Automatic recommendation
Not OK - siRNA is not specific
77 hits were found for AGGAGGAUGAAAUAGAUGG (42 guide strand hits and 35 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_021230 | MLL3 | 10841 | 10859 | g | u | G | A | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 81 | 3 | 16 | abc | false | <90% | 14358 | ||
NM_170606 | MLL3 | 13343 | 13361 | g | u | G | A | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 81 | 3 | 16 | abc | false | <90% | 16872 | ||
XM_939950 | LOC650865 | 1055 | 1073 | A | G | a | A | G | G | A | U | G | A | A | A | g | A | G | A | U | G | a | 65 | 3 | 9 | false | <90% | 1077 | |||
XM_371701 | LOC389217 | 1136 | 1154 | A | G | a | A | G | G | A | U | G | A | A | A | g | A | G | A | U | G | a | 65 | 3 | 9 | false | <90% | 1158 | |||
XM_936897 | KIAA1109 | 11099 | 11117 | A | G | a | A | G | G | A | U | G | A | A | A | a | A | G | A | U | G | a | 65 | 3 | 9 | false | <90% | 15440 | |||
XM_371706 | KIAA1109 | 11234 | 11252 | A | G | a | A | G | G | A | U | G | A | A | A | a | A | G | A | U | G | a | 65 | 3 | 9 | false | <90% | 15575 | |||
XM_937391 | LOC642869 | 980 | 998 | A | G | G | A | G | G | A | U | G | A | A | A | g | A | G | A | a | G | a | 61 | 3 | 12 | false | <90% | 1480 | |||
XM_926257 | LOC642869 | 980 | 998 | A | G | G | A | G | G | A | U | G | A | A | A | g | A | G | A | a | G | a | 61 | 3 | 12 | false | <90% | 1480 | |||
NM_182627 | WDR53 | 1004 | 1022 | A | G | G | A | G | G | A | U | G | A | A | A | c | A | G | A | a | G | a | 61 | 3 | 12 | false | <90% | 1584 | |||
NM_014829 | DDX46 | 587 | 605 | A | G | G | A | G | G | A | U | G | A | A | A | a | A | G | A | a | a | a | 58 | 4 | 12 | false | <90% | 5695 | |||
NM_133444 | ZNF526 | 872 | 890 | A | G | G | A | G | G | A | U | G | A | A | g | a | A | G | A | U | G | a | 50 | 3 | 11 | false | <90% | 3954 | |||
XR_017036 | LOC645771 | 4048 | 4066 | A | G | G | A | G | G | A | U | G | A | A | A | U | A | G | u | g | u | G | 47 | 3 | 15 | c | false | <90% | 4735 | ||
NM_001006614 | WBP5 | 440 | 458 | A | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 46 | 3 | 14 | bc | false | <90% | 1020 | ||
NM_001006613 | WBP5 | 443 | 461 | A | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 46 | 3 | 14 | bc | false | <90% | 1023 | ||
NM_001006612 | WBP5 | 519 | 537 | A | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 46 | 3 | 14 | bc | false | <90% | 1099 | ||
NM_016303 | WBP5 | 522 | 540 | A | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 46 | 3 | 14 | bc | false | <90% | 1102 | ||
NM_018557 | LRP1B | 2966 | 2984 | A | G | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | a | 43 | 2 | 13 | bc | false | <90% | 16557 | ||
NM_175876 | EXOC8 | 1813 | 1831 | A | G | G | A | G | G | A | U | G | A | A | c | U | u | G | A | U | G | a | 41 | 3 | 11 | false | <90% | 5099 | |||
NM_016447 | MPP6 | 1432 | 1450 | g | G | G | A | a | G | A | U | G | A | A | A | a | A | G | A | U | G | G | 36 | 3 | 7 | false | <90% | 2201 | |||
NM_014217 | KCNK2 | 1962 | 1980 | c | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | 30 | 4 | 13 | bc | false | <90% | 3274 | ||
NM_001017425 | KCNK2 | 2086 | 2104 | c | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | 30 | 4 | 13 | bc | false | <90% | 3398 | ||
NM_001017424 | KCNK2 | 2285 | 2303 | c | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | 30 | 4 | 13 | bc | false | <90% | 3597 | ||
NM_006360 | PCID1 | 204 | 222 | A | G | G | A | G | G | A | U | G | A | u | A | a | A | G | A | U | G | u | 23 | 3 | 10 | false | <90% | 1259 | |||
NM_006574 | CSPG5 | 1021 | 1039 | A | G | G | A | G | G | A | U | G | A | c | A | a | A | G | A | U | G | c | 23 | 3 | 10 | false | <90% | 2175 | |||
NM_004728 | DDX21 | 452 | 470 | c | u | G | A | G | G | A | a | G | A | A | A | U | A | G | A | U | G | c | 19 | 4 | 10 | bc | false | <90% | 4153 | ||
NM_001231 | CASQ1 | 1004 | 1022 | g | G | G | A | G | G | A | U | G | A | u | A | U | g | G | A | U | G | G | 17 | 3 | 9 | c | false | <90% | 1886 | ||
NM_152330 | FRMD6 | 1613 | 1631 | A | G | G | A | c | G | A | U | G | A | A | A | U | A | G | A | g | a | u | 17 | 4 | 11 | c | false | <90% | 4842 | ||
NM_001042481 | FRMD6 | 1821 | 1839 | A | G | G | A | c | G | A | U | G | A | A | A | U | A | G | A | g | a | u | 17 | 4 | 11 | c | false | <90% | 5050 | ||
NM_020871 | LRCH2 | 1623 | 1641 | A | G | a | A | G | G | A | U | c | A | A | A | U | A | G | A | U | G | a | 15 | 3 | 9 | bc | false | <90% | 4943 | ||
NM_025135 | FHOD3 | 2577 | 2595 | A | G | G | A | G | G | A | U | G | A | c | A | U | u | G | A | U | G | u | 14 | 3 | 10 | c | false | <90% | 4942 | ||
XM_936559 | LOC647500 | 779 | 797 | A | G | G | A | G | G | A | a | G | A | A | A | U | g | G | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 1110 | ||
XM_001134447 | FAM92A3 | 89 | 107 | A | G | G | A | G | G | A | a | G | A | A | A | U | g | G | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 1228 | ||
XM_001134466 | FAM92A3 | 89 | 107 | A | G | G | A | G | G | A | a | G | A | A | A | U | g | G | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 1228 | ||
NM_005926 | MFAP1 | 591 | 609 | A | G | G | A | G | G | A | g | G | A | A | A | U | u | G | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 2063 | ||
XM_001129593 | LOC729182 | 779 | 797 | A | G | G | A | G | G | A | a | G | A | A | A | U | g | G | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 2298 | ||
NR_002784 | SMEK3P | 1508 | 1526 | A | G | G | A | G | G | A | U | G | A | u | A | U | A | G | c | U | G | G | 12 | 2 | 10 | c | false | <90% | 3133 | ||
NM_181644 | MFSD4 | 2586 | 2604 | A | G | G | A | G | a | A | U | G | A | A | A | U | g | G | A | U | G | u | 12 | 3 | 7 | c | false | <90% | 3343 | ||
NM_003772 | JRKL | 1391 | 1409 | A | G | G | A | G | G | A | g | G | A | A | A | U | A | G | A | a | c | u | 6 | 4 | 8 | c | false | <90% | 2930 | ||
NM_002161 | IARS | 2165 | 2183 | A | G | G | A | G | G | A | a | G | A | A | A | U | A | G | A | a | u | u | 6 | 4 | 8 | c | false | <90% | 4403 | ||
NM_013417 | IARS | 2272 | 2290 | A | G | G | A | G | G | A | a | G | A | A | A | U | A | G | A | a | u | u | 6 | 4 | 8 | c | false | <90% | 4510 | ||
NM_144963 | FAM91A1 | 4441 | 4459 | A | G | G | A | G | G | A | a | G | A | A | A | U | A | G | A | a | c | c | 6 | 4 | 8 | c | false | <90% | 5347 | ||
NM_001365 | DLG4 | 2700 | 2718 | g | G | G | A | G | u | A | U | G | A | g | A | U | A | G | A | U | G | G | -26 | 3 | 8 | c | false | <90% | 3995 |
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_178505 | TMEM26 | 5017 | 5035 | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | C | u | g | 90 | 3 | 16 | ac | false | <90% | 5170 | ||
NM_000350 | ABCA4 | 2404 | 2422 | u | C | A | U | C | U | A | U | U | U | C | A | c | C | C | U | C | u | a | 79 | 4 | 11 | false | <90% | 7326 | |||
NM_001005407 | CACNA1H | 1437 | 1455 | u | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | g | C | U | 74 | 2 | 15 | ac | false | <90% | 8079 | ||
NM_021098 | CACNA1H | 1437 | 1455 | u | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | g | C | U | 74 | 2 | 15 | ac | false | <90% | 8097 | ||
NM_052867 | NALCN | 1915 | 1933 | C | C | A | U | C | U | A | U | U | U | C | A | U | u | C | U | C | u | a | 72 | 3 | 13 | c | false | <90% | 6923 | ||
NM_033067 | DMRTB1 | 1449 | 1467 | C | C | A | U | C | U | A | U | U | U | C | A | g | C | C | U | u | C | U | 66 | 2 | 12 | false | <90% | 1907 | |||
NM_054020 | CATSPER2 | 1167 | 1185 | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | u | u | g | 66 | 4 | 15 | ac | false | <90% | 1942 | ||
NM_172095 | CATSPER2 | 1167 | 1185 | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | u | u | g | 66 | 4 | 15 | ac | false | <90% | 1948 | ||
NM_005985 | SNAI1 | 1390 | 1408 | g | C | A | g | C | U | A | U | U | U | C | A | g | C | C | U | C | C | U | 50 | 3 | 8 | false | <90% | 1708 | |||
NM_005183 | CACNA1F | 2268 | 2286 | g | C | A | U | C | U | A | U | U | U | C | A | U | C | a | U | u | C | U | 49 | 3 | 13 | c | false | <90% | 6080 | ||
NM_001004729 | OR5AN1 | 31 | 49 | u | C | A | c | C | U | A | U | U | U | C | A | U | C | C | U | g | C | U | 37 | 3 | 12 | c | false | <90% | 936 | ||
NM_198397 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 5243 | ||
NM_198376 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7207 | ||
NM_198388 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7450 | ||
NM_198387 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7471 | ||
NM_198382 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7477 | ||
NM_198386 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7492 | ||
NM_198378 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7513 | ||
NM_198384 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7546 | ||
NM_198379 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7588 | ||
NM_198383 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7612 | ||
NM_198380 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7657 | ||
NM_198385 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7690 | ||
NM_198377 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7756 | ||
NM_018896 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7825 | ||
NM_198396 | CACNA1G | 1489 | 1507 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | U | 35 | 2 | 11 | bc | false | <90% | 7834 | ||
NM_001004757 | OR51Q1 | 32 | 50 | g | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | a | c | 28 | 4 | 9 | c | false | <90% | 954 | ||
NM_001003406 | CACNA1I | 1126 | 1144 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | g | C | U | 12 | 3 | 8 | c | false | <90% | 9902 | ||
NM_021096 | CACNA1I | 1126 | 1144 | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | g | C | U | 12 | 3 | 8 | c | false | <90% | 10007 | ||
NM_000720 | CACNA1D | 2366 | 2384 | g | C | A | U | C | U | A | c | U | U | C | A | U | C | a | U | C | C | U | 11 | 3 | 6 | c | false | <90% | 7193 | ||
NM_001005494 | OR6C4 | 167 | 185 | C | C | A | U | g | U | A | U | U | U | C | u | U | C | C | U | C | C | g | 9 | 3 | 6 | false | <90% | 930 | |||
NM_001005490 | OR6C74 | 167 | 185 | C | C | A | U | g | U | A | U | U | U | C | u | U | C | C | U | C | C | g | 9 | 3 | 6 | false | <90% | 939 | |||
NM_058241 | CCNT2 | 1964 | 1982 | u | C | A | U | C | U | A | g | U | U | C | u | U | C | C | U | C | C | U | 2 | 3 | 7 | false | <90% | 4614 | |||
NM_152500 | CCDC17 | 11 | 29 | a | u | g | U | C | U | c | U | U | U | C | A | U | C | C | U | C | C | U | 0 | 4 | 12 | bc | false | <90% | 1914 | ||
NM_018306 | TMEM40 | 313 | 331 | u | C | A | U | C | U | u | c | U | U | C | A | U | C | C | U | C | C | U | -30 | 3 | 11 | bc | false | <90% | 1710 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3515
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