Automatic recommendation
Not OK - siRNA is not specific
59 hits were found for UCUGUGACAUUGGAGAGUC (30 guide strand hits and 29 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_016616 | TXNDC3 | 1229 | 1247 | U | C | U | G | U | G | A | C | A | U | U | G | a | A | G | A | G | g | a | 81 | 3 | 12 | false | <90% | 2350 | |||
NM_016610 | TLR8 | 2535 | 2553 | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | U | u | 69 | 3 | 15 | ac | false | <90% | 3468 | ||
NM_138636 | TLR8 | 2398 | 2416 | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | U | u | 69 | 3 | 15 | ac | false | <90% | 4211 | ||
NM_007235 | XPOT | 1915 | 1933 | U | C | U | G | U | G | A | C | A | U | U | G | G | A | G | u | u | c | u | 42 | 4 | 15 | c | false | <90% | 3881 | ||
NM_002111 | HD | 2151 | 2169 | a | a | g | G | U | G | A | C | A | U | U | G | G | A | c | A | G | U | C | 42 | 4 | 11 | c | false | <90% | 13481 | ||
NM_153280 | UBE1 | 686 | 704 | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | g | a | 32 | 3 | 8 | c | false | <90% | 3483 | ||
NM_003334 | UBE1 | 725 | 743 | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | g | a | 32 | 3 | 8 | c | false | <90% | 3504 | ||
NM_001077685 | CTGLF4 | 553 | 571 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 2420 | ||
NM_001077686 | CTGLF5 | 553 | 571 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 2420 | ||
NM_133446 | CTGLF1 | 553 | 571 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 2420 | ||
NM_001077665 | CTGLF3 | 553 | 571 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 2429 | ||
XM_370567 | KIAA1975 | 1217 | 1235 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3182 | ||
XM_937229 | KIAA1975 | 1217 | 1235 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3182 | ||
XM_001127181 | LOC728005 | 1403 | 1421 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3293 | ||
XM_001132582 | LOC729092 | 1404 | 1422 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3295 | ||
XR_016668 | LOC653234 | 1669 | 1687 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3558 | ||
XR_015281 | LOC728127 | 1933 | 1951 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3817 | ||
XR_015233 | LOC642517 | 1933 | 1951 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 3817 | ||
XM_001132574 | LOC729092 | 2595 | 2613 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 4402 | ||
XM_001132585 | LOC729092 | 2526 | 2544 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 4417 | ||
XM_001127197 | LOC728005 | 2566 | 2584 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 4456 | ||
XM_001132588 | LOC729092 | 2595 | 2613 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 4486 | ||
XR_016708 | LOC653259 | 2643 | 2661 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 4536 | ||
XM_001127140 | LOC728005 | 5285 | 5303 | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | a | C | 13 | 3 | 8 | c | false | <90% | 7115 | ||
NM_002649 | PIK3CG | 3851 | 3869 | U | C | U | G | U | G | g | C | A | U | U | G | G | A | G | A | a | U | a | 5 | 3 | 9 | c | false | <90% | 5379 | ||
NM_138732 | NRXN2 | 1826 | 1844 | c | C | U | G | U | G | A | C | c | U | U | u | G | A | G | A | G | U | C | 4 | 3 | 7 | false | <90% | 6390 | |||
NM_015080 | NRXN2 | 1919 | 1937 | c | C | U | G | U | G | A | C | c | U | U | u | G | A | G | A | G | U | C | 4 | 3 | 7 | false | <90% | 6616 | |||
NM_021977 | SLC22A3 | 5154 | 5172 | U | C | U | c | U | G | A | C | c | U | U | G | G | A | G | A | G | U | g | -1 | 3 | 9 | bc | false | <90% | 5624 | ||
XM_932109 | CEP78 | 1456 | 1474 | a | C | U | G | U | G | A | C | A | g | U | a | G | A | G | A | G | U | C | -18 | 3 | 8 | false | <90% | 2304 | |||
XM_943379 | CEP78 | 1456 | 1474 | a | C | U | G | U | G | A | C | A | g | U | a | G | A | G | A | G | U | C | -18 | 3 | 8 | false | <90% | 2304 |
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_005215 | DCC | 1478 | 1496 | u | u | a | U | C | U | C | C | A | A | U | G | U | g | A | C | A | G | A | 47 | 4 | 10 | c | false | <90% | 5690 | ||
NM_001008657 | TCOF1 | 3405 | 3423 | c | A | C | U | u | U | C | C | A | A | U | G | g | C | A | C | A | G | A | 36 | 3 | 7 | false | <90% | 3827 | |||
NM_001846 | COL4A2 | 5733 | 5751 | c | A | C | U | u | U | C | C | A | A | U | G | c | C | A | C | A | G | A | 36 | 3 | 7 | false | <90% | 6264 | |||
XM_939510 | DUB3 | 593 | 611 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 945 | ||
XM_939458 | LOC650373 | 320 | 338 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1068 | ||
XR_017907 | DUB4 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1197 | ||
XR_019571 | LOC652732 | 846 | 864 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1200 | ||
XR_018109 | LOC647334 | 846 | 864 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1200 | ||
XR_016895 | LOC402329 | 846 | 864 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1201 | ||
XR_016952 | LOC392187 | 846 | 864 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1201 | ||
NR_003275 | LOC392196 | 844 | 862 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1438 | ||
XM_373243 | LOC392197 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_938441 | LOC649368 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
NM_201402 | DUB3 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130410 | LOC728369 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130417 | LOC728373 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130428 | LOC728379 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130437 | LOC728386 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130444 | LOC728393 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130452 | LOC728400 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130464 | LOC728405 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_001130476 | LOC728419 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
XM_376305 | DUB3 | 845 | 863 | G | A | u | U | C | U | C | C | g | A | U | G | U | C | A | C | A | G | g | 15 | 3 | 9 | bc | false | <90% | 1593 | ||
NM_015431 | TRIM58 | 1318 | 1336 | c | A | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | 12 | 3 | 12 | bc | false | <90% | 5158 | ||
NM_152536 | FGD5 | 2996 | 3014 | u | c | a | U | C | U | C | C | A | A | a | G | U | C | A | C | A | G | A | 5 | 4 | 8 | c | false | <90% | 5384 | ||
NM_172016 | TRIM39 | 1916 | 1934 | c | u | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | 0 | 4 | 12 | bc | false | <90% | 3545 | ||
NM_021253 | TRIM39 | 2006 | 2024 | c | u | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | 0 | 4 | 12 | bc | false | <90% | 3635 | ||
NM_003637 | ITGA10 | 1078 | 1096 | u | c | u | U | C | U | u | C | A | A | U | G | U | C | A | C | A | G | A | 0 | 4 | 12 | bc | false | <90% | 5189 | ||
XM_001133842 | LOC729446 | 6669 | 6687 | G | A | C | U | C | U | C | C | A | g | U | G | U | C | A | C | g | a | g | -13 | 4 | 9 | c | false | <90% | 7377 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3504
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