Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
52 hits were found for UUCUUUCCCUUCUCUCGUC (20 guide strand hits and 32 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_003220 | TFAP2A | 8 | 26 | c | U | C | U | U | U | C | C | C | U | U | C | U | C | U | C | c | U | C | 74 | 2 | 15 | ac | false | <90% | 3300 | ||
NM_153456 | HS6ST3 | 4492 | 4510 | U | U | C | U | U | U | C | C | C | U | U | C | U | C | U | u | G | g | C | 71 | 2 | 15 | c | false | <90% | 7817 | ||
XM_001125720 | VAC14 | 2023 | 2041 | c | U | C | U | U | U | C | C | C | U | U | C | U | C | U | C | u | c | C | 71 | 3 | 15 | ac | false | <90% | 3996 | ||
NM_005568 | LHX1 | 298 | 316 | c | U | C | U | U | U | C | C | C | U | U | C | U | C | c | C | G | c | g | 65 | 4 | 13 | c | false | <90% | 2283 | ||
NM_201998 | SF1 | 2243 | 2261 | U | c | C | U | U | U | C | C | C | U | U | C | U | C | U | C | c | a | g | 57 | 4 | 14 | ac | false | <90% | 2890 | ||
NM_201995 | SF1 | 2448 | 2466 | U | c | C | U | U | U | C | C | C | U | U | C | U | C | U | C | c | a | g | 57 | 4 | 14 | ac | false | <90% | 3095 | ||
NM_004630 | SF1 | 2880 | 2898 | U | c | C | U | U | U | C | C | C | U | U | C | U | C | U | C | c | a | g | 57 | 4 | 14 | ac | false | <90% | 3527 | ||
XM_932168 | LOC644403 | 863 | 881 | c | a | u | U | U | U | C | C | C | U | U | C | U | C | U | C | u | U | C | 43 | 4 | 13 | c | false | <90% | 1194 | ||
XM_943951 | LOC649842 | 863 | 881 | c | a | u | U | U | U | C | C | C | U | U | C | U | C | U | C | u | U | C | 43 | 4 | 13 | c | false | <90% | 1194 | ||
NM_032947 | MST150 | 325 | 343 | g | U | C | U | c | U | C | C | C | U | U | C | U | C | U | C | G | c | a | 38 | 4 | 12 | c | false | <90% | 1993 | ||
NM_144579 | SFXN5 | 2254 | 2272 | U | U | C | a | U | U | C | C | C | U | U | C | U | C | U | C | a | g | C | 37 | 3 | 12 | c | false | <90% | 4140 | ||
NM_006359 | SLC9A6 | 2567 | 2585 | U | U | C | U | U | U | C | C | C | U | U | u | U | C | U | C | u | g | g | 35 | 4 | 11 | false | <90% | 4646 | |||
NM_001042537 | SLC9A6 | 2663 | 2681 | U | U | C | U | U | U | C | C | C | U | U | u | U | C | U | C | u | g | g | 35 | 4 | 11 | false | <90% | 4742 | |||
NM_005902 | SMAD3 | 2643 | 2661 | U | U | C | U | c | U | C | C | C | U | U | C | U | C | U | C | u | c | C | 22 | 3 | 11 | c | false | <90% | 6256 | ||
NM_170736 | KCNJ15 | 25 | 43 | c | U | C | U | U | U | C | C | u | U | U | C | U | C | U | C | u | U | C | 14 | 3 | 7 | c | false | <90% | 2919 | ||
NM_170741 | KCNJ16 | 3122 | 3140 | U | U | C | U | U | U | C | u | C | U | U | C | U | C | U | C | u | c | C | 11 | 3 | 8 | c | false | <90% | 3926 | ||
NM_018658 | KCNJ16 | 3203 | 3221 | U | U | C | U | U | U | C | u | C | U | U | C | U | C | U | C | u | c | C | 11 | 3 | 8 | c | false | <90% | 4021 | ||
NM_170742 | KCNJ16 | 3210 | 3228 | U | U | C | U | U | U | C | u | C | U | U | C | U | C | U | C | u | c | C | 11 | 3 | 8 | c | false | <90% | 4025 | ||
NM_138809 | CMBL | 144 | 162 | c | U | C | c | c | U | C | C | C | U | U | C | U | C | U | C | G | U | C | 9 | 3 | 14 | bc | false | <90% | 4047 | ||
NM_004267 | CHST2 | 2725 | 2743 | U | U | C | U | U | U | g | C | C | U | U | C | U | C | U | u | G | U | C | 7 | 2 | 8 | c | false | <90% | 3046 |
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_007207 | DUSP10 | 960 | 978 | G | A | a | G | A | G | A | G | A | A | G | G | c | A | A | A | G | A | A | 70 | 2 | 9 | false | <90% | 2619 | |||
NM_013275 | ANKRD11 | 3480 | 3498 | c | A | C | G | A | G | A | G | A | A | G | G | a | g | A | A | G | A | A | 68 | 3 | 11 | false | <90% | 9326 | |||
XR_016397 | LOC643586 | 936 | 954 | u | g | g | G | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 67 | 3 | 16 | bc | false | <90% | 1702 | ||
XR_018713 | LOC649845 | 936 | 954 | u | g | g | G | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 67 | 3 | 16 | bc | false | <90% | 1702 | ||
NM_002654 | PKM2 | 1018 | 1036 | u | g | g | G | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 67 | 3 | 16 | bc | false | <90% | 2479 | ||
NM_182471 | PKM2 | 1018 | 1036 | u | g | g | G | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 67 | 3 | 16 | bc | false | <90% | 2498 | ||
NM_182470 | PKM2 | 1234 | 1252 | u | g | g | G | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 67 | 3 | 16 | bc | false | <90% | 2674 | ||
NM_144982 | CCDC131 | 1746 | 1764 | G | A | a | G | A | G | A | G | A | A | G | G | a | A | A | A | G | A | g | 65 | 3 | 9 | false | <90% | 7158 | |||
NM_001007525 | NWD1 | 395 | 413 | a | A | C | G | A | G | A | G | A | A | G | G | a | A | c | A | G | A | A | 62 | 3 | 11 | false | <90% | 8418 | |||
NM_020347 | LZTFL1 | 2403 | 2421 | G | A | u | G | A | G | A | G | A | A | G | G | G | A | g | A | G | A | A | 55 | 2 | 11 | c | false | <90% | 3398 | ||
NM_014258 | SYCP2 | 1233 | 1251 | c | A | a | a | A | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 41 | 3 | 15 | bc | false | <90% | 5497 | ||
NM_015116 | LRCH1 | 1954 | 1972 | G | A | u | G | A | G | A | G | A | A | G | a | G | A | A | A | G | A | g | 41 | 3 | 8 | false | <90% | 4163 | |||
NM_000486 | AQP2 | 2204 | 2222 | G | A | C | c | A | G | A | G | A | A | G | G | G | A | A | A | u | g | A | 37 | 3 | 12 | c | false | <90% | 4222 | ||
NM_001010877 | ZNF311 | 1123 | 1141 | a | c | u | G | A | G | A | G | A | A | G | a | G | A | A | A | G | A | A | 33 | 4 | 8 | false | <90% | 2698 | |||
XM_933339 | LOC646021 | 359 | 377 | G | A | C | G | A | G | A | G | g | A | G | G | G | A | A | A | G | g | c | 32 | 3 | 8 | c | false | <90% | 1031 | ||
XM_944724 | LOC651501 | 359 | 377 | G | A | C | G | A | G | A | G | g | A | G | G | G | A | A | A | G | g | c | 32 | 3 | 8 | c | false | <90% | 1138 | ||
NM_022739 | SMURF2 | 73 | 91 | G | A | C | G | A | G | A | G | g | A | G | G | G | A | A | A | G | g | c | 32 | 3 | 8 | c | false | <90% | 3866 | ||
XM_001132389 | LOC728857 | 115 | 133 | G | A | u | G | u | G | A | G | A | A | G | G | G | A | A | A | G | A | c | 23 | 3 | 13 | bc | false | <90% | 494 | ||
XM_001132135 | LOC731163 | 115 | 133 | G | A | u | G | u | G | A | G | A | A | G | G | G | A | A | A | G | A | c | 23 | 3 | 13 | bc | false | <90% | 494 | ||
NM_015086 | DDN | 1131 | 1149 | c | u | C | G | A | G | g | G | A | A | G | G | G | A | A | A | G | A | A | 20 | 3 | 12 | bc | false | <90% | 3744 | ||
XR_018772 | LOC650301 | 758 | 776 | u | u | g | G | g | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 15 | 4 | 14 | bc | false | <90% | 1569 | ||
XR_016877 | LOC402408 | 758 | 776 | u | u | g | G | g | G | A | G | A | A | G | G | G | A | A | A | G | A | A | 15 | 4 | 14 | bc | false | <90% | 1569 | ||
NM_015726 | WDR42A | 3338 | 3356 | G | A | a | G | A | G | u | G | A | A | G | G | G | A | A | A | G | A | c | 9 | 3 | 11 | bc | false | <90% | 3849 | ||
NM_019049 | FLJ20054 | 1066 | 1084 | G | g | a | G | A | a | A | G | A | A | G | G | G | A | A | A | G | A | A | 5 | 3 | 13 | bc | false | <90% | 2035 | ||
XR_018496 | LOC648895 | 1436 | 1454 | u | g | g | G | A | G | A | G | A | A | a | G | G | A | A | A | G | A | A | 5 | 4 | 8 | c | false | <90% | 2264 | ||
XR_016461 | LOC442156 | 1436 | 1454 | u | g | g | G | A | G | A | G | A | A | a | G | G | A | A | A | G | A | A | 5 | 4 | 8 | c | false | <90% | 2264 | ||
XM_001127181 | LOC728005 | 2583 | 2601 | c | A | C | G | A | G | g | G | A | A | G | a | G | A | A | A | G | A | A | -2 | 3 | 7 | false | <90% | 3293 | |||
XM_001127197 | LOC728005 | 3746 | 3764 | c | A | C | G | A | G | g | G | A | A | G | a | G | A | A | A | G | A | A | -2 | 3 | 7 | false | <90% | 4456 | |||
XM_001127212 | LOC728005 | 3815 | 3833 | c | A | C | G | A | G | g | G | A | A | G | a | G | A | A | A | G | A | A | -2 | 3 | 7 | false | <90% | 4525 | |||
XM_001127140 | LOC728005 | 6405 | 6423 | c | A | C | G | A | G | g | G | A | A | G | a | G | A | A | A | G | A | A | -2 | 3 | 7 | false | <90% | 7115 | |||
NM_001040151 | SCN3B | 2802 | 2820 | G | A | C | a | A | G | A | G | A | g | G | G | G | A | A | A | G | A | u | -24 | 3 | 8 | bc | false | <90% | 5682 | ||
NM_018400 | SCN3B | 3201 | 3219 | G | A | C | a | A | G | A | G | A | g | G | G | G | A | A | A | G | A | u | -24 | 3 | 8 | bc | false | <90% | 6081 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4990
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