Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
45 hits were found for GAUGCAGCUUCCAGUGGUG (14 guide strand hits and 31 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_017978 | ANKHD1 | 920 | 938 | a | u | g | G | C | A | G | C | U | U | C | C | A | G | U | G | G | a | G | 64 | 4 | 14 | c | false | <90% | 2149 | ||
NM_024668 | ANKHD1 | 953 | 971 | a | u | g | G | C | A | G | C | U | U | C | C | A | G | U | G | G | a | G | 64 | 4 | 14 | c | false | <90% | 2164 | ||
NM_017747 | ANKHD1 | 953 | 971 | a | u | g | G | C | A | G | C | U | U | C | C | A | G | U | G | G | a | G | 64 | 4 | 14 | c | false | <90% | 8196 | ||
NM_020690 | MASK-BP3 | 953 | 971 | a | u | g | G | C | A | G | C | U | U | C | C | A | G | U | G | G | a | G | 64 | 4 | 14 | c | false | <90% | 8319 | ||
NM_199459 | C10orf71 | 171 | 189 | c | c | U | G | C | A | G | C | U | U | C | C | A | G | U | G | c | U | G | 63 | 3 | 14 | ac | false | <90% | 2970 | ||
XM_937807 | DYNC2H1 | 10288 | 10306 | G | A | U | G | C | A | G | C | U | U | C | C | A | u | U | G | u | U | a | 51 | 3 | 13 | c | false | <90% | 13436 | ||
XM_931085 | DYNC2H1 | 10288 | 10306 | G | A | U | G | C | A | G | C | U | U | C | C | A | u | U | G | u | U | a | 51 | 3 | 13 | c | false | <90% | 13436 | ||
NM_001080463 | DYNC2H1 | 10309 | 10327 | G | A | U | G | C | A | G | C | U | U | C | C | A | u | U | G | u | U | a | 51 | 3 | 13 | c | false | <90% | 13699 | ||
NM_012346 | NUP62 | 3025 | 3043 | G | c | c | a | C | A | G | C | U | U | C | C | A | G | U | G | G | U | G | 32 | 3 | 15 | bc | false | <90% | 3253 | ||
NM_153718 | NUP62 | 3049 | 3067 | G | c | c | a | C | A | G | C | U | U | C | C | A | G | U | G | G | U | G | 32 | 3 | 15 | bc | false | <90% | 3277 | ||
NM_016553 | NUP62 | 3171 | 3189 | G | c | c | a | C | A | G | C | U | U | C | C | A | G | U | G | G | U | G | 32 | 3 | 15 | bc | false | <90% | 3399 | ||
NM_153719 | NUP62 | 3204 | 3222 | G | c | c | a | C | A | G | C | U | U | C | C | A | G | U | G | G | U | G | 32 | 3 | 15 | bc | false | <90% | 3432 | ||
NM_015199 | ANKRD28 | 579 | 597 | c | A | U | G | C | A | G | C | U | U | u | C | A | G | U | G | G | a | c | 29 | 4 | 9 | c | false | <90% | 6339 | ||
NM_016323 | HERC5 | 1164 | 1182 | G | A | U | G | C | c | G | C | U | U | C | C | A | G | U | G | a | a | a | 5 | 4 | 10 | c | false | <90% | 3525 |
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 | |||||||||||||
XM_001134051 | FLJ32065 | 728 | 746 | g | A | C | C | A | C | U | G | G | A | A | G | g | U | a | C | A | U | C | 62 | 3 | 11 | false | <90% | 937 | |||
XM_001134063 | FLJ32065 | 728 | 746 | g | A | C | C | A | C | U | G | G | A | A | G | g | U | a | C | A | U | C | 62 | 3 | 11 | false | <90% | 937 | |||
NM_134445 | CD99L2 | 2121 | 2139 | a | A | C | C | A | C | U | G | G | A | A | u | C | U | G | C | A | g | C | 61 | 3 | 10 | false | <90% | 3419 | |||
NM_134446 | CD99L2 | 2190 | 2208 | a | A | C | C | A | C | U | G | G | A | A | u | C | U | G | C | A | g | C | 61 | 3 | 10 | false | <90% | 3488 | |||
NM_031462 | CD99L2 | 2337 | 2355 | a | A | C | C | A | C | U | G | G | A | A | u | C | U | G | C | A | g | C | 61 | 3 | 10 | false | <90% | 3635 | |||
NM_022131 | CLSTN2 | 1337 | 1355 | u | u | C | C | A | C | U | G | G | A | A | G | C | U | G | g | A | U | C | 60 | 3 | 13 | c | false | <90% | 4421 | ||
NM_198717 | PTGER3 | 1353 | 1371 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 1817 | ||
NM_198716 | PTGER3 | 1380 | 1398 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 1844 | ||
NM_198714 | PTGER3 | 1472 | 1490 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 1936 | ||
NM_198713 | PTGER3 | 1522 | 1540 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 1986 | ||
NM_198712 | PTGER3 | 1549 | 1567 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 2011 | ||
NM_000957 | PTGER3 | 1618 | 1636 | C | A | u | C | A | C | U | G | G | A | A | G | C | U | c | C | A | U | g | 50 | 3 | 11 | c | false | <90% | 2082 | ||
NM_002460 | IRF4 | 2651 | 2669 | C | A | C | C | A | C | U | G | G | A | A | G | C | a | G | g | A | U | g | 49 | 3 | 13 | c | false | <90% | 5065 | ||
NM_003576 | STK24 | 3977 | 3995 | u | A | C | C | A | C | U | G | G | A | A | c | C | U | G | C | c | U | C | 40 | 3 | 10 | false | <90% | 4539 | |||
NM_001032296 | STK24 | 4062 | 4080 | u | A | C | C | A | C | U | G | G | A | A | c | C | U | G | C | c | U | C | 40 | 3 | 10 | false | <90% | 4624 | |||
NM_006715 | MAN2C1 | 1759 | 1777 | g | g | u | g | A | C | U | G | G | A | A | G | C | U | G | C | A | U | C | 30 | 4 | 15 | bc | false | <90% | 3254 | ||
NM_178819 | AGPAT6 | 568 | 586 | a | A | C | C | u | C | U | G | G | A | A | G | C | a | G | C | A | U | C | 27 | 3 | 8 | c | false | <90% | 2592 | ||
NM_001048209 | HNT | 1641 | 1659 | a | c | C | C | A | C | U | G | c | A | A | G | C | U | G | C | A | U | C | 26 | 3 | 10 | bc | false | <90% | 3048 | ||
NM_016522 | HNT | 1974 | 1992 | a | c | C | C | A | C | U | G | c | A | A | G | C | U | G | C | A | U | C | 26 | 3 | 10 | bc | false | <90% | 3381 | ||
NM_001079812 | DIAPH1 | 5199 | 5217 | a | A | C | C | A | C | a | G | G | A | A | G | C | U | G | C | A | a | u | 24 | 4 | 10 | c | false | <90% | 5718 | ||
NM_005219 | DIAPH1 | 5226 | 5244 | a | A | C | C | A | C | a | G | G | A | A | G | C | U | G | C | A | a | u | 24 | 4 | 10 | c | false | <90% | 5745 | ||
NM_001077706 | LFDH | 1884 | 1902 | C | A | C | C | A | C | U | G | a | A | A | G | C | a | G | C | A | U | u | 15 | 3 | 8 | c | false | <90% | 4261 | ||
NR_002723 | GABPAP | 36565 | 36583 | C | A | C | C | A | g | U | G | G | A | A | G | C | a | G | C | A | U | g | 12 | 3 | 7 | c | false | <90% | 194142 | ||
NM_014820 | TOMM70A | 4282 | 4300 | C | u | g | C | A | C | U | G | a | A | A | G | C | U | G | C | A | U | C | 8 | 3 | 10 | bc | false | <90% | 4376 | ||
NM_003874 | CD84 | 1357 | 1375 | C | A | C | u | u | C | U | G | G | A | A | G | C | U | G | C | A | U | a | 6 | 3 | 13 | bc | false | <90% | 3299 | ||
XM_942334 | TANC2 | 1129 | 1147 | C | A | C | C | A | g | U | G | G | A | A | G | C | U | G | C | c | c | a | 5 | 4 | 10 | c | false | <90% | 11577 | ||
XM_371074 | TANC2 | 1129 | 1147 | C | A | C | C | A | g | U | G | G | A | A | G | C | U | G | C | c | c | a | 5 | 4 | 10 | c | false | <90% | 11577 | ||
NM_002831 | PTPN6 | 131 | 149 | C | g | g | C | A | C | U | G | G | g | A | G | C | U | G | C | A | U | C | -13 | 3 | 9 | bc | false | <90% | 2312 | ||
NM_000102 | CYP17A1 | 531 | 549 | g | c | a | C | A | C | U | G | G | c | A | G | C | U | G | C | A | U | C | -15 | 4 | 9 | bc | false | <90% | 1895 | ||
NM_001376 | DYNC1H1 | 13527 | 13545 | u | c | u | C | A | C | U | G | G | c | A | G | C | U | G | C | A | U | C | -15 | 4 | 9 | bc | false | <90% | 14229 | ||
NM_015168 | C19orf7 | 1395 | 1413 | C | A | C | C | A | C | U | G | G | g | A | a | C | U | G | C | A | U | C | -16 | 2 | 9 | false | <90% | 6131 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2044
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