a | -27 | 3 | 9 | bc | false | <90% | 5251 | ||
| NM_001438 | ESRRG | 1262 | 1280 | U | U | U | G | U | C | A | c | c | C | U | C | A | A | A | G | C | U | a | -27 | 3 | 9 | bc | false | <90% | 5253 | ||
| NM_206594 | ESRRG | 1378 | 1396 | U | U | U | G | U | C | A | c | c | C | U | C | A | A | A | G | C | U | a | -27 | 3 | 9 | bc | false | <90% | 5369 | ||
| NM_017656 | ZNF562 | 3027 | 3045 | U | U | U | G | U | C | A | g | U | u | U | C | A | A | A | G | C | U | g | -49 | 3 | 8 | bc | false | <90% | 5539 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2360
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