Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
37 hits were found for CCUUUGGAGAAGAUACUGU (23 guide strand hits and 14 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_000084 | CLCN5 | 6929 | 6947 | C | C | U | U | U | G | G | A | G | A | A | G | A | a | A | C | U | a | a | 72 | 3 | 13 | c | false | <90% | 9505 | ||
NM_144720 | JAKMIP1 | 2062 | 2080 | g | a | U | U | U | G | G | A | G | A | A | G | u | U | A | C | U | G | g | 71 | 4 | 10 | false | <90% | 2551 | |||
XM_001129178 | JAKMIP1 | 1828 | 1846 | g | a | U | U | U | G | G | A | G | A | A | G | u | U | A | C | U | G | g | 71 | 4 | 10 | false | <90% | 2880 | |||
NM_199191 | BRE | 431 | 449 | u | C | U | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | a | 68 | 3 | 13 | c | false | <90% | 1720 | ||
NM_199192 | BRE | 431 | 449 | u | C | U | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | a | 68 | 3 | 13 | c | false | <90% | 1791 | ||
NM_199194 | BRE | 572 | 590 | u | C | U | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | a | 68 | 3 | 13 | c | false | <90% | 1860 | ||
NM_004899 | BRE | 431 | 449 | u | C | U | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | a | 68 | 3 | 13 | c | false | <90% | 1893 | ||
NM_199193 | BRE | 572 | 590 | u | C | U | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | a | 68 | 3 | 13 | c | false | <90% | 1932 | ||
NM_006842 | SF3B2 | 854 | 872 | g | C | U | U | U | G | G | A | G | A | A | G | A | U | c | C | U | G | c | 68 | 3 | 13 | c | false | <90% | 2902 | ||
NM_019118 | C1orf91 | 305 | 323 | C | C | c | U | U | G | G | A | G | A | A | G | A | U | A | u | U | G | g | 49 | 3 | 12 | c | false | <90% | 1108 | ||
NM_002286 | LAG3 | 1765 | 1783 | C | C | U | U | U | G | G | A | G | A | A | G | A | c | A | g | U | G | g | 49 | 3 | 13 | c | false | <90% | 1991 | ||
XM_927355 | LOC644145 | 22 | 40 | g | a | c | U | U | G | G | A | G | A | A | G | A | a | A | C | U | G | U | 47 | 4 | 10 | c | false | <90% | 519 | ||
XM_936785 | LOC644145 | 22 | 40 | g | a | c | U | U | G | G | A | G | A | A | G | A | a | A | C | U | G | U | 47 | 4 | 10 | c | false | <90% | 519 | ||
NR_003377 | LOC728939 | 9537 | 9555 | g | g | c | U | U | G | G | A | G | A | A | G | A | U | A | C | a | G | U | 43 | 4 | 13 | c | false | <90% | 18232 | ||
NM_015601 | HERC4 | 2512 | 2530 | u | u | g | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | U | 42 | 4 | 11 | c | false | <90% | 4507 | ||
NM_022079 | HERC4 | 2536 | 2554 | u | u | g | U | U | G | G | A | G | A | A | G | A | U | g | C | U | G | U | 42 | 4 | 11 | c | false | <90% | 4531 | ||
NM_018124 | RFWD3 | 352 | 370 | u | C | U | U | g | G | G | A | G | A | A | G | A | c | A | C | U | G | U | 27 | 3 | 8 | c | false | <90% | 4952 | ||
NM_148894 | FAM44A | 1370 | 1388 | C | u | U | U | U | G | a | A | G | A | A | G | A | U | A | C | U | G | a | 17 | 3 | 11 | bc | false | <90% | 10542 | ||
NM_018976 | SLC38A2 | 3883 | 3901 | g | u | a | U | g | G | G | A | G | A | A | G | A | U | A | C | U | G | U | 15 | 4 | 14 | bc | false | <90% | 4861 | ||
NM_014300 | SEC11A | 959 | 977 | u | g | U | U | U | G | G | A | G | u | A | G | A | U | A | C | U | G | g | -1 | 4 | 8 | bc | false | <90% | 1399 | ||
NM_001038702 | CDC42SE2 | 775 | 793 | g | C | U | c | U | G | a | A | G | A | A | G | A | U | A | C | U | G | U | -5 | 3 | 12 | bc | false | <90% | 3498 | ||
NM_020240 | CDC42SE2 | 944 | 962 | g | C | U | c | U | G | a | A | G | A | A | G | A | U | A | C | U | G | U | -5 | 3 | 12 | bc | false | <90% | 3667 | ||
NM_000919 | PAM | 3054 | 3072 | C | C | U | U | U | G | G | A | G | c | A | G | A | U | u | C | U | G | a | -12 | 3 | 9 | c | false | <90% | 3960 |
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_004525 | LRP2 | 1399 | 1417 | c | C | A | u | U | A | U | C | U | U | C | U | C | C | A | A | u | G | G | 37 | 3 | 12 | c | false | <90% | 15735 | ||
NM_015141 | GPD1L | 784 | 802 | c | C | A | G | g | A | U | C | U | U | C | U | g | C | A | A | A | G | G | 36 | 3 | 7 | false | <90% | 3954 | |||
XR_018392 | LOC390557 | 492 | 510 | g | a | A | G | c | A | U | C | U | U | C | U | C | C | A | A | A | G | c | 30 | 4 | 13 | bc | false | <90% | 922 | ||
XR_015425 | LOC728996 | 557 | 575 | A | C | A | G | U | A | U | g | U | U | C | U | g | C | A | A | A | G | c | 22 | 3 | 7 | false | <90% | 1121 | |||
XR_015453 | LOC731367 | 557 | 575 | A | C | A | G | U | A | U | g | U | U | C | U | g | C | A | A | A | G | c | 22 | 3 | 7 | false | <90% | 1121 | |||
NM_024770 | METTL8 | 1144 | 1162 | A | C | A | G | U | A | U | g | U | U | C | U | g | C | A | A | A | G | c | 22 | 3 | 7 | false | <90% | 2246 | |||
NM_145010 | C10orf63 | 331 | 349 | g | a | A | G | U | A | c | C | U | U | C | U | C | C | A | A | A | G | G | 20 | 3 | 12 | bc | false | <90% | 3318 | ||
XR_018470 | LOC390203 | 453 | 471 | u | C | A | G | U | g | U | C | U | U | C | U | C | C | A | A | u | G | G | 11 | 3 | 10 | c | false | <90% | 953 | ||
XR_016482 | LOC390203 | 453 | 471 | u | C | A | G | U | g | U | C | U | U | C | U | C | C | A | A | u | G | G | 11 | 3 | 10 | c | false | <90% | 953 | ||
NM_003919 | SGCE | 181 | 199 | A | C | A | G | U | A | U | u | U | U | C | U | C | C | A | A | g | G | u | 9 | 3 | 8 | c | false | <90% | 1658 | ||
NM_007038 | ADAMTS5 | 2158 | 2176 | g | u | g | G | U | A | U | u | U | U | C | U | C | C | A | A | A | G | G | 4 | 4 | 11 | bc | false | <90% | 9046 | ||
NM_014636 | RALGPS1 | 5617 | 5635 | A | C | A | G | U | A | U | C | U | g | C | U | C | C | A | u | A | G | G | -8 | 2 | 9 | c | false | <90% | 6336 | ||
XM_001125912 | LOC727899 | 351 | 369 | A | C | A | G | U | g | c | C | U | U | C | U | C | C | A | A | A | G | u | -34 | 3 | 11 | bc | false | <90% | 554 | ||
XM_001125962 | LOC727924 | 351 | 369 | A | C | A | G | U | g | c | C | U | U | C | U | C | C | A | A | A | G | u | -34 | 3 | 11 | bc | false | <90% | 554 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2863
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