Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
80 hits were found for UCAACCUCCUGAGUUCCUC (38 guide strand hits and 42 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_017656 | ZNF562 | 3299 | 3317 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | C | a | g | 72 | 3 | 14 | c | false | <90% | 5539 | ||
XM_001126035 | LOC727866 | 137 | 155 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 68 | 3 | 16 | ac | false | <90% | 2032 | ||
NM_014138 | TMEM29 | 263 | 281 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 68 | 3 | 16 | ac | false | <90% | 2339 | ||
NM_015425 | POLR1A | 3256 | 3274 | c | a | A | A | C | C | U | C | C | U | G | A | G | U | U | C | u | U | C | 63 | 3 | 14 | ac | false | <90% | 6637 | ||
NM_000362 | TIMP3 | 3267 | 3285 | g | C | c | A | C | C | U | C | C | U | G | A | G | a | U | C | C | U | C | 58 | 3 | 10 | c | false | <90% | 5496 | ||
NM_006336 | ZER1 | 228 | 246 | c | C | A | A | C | C | U | C | C | U | G | A | G | g | U | g | C | U | C | 52 | 3 | 12 | c | false | <90% | 4299 | ||
NM_002119 | HLA-DOA | 2241 | 2259 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 3485 | ||
NR_003102 | POT1 | 1613 | 1631 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 4215 | ||
NM_030777 | SLC2A10 | 2251 | 2269 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 4241 | ||
NM_181833 | NF2 | 2276 | 2294 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 4731 | ||
NM_181830 | NF2 | 3362 | 3380 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 5817 | ||
NM_181828 | NF2 | 3485 | 3503 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 5940 | ||
NM_181829 | NF2 | 3488 | 3506 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 5943 | ||
NM_000268 | NF2 | 3566 | 3584 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 6021 | ||
NM_016418 | NF2 | 3611 | 3629 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 6066 | ||
NM_181832 | NF2 | 3626 | 3644 | U | C | c | A | C | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 49 | 4 | 13 | c | false | <90% | 6081 | ||
NM_175883 | OR7D2 | 2616 | 2634 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 3226 | ||
NM_020748 | INTS2 | 4989 | 5007 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 5894 | ||
NM_024884 | L2HGDH | 2504 | 2522 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 6111 | ||
NM_003281 | TNNI1 | 1965 | 1983 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 6162 | ||
NR_002791 | EMX2OS | 5839 | 5857 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 7282 | ||
NM_024577 | SH3TC2 | 4977 | 4995 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 26588 | ||
NM_207361 | FREM2 | 15545 | 15563 | U | C | A | A | C | C | U | C | C | U | G | A | G | U | a | g | C | U | g | 44 | 3 | 14 | c | false | <90% | 16179 | ||
NM_025193 | HSD3B7 | 1436 | 1454 | U | C | A | A | C | C | U | C | C | U | G | g | G | U | U | C | a | a | g | 35 | 4 | 11 | false | <90% | 2189 | |||
NM_005419 | STAT2 | 3499 | 3517 | U | C | A | A | C | C | U | C | C | U | G | g | G | U | U | C | a | a | g | 35 | 4 | 11 | false | <90% | 4451 | |||
NR_002723 | GABPAP | 45130 | 45148 | U | C | A | g | C | C | U | C | C | U | G | A | G | U | a | C | C | U | g | 33 | 3 | 10 | c | false | <90% | 194142 | ||
NM_024758 | AGMAT | 1692 | 1710 | U | C | A | g | C | C | U | C | C | U | G | A | G | U | a | C | C | U | g | 33 | 3 | 10 | c | false | <90% | 2196 | ||
NM_207012 | AP3M1 | 413 | 431 | U | C | A | u | C | C | U | C | C | U | G | A | G | U | a | C | C | U | a | 33 | 3 | 10 | c | false | <90% | 5270 | ||
NM_144680 | ZNF18 | 496 | 514 | U | C | A | g | C | C | U | C | C | U | G | A | G | U | U | g | C | U | g | 32 | 3 | 11 | c | false | <90% | 2767 | ||
NM_007054 | KIF3A | 4581 | 4599 | U | C | A | g | C | C | U | C | C | U | G | A | G | U | U | g | C | U | g | 32 | 3 | 11 | c | false | <90% | 6257 | ||
XM_940069 | PPP1R3E | 4349 | 4367 | a | g | A | A | C | C | U | C | C | U | c | A | G | U | U | C | C | U | u | 20 | 4 | 8 | c | false | <90% | 6563 | ||
XM_927029 | PPP1R3E | 4349 | 4367 | a | g | A | A | C | C | U | C | C | U | c | A | G | U | U | C | C | U | u | 20 | 4 | 8 | c | false | <90% | 6564 | ||
NR_002723 | GABPAP | 40585 | 40603 | U | C | A | A | a | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 17 | 4 | 11 | c | false | <90% | 194142 | ||
NM_198586 | NHLRC1 | 1651 | 1669 | U | C | A | A | a | C | U | C | C | U | G | A | G | U | U | C | a | a | g | 17 | 4 | 11 | c | false | <90% | 2134 | ||
NM_080717 | TBX5 | 1928 | 1946 | U | C | A | g | C | C | c | C | C | U | G | A | G | U | U | C | C | U | C | -3 | 2 | 12 | bc | false | <90% | 3736 | ||
NM_181486 | TBX5 | 1941 | 1959 | U | C | A | g | C | C | c | C | C | U | G | A | G | U | U | C | C | U | C | -3 | 2 | 12 | bc | false | <90% | 3749 | ||
NM_000192 | TBX5 | 2113 | 2131 | U | C | A | g | C | C | c | C | C | U | G | A | G | U | U | C | C | U | C | -3 | 2 | 12 | bc | false | <90% | 3921 | ||
NM_032355 | MON1A | 1275 | 1293 | U | C | A | A | C | C | U | C | a | U | u | A | G | U | U | C | C | U | C | -21 | 2 | 8 | c | false | <90% | 2054 |
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_018152 | C20orf12 | 2672 | 2690 | G | A | G | G | A | A | C | U | C | A | G | G | A | G | a | U | U | u | u | 67 | 3 | 14 | c | false | <90% | 3291 | ||
NM_032325 | MGC11102 | 225 | 243 | a | A | G | G | A | A | C | U | C | A | G | G | A | G | G | a | g | G | A | 48 | 3 | 14 | c | false | <90% | 2836 | ||
NR_002723 | GABPAP | 193375 | 193393 | c | u | u | G | A | A | C | U | C | A | G | G | A | G | G | U | g | G | A | 43 | 4 | 13 | c | false | <90% | 194142 | ||
NM_052916 | RNF157 | 3477 | 3495 | c | u | u | G | A | A | C | U | C | A | G | G | A | G | G | U | g | G | A | 43 | 4 | 13 | c | false | <90% | 3570 | ||
NM_021629 | GNB4 | 4682 | 4700 | c | u | u | G | A | A | C | U | C | A | G | G | A | G | G | U | g | G | A | 43 | 4 | 13 | c | false | <90% | 6428 | ||
NM_144590 | ANKRD22 | 1057 | 1075 | c | u | u | G | A | A | C | U | C | A | G | G | A | G | u | U | U | G | A | 42 | 4 | 11 | c | false | <90% | 1135 | ||
NR_002723 | GABPAP | 19807 | 19825 | c | A | G | c | A | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 35 | 3 | 11 | c | false | <90% | 194142 | ||
NM_001001789 | C21orf24 | 3479 | 3497 | c | A | G | c | A | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 35 | 3 | 11 | c | false | <90% | 3620 | ||
NM_001039211 | ATAD3C | 831 | 849 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 1822 | ||
NM_198076 | FAM36A | 2203 | 2221 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 2632 | ||
NM_145278 | C1orf150 | 2502 | 2520 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 2646 | ||
NM_002649 | PIK3CG | 5239 | 5257 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 5379 | ||
NM_207116 | TRIAD3 | 4345 | 4363 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 5622 | ||
NM_207111 | TRIAD3 | 4516 | 4534 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 5793 | ||
NR_003266 | LOC220729 | 11847 | 11865 | c | A | G | G | u | A | C | U | C | A | G | G | A | G | G | c | U | G | A | 20 | 3 | 10 | c | false | <90% | 15309 | ||
NM_001081 | CUBN | 8660 | 8678 | c | A | G | G | A | A | C | U | g | A | G | G | A | G | G | U | g | G | A | 14 | 3 | 7 | c | false | <90% | 11933 | ||
NM_001032363 | C1orf151 | 2477 | 2495 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 2589 | ||
NM_001039891 | ZNF674 | 2506 | 2524 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 2689 | ||
NM_016641 | MIR16 | 2111 | 2129 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 2960 | ||
NM_004379 | CREB1 | 2838 | 2856 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 2964 | ||
NM_134442 | CREB1 | 2880 | 2898 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 3006 | ||
NM_170720 | KCNJ14 | 166 | 184 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 3120 | ||
NM_138450 | ARL11 | 1422 | 1440 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 3294 | ||
NM_002209 | ITGAL | 4771 | 4789 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 5133 | ||
NM_033425 | DIXDC1 | 4713 | 4731 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 5432 | ||
NM_001037954 | DIXDC1 | 5180 | 5198 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 5899 | ||
XM_001133581 | LOC729540 | 6460 | 6478 | c | A | G | c | u | A | C | U | C | A | G | G | A | G | G | U | U | G | A | 9 | 3 | 14 | bc | false | <90% | 6593 | ||
NM_005149 | TBX19 | 2227 | 2245 | c | u | u | G | A | u | C | U | C | A | G | G | A | G | G | U | U | G | A | 3 | 4 | 13 | bc | false | <90% | 2882 | ||
NM_000379 | XDH | 5072 | 5090 | u | u | u | G | A | g | C | U | C | A | G | G | A | G | G | U | U | G | A | 3 | 4 | 13 | bc | false | <90% | 5717 | ||
XM_001125733 | LOC727737 | 497 | 515 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 1152 | |||
XM_001126076 | LOC727737 | 566 | 584 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 2832 | |||
XM_001125996 | LOC727737 | 616 | 634 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 2862 | |||
NM_013325 | ATG4B | 632 | 650 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 2892 | |||
NM_178326 | ATG4B | 632 | 650 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 2912 | |||
XM_001126139 | LOC727737 | 878 | 896 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 3124 | |||
XM_001126088 | LOC727737 | 878 | 896 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 3160 | |||
XM_001126099 | LOC727737 | 1031 | 1049 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 3297 | |||
XM_001125933 | LOC727737 | 615 | 633 | G | A | G | G | A | A | a | U | C | A | G | a | A | G | G | U | U | G | u | -5 | 3 | 6 | false | <90% | 3646 | |||
NM_001013255 | LSP1 | 1342 | 1360 | u | A | G | G | A | A | g | U | u | A | G | G | A | G | G | U | U | G | A | -28 | 3 | 10 | bc | false | <90% | 1578 | ||
NM_002339 | LSP1 | 1520 | 1538 | u | A | G | G | A | A | g | U | u | A | G | G | A | G | G | U | U | G | A | -28 | 3 | 10 | bc | false | <90% | 1756 | ||
NM_001013253 | LSP1 | 1606 | 1624 | u | A | G | G | A | A | g | U | u | A | G | G | A | G | G | U | U | G | A | -28 | 3 | 10 | bc | false | <90% | 1842 | ||
NM_001013254 | LSP1 | 1836 | 1854 | u | A | G | G | A | A | g | U | u | A | G | G | A | G | G | U | U | G | A | -28 | 3 | 10 | bc | false | <90% | 2072 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1538
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