Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for ACAAGACGCACAACCUUUA (5 guide strand hits and 13 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 | |||||||||||||
| XM_939498 | LOC650412 | 2618 | 2636 | u | C | A | A | G | A | C | G | C | A | C | A | A | C | a | U | U | g | A | 70 | 3 | 13 | c | false | <90% | 12324 | ||
| XM_001125679 | LOC727756 | 257 | 275 | A | C | A | A | G | A | C | a | C | A | C | A | A | C | C | a | U | U | u | 6 | 3 | 7 | c | false | <90% | 1076 | ||
| NM_005359 | SMAD4 | 1868 | 1886 | u | g | c | A | G | A | C | c | C | A | C | A | A | C | C | U | U | U | A | 4 | 4 | 11 | bc | false | <90% | 3220 | ||
| XM_001129206 | KIAA1639 | 2357 | 2375 | A | C | A | A | G | A | g | G | C | A | C | A | A | C | C | U | g | g | c | 2 | 4 | 9 | c | false | <90% | 2781 | ||
| XM_001129220 | KIAA1639 | 5306 | 5324 | A | C | A | A | G | A | g | G | C | A | C | A | A | C | C | U | g | g | c | 2 | 4 | 9 | c | false | <90% | 5337 | ||
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 | |||||||||||||
| XM_945318 | LOC644511 | 325 | 343 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 587 | ||
| XM_934381 | LOC644511 | 325 | 343 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 587 | ||
| XM_941634 | LOC644511 | 393 | 411 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 676 | ||
| XM_001129044 | LOC387841 | 393 | 411 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 691 | ||
| XM_370681 | LOC387841 | 393 | 411 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 693 | ||
| XR_016947 | LOC441632 | 509 | 527 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 828 | ||
| XR_015367 | LOC731064 | 509 | 527 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 828 | ||
| XR_016232 | LOC284821 | 396 | 414 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 1143 | ||
| XR_019402 | LOC649564 | 398 | 416 | U | c | A | A | G | G | U | U | G | U | G | C | G | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 1145 | ||
| NM_004646 | NPHS1 | 2838 | 2856 | U | A | A | A | G | G | U | U | G | U | G | a | G | U | C | U | g | a | c | 35 | 4 | 11 | false | <90% | 4285 | |||
| NM_152996 | ST6GALNAC3 | 218 | 236 | U | g | c | u | G | G | U | U | G | U | G | C | G | U | C | U | U | G | U | 32 | 3 | 15 | bc | false | <90% | 3207 | ||
| XM_941099 | LOC646951 | 1217 | 1235 | a | A | A | A | G | c | U | U | G | U | G | C | G | U | C | U | U | a | c | 27 | 4 | 11 | c | false | <90% | 1383 | ||
| XM_929916 | LOC646951 | 1217 | 1235 | a | A | A | A | G | c | U | U | G | U | G | C | G | U | C | U | U | a | c | 27 | 4 | 11 | c | false | <90% | 1383 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1342
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