Automatic recommendation
Not OK - siRNA is not specific
31 hits were found for GACAGCUGUUCCUCACUCG (18 guide strand hits and 13 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 | |||||||||||||
XM_001134164 | ETV5 | 2283 | 2301 | a | A | C | A | G | C | U | G | U | U | C | C | c | C | A | C | U | C | c | 82 | 3 | 11 | false | <90% | 3434 | |||
NM_004454 | ETV5 | 2314 | 2332 | a | A | C | A | G | C | U | G | U | U | C | C | c | C | A | C | U | C | c | 82 | 3 | 11 | false | <90% | 4071 | |||
NM_000337 | SGCD | 2156 | 2174 | a | A | C | A | G | C | U | G | U | U | C | C | U | C | A | g | U | g | a | 64 | 4 | 14 | c | false | <90% | 8052 | ||
NM_198535 | ZNF699 | 778 | 796 | u | u | C | A | G | C | U | G | U | U | C | C | U | C | A | u | U | C | u | 55 | 4 | 13 | c | false | <90% | 2094 | ||
NM_018056 | TMEM39B | 593 | 611 | u | c | C | u | G | C | U | G | U | U | C | C | U | C | A | C | U | C | G | 49 | 3 | 15 | bc | false | <90% | 1790 | ||
NM_174899 | FBXO36 | 499 | 517 | G | A | C | A | G | C | U | G | U | U | C | u | U | C | A | C | c | a | a | 35 | 4 | 11 | false | <90% | 2832 | |||
NM_182573 | LYPD5 | 1037 | 1055 | c | A | C | A | G | C | U | G | U | U | a | C | U | C | A | C | U | g | a | 29 | 4 | 9 | c | false | <90% | 2118 | ||
NM_001031749 | LYPD5 | 1073 | 1091 | c | A | C | A | G | C | U | G | U | U | a | C | U | C | A | C | U | g | a | 29 | 4 | 9 | c | false | <90% | 2186 | ||
NM_144648 | LRGUK | 2573 | 2591 | u | c | C | A | G | C | U | G | U | U | u | C | U | C | A | C | U | C | a | 20 | 4 | 8 | c | false | <90% | 2700 | ||
NM_001508 | GPR39 | 2585 | 2603 | G | A | C | A | G | C | U | c | U | U | C | C | U | u | A | C | U | C | c | 13 | 3 | 7 | c | false | <90% | 2821 | ||
NM_004731 | SLC16A7 | 485 | 503 | u | A | C | A | G | C | U | G | U | a | C | C | U | C | A | C | U | a | u | 7 | 4 | 8 | c | false | <90% | 3575 | ||
NM_031268 | PDPK1 | 1184 | 1202 | G | A | C | A | G | C | U | G | U | U | g | C | U | C | A | C | a | g | a | 7 | 4 | 10 | c | false | <90% | 6873 | ||
NM_002613 | PDPK1 | 1565 | 1583 | G | A | C | A | G | C | U | G | U | U | g | C | U | C | A | C | a | g | a | 7 | 4 | 10 | c | false | <90% | 7254 | ||
XR_018665 | LOC440568 | 521 | 539 | G | A | C | A | G | C | U | G | U | c | C | C | U | C | A | C | c | u | G | -8 | 3 | 9 | c | false | <90% | 1377 | ||
XR_016997 | LOC440568 | 522 | 540 | G | A | C | A | G | C | U | G | U | c | C | C | U | C | A | C | c | u | G | -8 | 3 | 9 | c | false | <90% | 1378 | ||
XM_001129031 | C1orf117 | 712 | 730 | G | A | C | A | G | C | U | G | U | c | C | C | U | C | A | C | c | u | G | -8 | 3 | 9 | c | false | <90% | 1568 | ||
NM_182623 | FAM131C | 813 | 831 | G | A | C | A | G | C | U | G | U | c | C | C | U | C | A | C | c | u | G | -8 | 3 | 9 | c | false | <90% | 1740 | ||
NM_000545 | TCF1 | 2030 | 2048 | G | A | C | A | G | C | U | G | U | g | C | C | U | C | g | C | U | C | c | -12 | 3 | 9 | c | false | <90% | 3241 |
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_152686 | DNAJC18 | 203 | 221 | a | c | A | G | U | G | A | G | G | A | A | C | A | G | C | U | G | c | u | 78 | 4 | 15 | ac | false | <90% | 3606 | ||
NM_001079669 | TMTC4 | 1555 | 1573 | g | G | A | G | U | G | A | G | G | A | A | C | A | G | C | U | u | U | u | 69 | 3 | 15 | ac | false | <90% | 3561 | ||
NM_032813 | TMTC4 | 1765 | 1783 | g | G | A | G | U | G | A | G | G | A | A | C | A | G | C | U | u | U | u | 69 | 3 | 15 | ac | false | <90% | 3771 | ||
NM_024553 | CCDC132 | 823 | 841 | a | G | A | u | U | G | A | G | G | A | A | C | A | G | C | U | G | g | a | 53 | 4 | 13 | c | false | <90% | 1216 | ||
NM_017667 | CCDC132 | 823 | 841 | a | G | A | u | U | G | A | G | G | A | A | C | A | G | C | U | G | g | a | 53 | 4 | 13 | c | false | <90% | 3625 | ||
NM_001273 | CHD4 | 5545 | 5563 | u | G | A | u | U | G | A | G | G | A | A | C | A | G | C | U | G | c | g | 53 | 4 | 13 | c | false | <90% | 6511 | ||
NM_001025104 | CSN1S1 | 315 | 333 | C | G | A | G | U | G | A | G | G | A | A | C | A | G | u | U | u | U | g | 46 | 3 | 14 | c | false | <90% | 954 | ||
NM_003274 | TMEM1 | 3275 | 3293 | C | u | u | c | U | G | A | G | G | A | A | C | A | G | C | U | G | U | C | 32 | 3 | 15 | bc | false | <90% | 6982 | ||
NM_001040715 | LOC653319 | 1505 | 1523 | u | G | A | G | U | G | A | G | G | A | c | C | u | G | C | U | G | U | C | 26 | 3 | 9 | false | <90% | 3416 | |||
NM_207170 | SYF2 | 642 | 660 | g | G | A | a | a | G | A | G | G | A | A | C | A | G | C | U | G | U | C | 9 | 3 | 14 | bc | false | <90% | 1651 | ||
NM_015484 | SYF2 | 768 | 786 | g | G | A | a | a | G | A | G | G | A | A | C | A | G | C | U | G | U | C | 9 | 3 | 14 | bc | false | <90% | 1777 | ||
NM_015635 | GAPVD1 | 4099 | 4117 | C | G | A | G | U | G | A | a | G | A | A | C | A | G | C | U | u | c | a | 6 | 4 | 8 | c | false | <90% | 6906 | ||
NM_178229 | IQGAP3 | 2851 | 2869 | g | G | A | a | U | a | A | G | G | A | A | C | A | G | C | U | G | U | C | -2 | 3 | 13 | bc | false | <90% | 6069 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1956
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