Automatic recommendation
Not OK - siRNA is not specific
43 hits were found for GGAGGAUGAAAUAGAUGGU (17 guide strand hits and 26 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 | 10842 | 10860 | u | G | A | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | a | 90 | 3 | 16 | ac | false | <90% | 14358 | ||
NM_170606 | MLL3 | 13344 | 13362 | u | G | A | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | a | 90 | 3 | 16 | ac | false | <90% | 16872 | ||
NM_001006614 | WBP5 | 441 | 459 | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | g | 70 | 4 | 14 | c | false | <90% | 1020 | ||
NM_001006613 | WBP5 | 444 | 462 | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | g | 70 | 4 | 14 | c | false | <90% | 1023 | ||
NM_001006612 | WBP5 | 520 | 538 | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | g | 70 | 4 | 14 | c | false | <90% | 1099 | ||
NM_016303 | WBP5 | 523 | 541 | a | G | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | a | g | 70 | 4 | 14 | c | false | <90% | 1102 | ||
NM_002806 | PSMC6 | 713 | 731 | u | a | u | G | G | A | U | G | A | A | A | U | A | G | A | U | G | c | U | 64 | 4 | 14 | c | false | <90% | 1590 | ||
NM_018557 | LRP1B | 2967 | 2985 | G | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | a | c | 55 | 3 | 13 | c | false | <90% | 16557 | ||
NM_014217 | KCNK2 | 1963 | 1981 | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | c | 53 | 4 | 13 | c | false | <90% | 3274 | ||
NM_001017425 | KCNK2 | 2087 | 2105 | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | c | 53 | 4 | 13 | c | false | <90% | 3398 | ||
NM_001017424 | KCNK2 | 2286 | 2304 | c | G | A | a | G | A | U | G | A | A | A | U | A | G | A | U | G | c | c | 53 | 4 | 13 | c | false | <90% | 3597 | ||
NM_004728 | DDX21 | 453 | 471 | u | G | A | G | G | A | a | G | A | A | A | U | A | G | A | U | G | c | U | 29 | 3 | 10 | c | false | <90% | 4153 | ||
NM_016447 | MPP6 | 1433 | 1451 | G | G | A | a | G | A | U | G | A | A | A | a | A | G | A | U | G | G | c | 24 | 3 | 7 | false | <90% | 2201 | |||
NM_024546 | C13orf7 | 356 | 374 | u | G | A | G | G | A | c | G | A | A | A | U | A | G | A | U | u | G | U | 8 | 3 | 9 | c | false | <90% | 3552 | ||
NM_001231 | CASQ1 | 1005 | 1023 | G | G | A | G | G | A | U | G | A | u | A | U | g | G | A | U | G | G | a | 1 | 3 | 9 | false | <90% | 1886 | |||
NR_002784 | SMEK3P | 1509 | 1527 | G | G | A | G | G | A | U | G | A | u | A | U | A | G | c | U | G | G | a | -12 | 3 | 9 | c | false | <90% | 3133 | ||
NM_001365 | DLG4 | 2701 | 2719 | G | G | A | G | u | A | U | G | A | g | A | U | A | G | A | U | G | G | c | -39 | 3 | 8 | bc | 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_001005407 | CACNA1H | 1437 | 1455 | u | u | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | g | C | 83 | 3 | 15 | ac | false | <90% | 8079 | ||
NM_021098 | CACNA1H | 1437 | 1455 | u | u | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | g | C | 83 | 3 | 15 | ac | false | <90% | 8097 | ||
NM_178505 | TMEM26 | 5018 | 5036 | u | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | C | u | 81 | 3 | 16 | abc | false | <90% | 5170 | ||
NM_054020 | CATSPER2 | 1166 | 1184 | A | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | u | u | 80 | 3 | 15 | ac | false | <90% | 1942 | ||
NM_172095 | CATSPER2 | 1166 | 1184 | A | g | C | A | U | C | U | A | U | U | U | C | A | U | C | C | U | u | u | 80 | 3 | 15 | ac | false | <90% | 1948 | ||
NM_033067 | DMRTB1 | 1448 | 1466 | A | C | C | A | U | C | U | A | U | U | U | C | A | g | C | C | U | u | C | 77 | 2 | 13 | c | false | <90% | 1907 | ||
NM_052867 | NALCN | 1916 | 1934 | g | C | C | A | U | C | U | A | U | U | U | C | A | U | u | C | U | C | u | 68 | 3 | 13 | c | false | <90% | 6923 | ||
NM_000350 | ABCA4 | 2405 | 2423 | g | u | C | A | U | C | U | A | U | U | U | C | A | c | C | C | U | C | u | 62 | 4 | 11 | c | false | <90% | 7326 | ||
NM_198397 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 5243 | ||
NM_198376 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7207 | ||
NM_198388 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7450 | ||
NM_198387 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7471 | ||
NM_198382 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7477 | ||
NM_198386 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7492 | ||
NM_198378 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7513 | ||
NM_198384 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7546 | ||
NM_198379 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7588 | ||
NM_198383 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7612 | ||
NM_198380 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7657 | ||
NM_198385 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7690 | ||
NM_198377 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7756 | ||
NM_018896 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7825 | ||
NM_198396 | CACNA1G | 1489 | 1507 | u | u | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | C | 26 | 3 | 10 | bc | false | <90% | 7834 | ||
NM_001005494 | OR6C4 | 168 | 186 | c | C | C | A | U | g | U | A | U | U | U | C | u | U | C | C | U | C | C | 24 | 3 | 6 | false | <90% | 930 | |||
NM_001005490 | OR6C74 | 168 | 186 | c | C | C | A | U | g | U | A | U | U | U | C | u | U | C | C | U | C | C | 24 | 3 | 6 | false | <90% | 939 | |||
NM_001004757 | OR51Q1 | 33 | 51 | g | g | C | A | U | C | U | A | c | U | U | C | A | U | C | C | U | C | a | 21 | 4 | 9 | bc | false | <90% | 954 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2156
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