Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
58 hits were found for GCUCUGUGACAUUGGAGAG (41 guide strand hits and 17 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_007235 | XPOT | 1913 | 1931 | c | a | U | C | U | G | U | G | A | C | A | U | U | G | G | A | G | u | u | 78 | 4 | 15 | ac | false | <90% | 3881 | ||
NM_016616 | TXNDC3 | 1227 | 1245 | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | A | G | A | G | 75 | 1 | 14 | c | false | <90% | 2350 | ||
NM_003275 | TMOD1 | 415 | 433 | a | C | U | C | U | G | U | G | A | C | A | U | U | G | c | A | G | c | G | 70 | 3 | 13 | c | false | <90% | 2664 | ||
NM_016610 | TLR8 | 2533 | 2551 | c | a | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | 62 | 4 | 15 | bc | false | <90% | 3468 | ||
NM_138636 | TLR8 | 2396 | 2414 | c | a | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | u | 62 | 4 | 15 | bc | false | <90% | 4211 | ||
NM_002581 | PAPPA | 2441 | 2459 | a | C | U | C | U | G | U | G | A | C | A | c | U | G | G | A | G | u | G | 61 | 3 | 10 | false | <90% | 11025 | |||
XR_017424 | RPL23AP9 | 350 | 368 | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | u | G | c | G | 46 | 3 | 14 | c | false | <90% | 494 | ||
XR_019430 | RPL23AP9 | 350 | 368 | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | u | G | c | G | 46 | 3 | 14 | c | false | <90% | 494 | ||
XM_933869 | LOC23117 | 1044 | 1062 | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | G | 39 | 2 | 12 | c | false | <90% | 4880 | ||
XM_001134445 | LOC339047 | 742 | 760 | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | a | 34 | 3 | 12 | c | false | <90% | 3655 | ||
XR_016512 | LOC642778 | 755 | 773 | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | a | 34 | 3 | 12 | c | false | <90% | 3666 | ||
XR_016550 | LOC642799 | 755 | 773 | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | a | 34 | 3 | 12 | c | false | <90% | 3666 | ||
NM_153280 | UBE1 | 684 | 702 | c | u | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | 25 | 3 | 8 | c | false | <90% | 3483 | ||
NM_003334 | UBE1 | 723 | 741 | c | u | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | G | 25 | 3 | 8 | c | false | <90% | 3504 | ||
NM_001008704 | C6orf1 | 381 | 399 | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | c | 21 | 3 | 6 | false | <90% | 932 | |||
NM_001008703 | C6orf1 | 441 | 459 | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | c | 21 | 3 | 6 | false | <90% | 992 | |||
NM_178508 | C6orf1 | 693 | 711 | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | c | 21 | 3 | 6 | false | <90% | 1244 | |||
NM_002649 | PIK3CG | 3849 | 3867 | u | g | U | C | U | G | U | G | g | C | A | U | U | G | G | A | G | A | a | 21 | 4 | 9 | bc | false | <90% | 5379 | ||
NM_001077685 | CTGLF4 | 551 | 569 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 2420 | ||
NM_001077686 | CTGLF5 | 551 | 569 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 2420 | ||
NM_133446 | CTGLF1 | 551 | 569 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 2420 | ||
NM_001077665 | CTGLF3 | 551 | 569 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 2429 | ||
XM_370567 | KIAA1975 | 1215 | 1233 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3182 | ||
XM_937229 | KIAA1975 | 1215 | 1233 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3182 | ||
XM_001127181 | LOC728005 | 1401 | 1419 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3293 | ||
XM_001132582 | LOC729092 | 1402 | 1420 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3295 | ||
XR_016668 | LOC653234 | 1667 | 1685 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3558 | ||
XR_015281 | LOC728127 | 1931 | 1949 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3817 | ||
XR_015233 | LOC642517 | 1931 | 1949 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 3817 | ||
XM_001132574 | LOC729092 | 2593 | 2611 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 4402 | ||
XM_001132585 | LOC729092 | 2524 | 2542 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 4417 | ||
XM_001127197 | LOC728005 | 2564 | 2582 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 4456 | ||
XM_001132588 | LOC729092 | 2593 | 2611 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 4486 | ||
XR_016708 | LOC653259 | 2641 | 2659 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 4536 | ||
XM_001127140 | LOC728005 | 5283 | 5301 | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | u | 20 | 4 | 8 | c | false | <90% | 7115 | ||
XM_001127869 | ITGAX | 872 | 890 | G | C | U | C | U | G | U | G | A | C | c | U | U | G | G | A | c | c | u | 7 | 4 | 10 | c | false | <90% | 2617 | ||
NM_000887 | ITGAX | 2085 | 2103 | G | C | U | C | U | G | U | G | A | C | c | U | U | G | G | A | c | c | u | 7 | 4 | 10 | c | false | <90% | 4666 | ||
NM_015690 | STK36 | 639 | 657 | G | C | U | C | U | G | U | G | A | C | u | U | U | G | G | A | u | u | u | 7 | 4 | 10 | c | false | <90% | 4887 | ||
NM_021977 | SLC22A3 | 5152 | 5170 | a | C | U | C | U | c | U | G | A | C | c | U | U | G | G | A | G | A | G | -26 | 3 | 8 | c | false | <90% | 5624 | ||
NM_001918 | DBT | 237 | 255 | G | C | U | C | U | c | a | G | A | C | A | U | U | G | G | A | G | A | a | -34 | 3 | 11 | bc | false | <90% | 10831 | ||
NM_012224 | NEK1 | 66 | 84 | c | C | U | C | U | G | U | G | A | a | g | U | U | G | G | A | G | A | G | -46 | 3 | 8 | c | false | <90% | 5501 |
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_020231 | KTELC1 | 1023 | 1041 | C | U | C | U | C | C | A | A | U | G | U | C | c | a | A | G | A | G | C | 70 | 2 | 12 | false | <90% | 1973 | |||
NM_152305 | KTELC1 | 1023 | 1041 | C | U | C | U | C | C | A | A | U | G | U | C | c | a | A | G | A | G | C | 70 | 2 | 12 | false | <90% | 3538 | |||
NM_005215 | DCC | 1476 | 1494 | a | U | C | U | C | C | A | A | U | G | U | g | A | C | A | G | A | u | g | 56 | 4 | 10 | false | <90% | 5690 | |||
XM_925853 | LOC653053 | 862 | 880 | u | U | C | U | C | C | A | A | U | G | U | C | A | C | A | c | u | c | C | 45 | 4 | 14 | c | false | <90% | 1317 | ||
NM_172016 | TRIM39 | 1916 | 1934 | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | c | C | 43 | 3 | 12 | c | false | <90% | 3545 | ||
NM_021253 | TRIM39 | 2006 | 2024 | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | c | C | 43 | 3 | 12 | c | false | <90% | 3635 | ||
NM_015431 | TRIM58 | 1318 | 1336 | u | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | u | g | 38 | 4 | 12 | c | false | <90% | 5158 | ||
NM_003637 | ITGA10 | 1076 | 1094 | u | U | C | U | u | C | A | A | U | G | U | C | A | C | A | G | A | u | g | 38 | 4 | 12 | c | false | <90% | 5189 | ||
NM_152536 | FGD5 | 2996 | 3014 | a | U | C | U | C | C | A | A | a | G | U | C | A | C | A | G | A | c | C | 35 | 3 | 8 | c | false | <90% | 5384 | ||
XM_064152 | SRL | 2222 | 2240 | C | U | C | a | u | C | A | A | U | G | U | C | A | C | A | G | A | G | C | 11 | 2 | 14 | bc | false | <90% | 5587 | ||
XM_942054 | SRL | 2222 | 2240 | C | U | C | a | u | C | A | A | U | G | U | C | A | C | A | G | A | G | C | 11 | 2 | 14 | bc | false | <90% | 5587 | ||
XM_001132046 | LOC732164 | 528 | 546 | u | U | C | U | C | C | A | u | U | G | U | C | A | C | A | c | A | G | C | 9 | 3 | 7 | c | false | <90% | 999 | ||
XM_001132359 | LOC730091 | 528 | 546 | u | U | C | U | C | C | A | u | U | G | U | C | A | C | A | c | A | G | C | 9 | 3 | 7 | c | false | <90% | 999 | ||
NM_024569 | MPZL1 | 1800 | 1818 | C | U | C | U | C | C | A | A | U | c | U | C | c | C | A | G | A | G | C | 6 | 2 | 9 | false | <90% | 3795 | |||
NM_003953 | MPZL1 | 1903 | 1921 | C | U | C | U | C | C | A | A | U | c | U | C | c | C | A | G | A | G | C | 6 | 2 | 9 | false | <90% | 3898 | |||
NM_006977 | ZBTB25 | 1167 | 1185 | a | U | C | U | C | C | A | A | a | G | a | C | A | C | A | G | A | G | C | -23 | 3 | 8 | c | false | <90% | 1609 | ||
NM_000544 | TAP2 | 4088 | 4106 | C | U | C | U | C | a | A | A | U | u | U | C | A | C | A | G | A | G | g | -51 | 3 | 8 | bc | false | <90% | 5679 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3293
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