Automatic recommendation
Not OK - siRNA is not specific
65 hits were found for UUCCUCCUUGCUGAGGUUC (17 guide strand hits and 48 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_000560 | CD53 | 440 | 458 | a | U | C | C | U | C | C | U | U | G | C | U | G | A | G | G | U | g | a | 90 | 3 | 16 | ac | false | <90% | 1567 | ||
NM_001040033 | CD53 | 445 | 463 | a | U | C | C | U | C | C | U | U | G | C | U | G | A | G | G | U | g | a | 90 | 3 | 16 | ac | false | <90% | 1572 | ||
NM_001331 | CTNND1 | 339 | 357 | U | U | C | C | U | C | C | U | U | G | C | U | G | u | G | G | U | g | g | 72 | 3 | 13 | c | false | <90% | 6232 | ||
NM_148955 | SNX1 | 1009 | 1027 | U | U | C | C | U | C | C | U | U | G | C | U | G | A | G | c | U | c | C | 71 | 2 | 15 | c | false | <90% | 8026 | ||
NM_152826 | SNX1 | 1204 | 1222 | U | U | C | C | U | C | C | U | U | G | C | U | G | A | G | c | U | c | C | 71 | 2 | 15 | c | false | <90% | 8077 | ||
NM_003099 | SNX1 | 1204 | 1222 | U | U | C | C | U | C | C | U | U | G | C | U | G | A | G | c | U | c | C | 71 | 2 | 15 | c | false | <90% | 8221 | ||
NM_004672 | MAP3K6 | 2439 | 2457 | g | U | C | C | U | C | C | U | U | G | C | U | G | c | G | G | U | c | g | 70 | 4 | 12 | c | false | <90% | 4333 | ||
NM_032189 | ATP11A | 7337 | 7355 | U | g | C | C | U | C | C | U | U | G | C | U | G | A | G | G | g | g | C | 62 | 3 | 14 | ac | false | <90% | 8755 | ||
NM_015205 | ATP11A | 7364 | 7382 | U | g | C | C | U | C | C | U | U | G | C | U | G | A | G | G | g | g | C | 62 | 3 | 14 | ac | false | <90% | 8782 | ||
XM_940627 | LBA1 | 630 | 648 | U | U | a | u | U | C | C | U | U | G | C | U | G | A | G | G | U | U | g | 38 | 3 | 14 | bc | false | <90% | 10815 | ||
XM_047357 | LBA1 | 630 | 648 | U | U | a | u | U | C | C | U | U | G | C | U | G | A | G | G | U | U | g | 38 | 3 | 14 | bc | false | <90% | 10815 | ||
NM_153021 | PLB1 | 1618 | 1636 | a | U | C | C | U | C | C | a | U | G | C | U | G | A | G | G | U | U | C | 35 | 2 | 11 | bc | false | <90% | 5063 | ||
XM_001126010 | KIAA0146 | 2424 | 2442 | U | U | C | C | U | C | C | c | U | G | C | U | G | A | G | G | U | U | u | 32 | 2 | 10 | bc | false | <90% | 3067 | ||
NM_001080394 | KIAA0146 | 2577 | 2595 | U | U | C | C | U | C | C | c | U | G | C | U | G | A | G | G | U | U | u | 32 | 2 | 10 | bc | false | <90% | 3220 | ||
NM_017449 | EPHB2 | 1805 | 1823 | U | U | C | C | U | C | a | U | U | G | C | U | G | u | G | G | U | U | g | 9 | 3 | 6 | c | false | <90% | 4866 | ||
NM_004442 | EPHB2 | 1805 | 1823 | U | U | C | C | U | C | a | U | U | G | C | U | G | u | G | G | U | U | g | 9 | 3 | 6 | c | false | <90% | 4869 | ||
NM_000480 | AMPD3 | 126 | 144 | U | U | C | C | U | C | C | c | U | G | C | U | G | A | G | G | c | g | g | 6 | 4 | 8 | c | false | <90% | 4371 |
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_005154 | USP8 | 1814 | 1832 | a | A | A | C | C | U | C | A | G | C | A | A | a | G | A | G | G | g | g | 79 | 4 | 11 | false | <90% | 4250 | |||
XR_019481 | LOC651191 | 1072 | 1090 | c | A | u | C | C | U | C | A | G | C | A | A | G | G | A | G | G | A | A | 78 | 2 | 16 | bc | false | <90% | 1358 | ||
XR_017587 | LOC645668 | 1072 | 1090 | c | A | u | C | C | U | C | A | G | C | A | A | G | G | A | G | G | A | A | 78 | 2 | 16 | bc | false | <90% | 1358 | ||
NM_003321 | TUFM | 1135 | 1153 | c | A | u | C | C | U | C | A | G | C | A | A | G | G | A | G | G | A | A | 78 | 2 | 16 | bc | false | <90% | 1627 | ||
NM_006772 | SYNGAP1 | 3515 | 3533 | G | A | g | C | C | U | C | A | G | C | A | A | G | G | A | G | G | g | c | 72 | 3 | 14 | c | false | <90% | 6010 | ||
NM_178169 | RASSF3 | 263 | 281 | u | u | A | C | C | U | C | A | G | C | A | A | a | G | A | G | G | A | g | 71 | 4 | 10 | false | <90% | 1337 | |||
XM_499300 | TNRC18 | 377 | 395 | G | A | A | C | C | U | C | A | G | C | A | A | G | G | g | G | G | g | c | 67 | 3 | 14 | c | false | <90% | 2850 | ||
XM_376618 | TNRC18 | 377 | 395 | G | A | A | C | C | U | C | A | G | C | A | A | G | G | g | G | G | g | c | 67 | 3 | 14 | c | false | <90% | 2850 | ||
NM_017738 | C9orf39 | 2599 | 2617 | G | A | A | C | C | U | C | A | G | C | A | A | G | G | A | c | G | g | c | 66 | 3 | 15 | c | false | <90% | 5522 | ||
NM_152259 | C15orf42 | 4764 | 4782 | G | c | c | C | C | U | C | A | G | C | A | A | G | G | A | G | G | A | g | 64 | 3 | 15 | bc | false | <90% | 6688 | ||
NM_004241 | JMJD1C | 3849 | 3867 | u | A | A | C | C | U | C | A | G | C | A | A | a | G | A | G | a | A | A | 64 | 3 | 11 | false | <90% | 8415 | |||
NM_032776 | JMJD1C | 4142 | 4160 | u | A | A | C | C | U | C | A | G | C | A | A | a | G | A | G | a | A | A | 64 | 3 | 11 | false | <90% | 8762 | |||
XM_290527 | USP35 | 1008 | 1026 | G | A | A | C | C | U | C | A | G | C | A | A | u | G | A | u | G | A | c | 58 | 3 | 12 | false | <90% | 4213 | |||
XM_942438 | USP35 | 1008 | 1026 | G | A | A | C | C | U | C | A | G | C | A | A | u | G | A | u | G | A | c | 58 | 3 | 12 | false | <90% | 4213 | |||
XR_016955 | LOC645615 | 294 | 312 | G | u | g | C | C | U | C | A | G | C | A | A | a | G | A | G | G | A | A | 58 | 3 | 9 | false | <90% | 1800 | |||
XR_018878 | LOC645615 | 294 | 312 | G | u | g | C | C | U | C | A | G | C | A | A | a | G | A | G | G | A | A | 58 | 3 | 9 | false | <90% | 1800 | |||
NM_203301 | FBXO33 | 925 | 943 | a | u | A | C | C | U | C | A | G | C | A | A | G | G | u | G | G | A | c | 56 | 4 | 12 | c | false | <90% | 3742 | ||
NM_138709 | DAB2IP | 217 | 235 | G | g | A | C | C | U | C | A | G | C | A | u | G | G | A | G | G | A | A | 54 | 2 | 9 | false | <90% | 3500 | |||
NM_032552 | DAB2IP | 427 | 445 | G | g | A | C | C | U | C | A | G | C | A | u | G | G | A | G | G | A | A | 54 | 2 | 9 | false | <90% | 5472 | |||
NM_173586 | MGC34821 | 637 | 655 | G | A | c | C | C | U | C | A | G | C | A | A | G | G | A | u | G | A | c | 49 | 3 | 12 | c | false | <90% | 1717 | ||
XR_019352 | LOC650252 | 1192 | 1210 | a | c | c | C | C | U | C | A | G | C | A | A | G | G | A | a | G | A | A | 40 | 4 | 12 | c | false | <90% | 1233 | ||
XR_019473 | LOC652073 | 1226 | 1244 | a | c | c | C | C | U | C | A | G | C | A | A | G | G | A | a | G | A | A | 40 | 4 | 12 | c | false | <90% | 1267 | ||
XR_019576 | LOC652749 | 1227 | 1245 | a | c | c | C | C | U | C | A | G | C | A | A | G | G | A | a | G | A | A | 40 | 4 | 12 | c | false | <90% | 1268 | ||
XM_942399 | HPX-2 | 1227 | 1245 | a | c | c | C | C | U | C | A | G | C | A | A | G | G | A | a | G | A | A | 40 | 4 | 12 | c | false | <90% | 1268 | ||
NM_130772 | S100Z | 413 | 431 | c | A | A | g | C | U | C | A | G | C | A | A | G | G | g | G | G | A | A | 36 | 3 | 10 | c | false | <90% | 1047 | ||
NM_014452 | TNFRSF21 | 1271 | 1289 | c | A | A | g | C | U | C | A | G | C | A | A | G | G | g | G | G | A | A | 36 | 3 | 10 | c | false | <90% | 3662 | ||
NM_007130 | ZNF41 | 508 | 526 | G | g | A | C | u | U | C | A | G | C | A | A | G | G | A | G | G | A | g | 32 | 3 | 13 | bc | false | <90% | 3172 | ||
NM_153380 | ZNF41 | 742 | 760 | G | g | A | C | u | U | C | A | G | C | A | A | G | G | A | G | G | A | g | 32 | 3 | 13 | bc | false | <90% | 3406 | ||
NM_013279 | C11orf9 | 113 | 131 | G | u | A | C | a | U | C | A | G | C | A | A | G | G | A | G | G | A | u | 32 | 3 | 13 | bc | false | <90% | 5745 | ||
NM_005479 | FRAT1 | 819 | 837 | a | A | A | C | C | U | C | A | u | C | A | A | G | G | A | G | G | c | c | 30 | 4 | 8 | c | false | <90% | 2653 | ||
NM_000912 | OPRK1 | 4137 | 4155 | u | g | A | C | C | U | C | A | a | C | A | A | G | G | A | G | G | A | c | 21 | 4 | 9 | bc | false | <90% | 4959 | ||
XM_001134164 | ETV5 | 1612 | 1630 | c | c | A | C | C | U | C | A | G | C | g | A | G | G | A | G | G | A | c | 20 | 4 | 8 | c | false | <90% | 3434 | ||
NM_004454 | ETV5 | 1644 | 1662 | c | c | A | C | C | U | C | A | G | C | g | A | G | G | A | G | G | A | c | 20 | 4 | 8 | c | false | <90% | 4071 | ||
NM_006623 | PHGDH | 238 | 256 | G | A | A | C | C | U | u | A | G | C | A | A | a | G | A | G | G | A | g | 18 | 3 | 6 | false | <90% | 1968 | |||
XM_001134298 | LAD1 | 1064 | 1082 | a | A | u | C | C | c | C | A | G | C | A | A | G | G | A | G | G | A | A | 15 | 3 | 13 | bc | false | <90% | 2261 | ||
NM_005558 | LAD1 | 1269 | 1287 | a | A | u | C | C | c | C | A | G | C | A | A | G | G | A | G | G | A | A | 15 | 3 | 13 | bc | false | <90% | 2869 | ||
NM_033308 | ABCA7 | 4137 | 4155 | G | A | A | C | C | U | C | A | c | C | A | A | G | G | A | G | c | A | g | 11 | 3 | 8 | c | false | <90% | 6174 | ||
NM_019112 | ABCA7 | 4667 | 4685 | G | A | A | C | C | U | C | A | c | C | A | A | G | G | A | G | c | A | g | 11 | 3 | 8 | c | false | <90% | 6704 | ||
XM_942162 | LOC649622 | 1544 | 1562 | G | A | u | C | C | U | g | A | G | C | A | A | G | G | A | G | G | A | c | 9 | 3 | 11 | bc | false | <90% | 1877 | ||
XM_945762 | LOC649622 | 1557 | 1575 | G | A | u | C | C | U | g | A | G | C | A | A | G | G | A | G | G | A | c | 9 | 3 | 11 | bc | false | <90% | 1890 | ||
NM_032243 | TXNDC2 | 1523 | 1541 | G | A | u | C | C | U | g | A | G | C | A | A | G | G | A | G | G | A | c | 9 | 3 | 11 | bc | false | <90% | 1893 | ||
NM_181722 | LOC285908 | 4262 | 4280 | G | A | A | C | C | U | C | A | u | C | A | A | G | G | A | G | a | c | u | 8 | 4 | 8 | c | false | <90% | 4429 | ||
NM_000458 | TCF2 | 956 | 974 | G | A | A | C | C | c | C | A | G | C | A | A | G | G | A | a | G | A | g | 5 | 3 | 9 | c | false | <90% | 2816 | ||
NM_006481 | TCF2 | 956 | 974 | G | A | A | C | C | c | C | A | G | C | A | A | G | G | A | a | G | A | g | 5 | 3 | 9 | c | false | <90% | 4192 | ||
NM_000242 | MBL2 | 591 | 609 | G | A | A | u | C | U | C | A | u | C | A | A | G | G | A | G | G | A | A | 3 | 2 | 10 | bc | false | <90% | 3605 | ||
NM_017662 | TRPM6 | 3648 | 3666 | c | u | A | C | C | U | C | A | G | u | A | A | G | G | A | G | G | A | u | -1 | 4 | 8 | bc | false | <90% | 8429 | ||
NM_001389 | DSCAM | 6083 | 6101 | a | A | A | C | C | U | C | A | G | g | A | u | G | G | A | G | G | A | A | -18 | 3 | 8 | false | <90% | 7110 | |||
NM_000545 | TCF1 | 689 | 707 | G | A | A | C | C | c | u | A | G | C | A | A | G | G | A | G | G | A | g | -34 | 3 | 11 | bc | false | <90% | 3241 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3902
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