Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
66 hits were found for CCAGAAGAAACAACUUCUG (35 guide strand hits and 31 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_014388 | C1orf107 | 133 | 151 | g | C | A | G | A | A | G | A | A | A | C | A | u | C | U | U | C | g | a | 79 | 4 | 11 | false | <90% | 8463 | |||
XR_018808 | LOC441641 | 481 | 499 | C | C | A | G | A | A | G | A | A | A | C | A | A | C | U | c | C | U | G | 73 | 1 | 15 | c | false | <90% | 586 | ||
XR_016792 | LOC441641 | 481 | 499 | C | C | A | G | A | A | G | A | A | A | C | A | A | C | U | c | C | U | G | 73 | 1 | 15 | c | false | <90% | 586 | ||
XM_943648 | LOC389365 | 304 | 322 | u | C | A | G | A | A | G | A | A | A | C | A | A | u | U | U | C | c | a | 70 | 4 | 12 | c | false | <90% | 650 | ||
XM_371797 | LOC389365 | 304 | 322 | u | C | A | G | A | A | G | A | A | A | C | A | A | u | U | U | C | c | a | 70 | 4 | 12 | c | false | <90% | 650 | ||
XM_940627 | LBA1 | 1902 | 1920 | g | C | g | G | A | A | G | A | A | A | C | A | g | C | U | U | C | U | G | 68 | 3 | 9 | false | <90% | 10815 | |||
XM_047357 | LBA1 | 1902 | 1920 | g | C | g | G | A | A | G | A | A | A | C | A | g | C | U | U | C | U | G | 68 | 3 | 9 | false | <90% | 10815 | |||
NM_153182 | MINA | 1822 | 1840 | u | u | g | G | A | A | G | A | A | A | C | A | A | C | U | U | C | U | u | 62 | 4 | 15 | bc | false | <90% | 4893 | ||
NM_032778 | MINA | 2215 | 2233 | u | u | g | G | A | A | G | A | A | A | C | A | A | C | U | U | C | U | u | 62 | 4 | 15 | bc | false | <90% | 5286 | ||
NM_001042533 | MINA | 2218 | 2236 | u | u | g | G | A | A | G | A | A | A | C | A | A | C | U | U | C | U | u | 62 | 4 | 15 | bc | false | <90% | 5289 | ||
NM_032900 | ARHGAP19 | 1190 | 1208 | a | a | A | G | A | A | G | A | A | A | C | A | A | C | U | U | a | U | u | 58 | 4 | 14 | ac | false | <90% | 5478 | ||
NM_020641 | C9orf11 | 415 | 433 | g | a | A | G | A | A | G | A | A | A | C | A | A | C | U | a | C | U | a | 55 | 4 | 13 | c | false | <90% | 1023 | ||
NM_015186 | VPS13A | 5286 | 5304 | C | C | A | G | A | A | G | A | A | A | C | g | g | C | U | U | C | U | u | 50 | 3 | 11 | false | <90% | 10052 | |||
NM_001018038 | VPS13A | 5286 | 5304 | C | C | A | G | A | A | G | A | A | A | C | g | g | C | U | U | C | U | u | 50 | 3 | 11 | false | <90% | 10135 | |||
NM_001018037 | VPS13A | 5169 | 5187 | C | C | A | G | A | A | G | A | A | A | C | g | g | C | U | U | C | U | u | 50 | 3 | 11 | false | <90% | 11145 | |||
NM_033305 | VPS13A | 5286 | 5304 | C | C | A | G | A | A | G | A | A | A | C | g | g | C | U | U | C | U | u | 50 | 3 | 11 | false | <90% | 11262 | |||
XM_499123 | FLJ46284 | 3201 | 3219 | g | a | A | c | A | A | G | A | A | A | C | A | A | C | U | U | C | U | G | 49 | 3 | 15 | bc | false | <90% | 3370 | ||
XM_942952 | FLJ46284 | 3201 | 3219 | g | a | A | c | A | A | G | A | A | A | C | A | A | C | U | U | C | U | G | 49 | 3 | 15 | bc | false | <90% | 3370 | ||
XM_001126100 | LOC730547 | 403 | 421 | a | C | A | G | c | A | G | A | A | A | C | A | A | C | U | U | C | c | u | 38 | 4 | 12 | c | false | <90% | 531 | ||
XM_001126089 | LOC727925 | 403 | 421 | a | C | A | G | c | A | G | A | A | A | C | A | A | C | U | U | C | c | u | 38 | 4 | 12 | c | false | <90% | 531 | ||
NM_017922 | PRPF39 | 2347 | 2365 | a | C | A | G | A | A | G | A | u | A | C | A | A | C | U | U | C | a | u | 30 | 4 | 8 | c | false | <90% | 3179 | ||
NM_005445 | SMC3 | 1599 | 1617 | a | a | A | G | A | A | G | c | A | A | C | A | A | C | U | U | C | U | u | 19 | 4 | 10 | bc | false | <90% | 4131 | ||
NM_000975 | RPL11 | 301 | 319 | u | a | A | G | A | A | a | A | A | A | C | A | A | C | U | U | C | U | c | 15 | 4 | 11 | bc | false | <90% | 609 | ||
XR_018108 | LOC441811 | 3114 | 3132 | u | C | A | G | A | A | c | A | A | A | C | A | A | u | U | U | C | U | G | 12 | 3 | 6 | c | false | <90% | 3795 | ||
XR_017184 | LOC441811 | 3114 | 3132 | u | C | A | G | A | A | c | A | A | A | C | A | A | u | U | U | C | U | G | 12 | 3 | 6 | c | false | <90% | 3795 | ||
XM_931354 | FMN1 | 2415 | 2433 | a | C | A | G | A | A | G | A | A | A | a | A | A | C | c | U | C | U | G | 11 | 3 | 9 | c | false | <90% | 3757 | ||
XM_943337 | FMN1 | 2415 | 2433 | a | C | A | G | A | A | G | A | A | A | a | A | A | C | c | U | C | U | G | 11 | 3 | 9 | c | false | <90% | 3757 | ||
NM_182984 | HTF9C | 2331 | 2349 | C | C | A | G | A | A | u | A | A | A | C | A | A | C | U | g | C | U | c | 2 | 3 | 8 | c | false | <90% | 2793 | ||
NM_022727 | HTF9C | 2455 | 2473 | C | C | A | G | A | A | u | A | A | A | C | A | A | C | U | g | C | U | c | 2 | 3 | 8 | c | false | <90% | 2917 | ||
NM_024523 | GCC1 | 487 | 505 | C | C | A | G | A | A | G | A | A | g | C | A | g | C | U | U | C | U | c | 1 | 3 | 9 | false | <90% | 4152 | |||
XM_001126157 | LOC730512 | 2536 | 2554 | u | C | A | G | A | A | G | c | c | A | C | A | A | C | U | U | C | U | G | -24 | 3 | 10 | bc | false | <90% | 3201 | ||
NR_003135 | CEP170L | 60795 | 60813 | C | C | A | u | A | A | G | A | A | g | C | A | A | C | U | U | C | U | c | -24 | 3 | 8 | bc | false | <90% | 90477 | ||
NM_017628 | KIAA1546 | 5013 | 5031 | C | C | A | u | A | A | G | A | A | g | C | A | A | C | U | U | C | U | u | -24 | 3 | 8 | bc | false | <90% | 9215 | ||
XM_497341 | MUC19 | 21322 | 21340 | u | C | A | G | A | A | G | c | c | A | C | A | A | C | U | U | C | U | G | -24 | 3 | 10 | bc | false | <90% | 21987 | ||
NM_004482 | GALNT3 | 1773 | 1791 | C | C | A | G | A | A | G | g | A | u | C | A | A | C | U | U | C | U | a | -49 | 3 | 8 | bc | false | <90% | 3874 |
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_001128517 | LOC728601 | 467 | 485 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 1603 | ||
XM_001125884 | LOC727836 | 467 | 485 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 1603 | ||
XM_928871 | LOC644038 | 488 | 506 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 1621 | ||
XM_926379 | LOC440839 | 488 | 506 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 1621 | ||
XM_926363 | LOC642313 | 485 | 503 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 1637 | ||
XR_016371 | LOC642617 | 505 | 523 | g | A | G | A | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 71 | 2 | 14 | c | false | <90% | 2124 | ||
NM_006577 | B3GNT2 | 1114 | 1132 | C | A | G | A | A | G | U | U | G | U | U | U | a | c | U | C | U | G | G | 70 | 2 | 12 | false | <90% | 2788 | |||
NM_153605 | DKFZp667G2110 | 4670 | 4688 | a | A | G | A | A | G | U | U | G | U | U | U | C | U | U | C | c | a | a | 66 | 4 | 15 | ac | false | <90% | 4802 | ||
NM_005033 | EXOSC9 | 1074 | 1092 | C | A | G | A | A | G | U | U | G | U | U | U | C | U | a | C | a | c | c | 44 | 4 | 14 | c | false | <90% | 1593 | ||
NM_001034194 | EXOSC9 | 1074 | 1092 | C | A | G | A | A | G | U | U | G | U | U | U | C | U | a | C | a | c | c | 44 | 4 | 14 | c | false | <90% | 1644 | ||
NM_145702 | TIGD1 | 2008 | 2026 | g | A | G | g | A | G | U | U | G | U | U | U | C | U | U | a | U | G | G | 35 | 3 | 11 | c | false | <90% | 2448 | ||
NM_207040 | TCF12 | 3349 | 3367 | C | A | G | A | A | G | U | U | G | U | U | g | C | U | U | a | U | G | a | 35 | 3 | 11 | false | <90% | 3995 | |||
NM_207038 | TCF12 | 4078 | 4096 | C | A | G | A | A | G | U | U | G | U | U | g | C | U | U | a | U | G | a | 35 | 3 | 11 | false | <90% | 4717 | |||
NM_003205 | TCF12 | 4088 | 4106 | C | A | G | A | A | G | U | U | G | U | U | g | C | U | U | a | U | G | a | 35 | 3 | 11 | false | <90% | 4734 | |||
NM_207036 | TCF12 | 4150 | 4168 | C | A | G | A | A | G | U | U | G | U | U | g | C | U | U | a | U | G | a | 35 | 3 | 11 | false | <90% | 4796 | |||
NM_207037 | TCF12 | 4160 | 4178 | C | A | G | A | A | G | U | U | G | U | U | g | C | U | U | a | U | G | a | 35 | 3 | 11 | false | <90% | 4806 | |||
XM_939208 | LOC648149 | 2928 | 2946 | a | u | G | A | A | u | U | U | G | U | U | U | C | U | U | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 2989 | ||
XM_001133680 | LOC648149 | 2928 | 2946 | a | u | G | A | A | u | U | U | G | U | U | U | C | U | U | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 2989 | ||
NM_014691 | AQR | 5024 | 5042 | a | g | G | A | A | c | U | U | G | U | U | U | C | U | U | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 5106 | ||
NM_002222 | ITPR1 | 7149 | 7167 | C | c | c | A | c | G | U | U | G | U | U | U | C | U | U | C | U | G | G | 17 | 3 | 14 | bc | false | <90% | 9517 | ||
NM_015942 | MTERFD1 | 548 | 566 | C | A | G | A | A | G | U | U | G | g | U | U | C | U | U | C | U | a | G | 14 | 2 | 9 | c | false | <90% | 1424 | ||
NM_133378 | TTN | 10216 | 10234 | C | A | G | A | A | G | U | U | G | U | g | U | C | U | c | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 101519 | ||
NM_133437 | TTN | 10078 | 10096 | C | A | G | A | A | G | U | U | G | U | g | U | C | U | c | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 82604 | ||
NM_133432 | TTN | 10078 | 10096 | C | A | G | A | A | G | U | U | G | U | g | U | C | U | c | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 82403 | ||
NM_003319 | TTN | 10078 | 10096 | C | A | G | A | A | G | U | U | G | U | g | U | C | U | c | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 82028 | ||
NM_022841 | RFXDC2 | 4324 | 4342 | C | A | G | A | A | G | U | g | G | U | U | U | C | U | U | C | a | G | u | 9 | 3 | 8 | c | false | <90% | 10268 | ||
NM_133379 | TTN | 10216 | 10234 | C | A | G | A | A | G | U | U | G | U | g | U | C | U | c | C | U | G | a | 9 | 3 | 10 | c | false | <90% | 17306 | ||
NM_002664 | PLEK | 1790 | 1808 | g | g | a | A | A | G | U | U | G | U | g | U | C | U | U | C | U | G | G | 5 | 4 | 8 | c | false | <90% | 2745 | ||
NM_020964 | KIAA1632 | 4037 | 4055 | C | A | G | A | A | G | U | U | c | U | U | c | C | U | U | C | U | G | u | 1 | 3 | 8 | false | <90% | 12715 | |||
NM_003117 | SPAM1 | 1914 | 1932 | C | A | G | A | A | u | U | g | G | U | U | U | C | U | U | C | U | G | a | -30 | 3 | 10 | bc | false | <90% | 2395 | ||
NM_003777 | DNAH11 | 11687 | 11705 | C | A | G | A | A | G | c | U | G | a | U | U | C | U | U | C | U | G | a | -54 | 3 | 8 | bc | false | <90% | 14188 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3131
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