Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for ACAGCAGAAUGCUGUGGAU (31 guide strand hits and 8 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 | |||||||||||||
NR_003263 | SDHAP3 | 1678 | 1696 | c | a | c | G | C | A | G | A | A | U | G | C | U | G | U | G | G | A | g | 62 | 4 | 15 | bc | false | <90% | 21323 | ||
NR_003265 | SDHALP2 | 17481 | 17499 | c | a | c | G | C | A | G | A | A | U | G | C | U | G | U | G | G | A | g | 62 | 4 | 15 | bc | false | <90% | 30843 | ||
NR_003264 | SDHALP1 | 16662 | 16680 | c | a | c | G | C | A | G | A | A | U | G | C | U | G | U | G | G | A | g | 62 | 4 | 15 | bc | false | <90% | 30398 | ||
NM_001040060 | SPP1 | 252 | 270 | A | a | A | G | C | A | G | A | A | U | G | C | U | G | U | G | u | c | c | 57 | 4 | 14 | ac | false | <90% | 1560 | ||
NM_015061 | JMJD2C | 2821 | 2839 | A | C | A | G | C | A | G | A | A | U | G | C | U | G | U | c | u | c | U | 47 | 3 | 15 | c | false | <90% | 4674 | ||
NM_001037339 | PDE4B | 607 | 625 | c | a | A | G | C | A | G | A | A | U | G | a | U | G | U | G | G | A | g | 47 | 4 | 9 | false | <90% | 3882 | |||
NM_002600 | PDE4B | 989 | 1007 | c | a | A | G | C | A | G | A | A | U | G | a | U | G | U | G | G | A | g | 47 | 4 | 9 | false | <90% | 4264 | |||
NM_001037340 | PDE4B | 998 | 1016 | c | a | A | G | C | A | G | A | A | U | G | a | U | G | U | G | G | A | g | 47 | 4 | 9 | false | <90% | 4273 | |||
NM_001037341 | PDE4B | 1034 | 1052 | c | a | A | G | C | A | G | A | A | U | G | a | U | G | U | G | G | A | g | 47 | 4 | 9 | false | <90% | 4309 | |||
XM_212241 | DKFZp434M131 | 3335 | 3353 | A | C | A | G | C | A | G | A | A | U | G | C | U | G | a | G | c | u | a | 44 | 4 | 14 | c | false | <90% | 3606 | ||
NM_015662 | IFT172 | 2160 | 2178 | g | g | A | a | C | A | G | A | A | U | G | C | U | G | U | G | G | A | g | 44 | 4 | 14 | bc | false | <90% | 5430 | ||
NM_207311 | CCDC64 | 1462 | 1480 | A | a | A | G | a | A | G | A | A | U | G | C | U | G | U | G | G | A | g | 32 | 3 | 13 | bc | false | <90% | 3081 | ||
NM_207303 | ATRNL1 | 1604 | 1622 | u | C | A | G | C | A | G | u | A | U | G | C | U | G | U | G | G | A | g | 30 | 3 | 10 | bc | false | <90% | 8732 | ||
NM_012101 | TRIM29 | 1129 | 1147 | g | g | A | G | C | A | G | g | A | U | G | C | U | G | U | G | G | A | c | 19 | 4 | 10 | bc | false | <90% | 3037 | ||
XM_941485 | LOC652147 | 3699 | 3717 | c | a | A | G | C | A | G | g | A | U | G | C | U | G | U | G | G | A | c | 19 | 4 | 10 | bc | false | <90% | 4869 | ||
NM_014014 | ASCC3L1 | 5327 | 5345 | c | a | A | G | C | A | G | g | A | U | G | C | U | G | U | G | G | A | c | 19 | 4 | 10 | bc | false | <90% | 7184 | ||
XM_001131304 | LOC728635 | 554 | 572 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1138 | ||
XM_001133065 | LOC731356 | 554 | 572 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1138 | ||
NM_001082488 | LOC728635 | 665 | 683 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1249 | ||
XM_001133102 | LOC731356 | 665 | 683 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1249 | ||
NM_021004 | DHRS4 | 689 | 707 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1289 | ||
NM_198083 | DHRS4L2 | 785 | 803 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1382 | ||
XM_001133105 | LOC731356 | 981 | 999 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1565 | ||
XM_001133116 | LOC731356 | 1083 | 1101 | u | C | A | G | C | A | G | g | A | U | G | C | U | c | U | G | G | A | U | 16 | 3 | 6 | c | false | <90% | 1667 | ||
XM_370997 | LOC146429 | 1113 | 1131 | A | C | g | G | C | A | G | A | u | U | G | C | U | G | U | G | G | A | c | 15 | 3 | 9 | bc | false | <90% | 1860 | ||
XM_946336 | LOC146429 | 1113 | 1131 | A | C | g | G | C | A | G | A | u | U | G | C | U | G | U | G | G | A | c | 15 | 3 | 9 | bc | false | <90% | 1860 | ||
NM_005651 | TDO2 | 1235 | 1253 | A | C | A | G | C | A | G | A | A | U | a | C | U | G | U | G | a | u | a | 7 | 4 | 10 | c | false | <90% | 1712 | ||
XM_935384 | LOC646483 | 763 | 781 | u | g | A | G | C | A | G | A | A | a | G | C | U | G | U | G | G | A | c | -1 | 4 | 8 | bc | false | <90% | 919 | ||
XM_935998 | LOC641814 | 766 | 784 | u | g | A | G | C | A | G | A | A | a | G | C | U | G | U | G | G | A | c | -1 | 4 | 8 | bc | false | <90% | 922 | ||
NM_033224 | PURB | 3901 | 3919 | A | u | u | G | C | A | G | A | A | g | G | C | U | G | U | G | G | A | U | -13 | 3 | 9 | bc | false | <90% | 9074 | ||
NM_173562 | KCTD20 | 2471 | 2489 | g | C | A | G | C | A | c | A | u | U | G | C | U | G | U | G | G | A | U | -28 | 3 | 10 | bc | false | <90% | 5032 |
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_021574 | BCR | 3271 | 3289 | g | U | C | C | A | C | A | G | C | A | U | U | C | c | G | C | U | G | a | 73 | 3 | 12 | c | false | <90% | 6795 | ||
NM_004327 | BCR | 3271 | 3289 | g | U | C | C | A | C | A | G | C | A | U | U | C | c | G | C | U | G | a | 73 | 3 | 12 | c | false | <90% | 6927 | ||
NM_001031746 | C10orf72 | 594 | 612 | A | U | C | C | u | C | A | G | C | A | U | U | C | U | G | C | U | c | U | 45 | 2 | 12 | c | false | <90% | 2449 | ||
NM_012434 | SLC17A5 | 335 | 353 | g | U | C | C | A | g | A | G | C | A | U | U | C | U | G | C | U | c | c | 27 | 4 | 11 | c | false | <90% | 3292 | ||
NM_014704 | KIAA0562 | 1419 | 1437 | c | U | C | C | u | C | A | G | C | A | U | U | C | U | G | C | a | G | U | 23 | 3 | 11 | c | false | <90% | 3770 | ||
NM_015196 | KIAA0922 | 631 | 649 | g | U | C | C | A | g | A | G | C | A | U | U | C | a | G | C | U | G | U | 15 | 3 | 7 | c | false | <90% | 4980 | ||
NM_015394 | ZNF10 | 136 | 154 | c | U | C | C | u | C | A | G | C | A | c | U | C | U | G | C | U | G | U | -14 | 3 | 8 | c | false | <90% | 4417 | ||
NM_005226 | EDG3 | 1772 | 1790 | A | U | C | C | A | C | u | G | C | c | U | U | C | U | G | C | U | G | c | -54 | 3 | 8 | bc | false | <90% | 4221 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3012
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