Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
82 hits were found for GGCAACAUUGCAAGACAUU (43 guide strand hits and 39 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_001001661 | ZNF425 | 2519 | 2537 | G | G | C | A | A | C | A | U | U | G | C | A | A | G | A | C | u | c | c | 68 | 3 | 16 | ac | false | <90% | 3184 | ||
NM_004788 | UBE4A | 3199 | 3217 | u | c | C | A | c | C | A | U | U | G | C | A | A | G | A | C | A | U | U | 35 | 3 | 14 | bc | false | <90% | 6138 | ||
NM_022497 | MRPS25 | 1687 | 1705 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | U | U | 16 | 2 | 8 | c | false | <90% | 4574 | ||
NM_017712 | PGPEP1 | 5546 | 5564 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | u | c | U | 13 | 3 | 8 | c | false | <90% | 7084 | ||
NM_032683 | FKSG24 | 1302 | 1320 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1360 | ||
XR_015984 | LOC731943 | 402 | 420 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1618 | ||
XR_015591 | LOC730861 | 442 | 460 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1662 | ||
XR_015276 | LOC727951 | 442 | 460 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1662 | ||
XR_015810 | LOC731051 | 443 | 461 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1663 | ||
XR_015570 | LOC728309 | 443 | 461 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1663 | ||
XR_015819 | LOC729150 | 442 | 460 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1664 | ||
XR_015774 | LOC731260 | 442 | 460 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1664 | ||
NM_173811 | C11orf77 | 1775 | 1793 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 1966 | ||
NM_024895 | PDZD7 | 1919 | 1937 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 2037 | ||
XR_015289 | LOC645431 | 1868 | 1886 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 2108 | ||
XR_015673 | LOC645431 | 1871 | 1889 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 2111 | ||
NM_014039 | C11orf54 | 1189 | 1207 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 2403 | ||
NM_003677 | DENR | 2872 | 2890 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 3061 | ||
NM_001001412 | FAM26C | 2971 | 2989 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | u | c | U | 13 | 3 | 8 | c | false | <90% | 3099 | ||
NM_001003715 | RECQL5 | 3208 | 3226 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 3243 | ||
NM_001003716 | RECQL5 | 3675 | 3693 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 3710 | ||
NR_003262 | FDPSL2A | 739 | 757 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 4981 | ||
NM_020844 | KIAA1456 | 2547 | 2565 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | u | c | U | 13 | 3 | 8 | c | false | <90% | 5759 | ||
NM_031483 | ITCH | 5758 | 5776 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 6357 | ||
NM_005665 | EVI5 | 6565 | 6583 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 7403 | ||
NM_001001928 | PPARA | 3617 | 3635 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 9965 | ||
NM_005036 | PPARA | 3701 | 3719 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | U | 13 | 3 | 8 | c | false | <90% | 10049 | ||
NM_148672 | CCL28 | 747 | 765 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | U | c | 11 | 3 | 8 | c | false | <90% | 816 | ||
NR_001282 | PCDHB19P | 4417 | 4435 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | U | c | 11 | 3 | 8 | c | false | <90% | 4613 | ||
NM_020448 | NPAL3 | 3756 | 3774 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | U | c | 11 | 3 | 8 | c | false | <90% | 5293 | ||
NM_020299 | AKR1B10 | 176 | 194 | G | G | C | A | A | C | A | g | U | G | C | A | A | G | A | C | u | g | U | 11 | 3 | 8 | c | false | <90% | 1551 | ||
NM_133444 | ZNF526 | 3929 | 3947 | G | G | C | A | A | C | A | g | U | G | C | A | A | G | A | C | c | c | U | 11 | 3 | 8 | c | false | <90% | 3954 | ||
NM_017712 | PGPEP1 | 4094 | 4112 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | g | A | U | c | 8 | 3 | 8 | c | false | <90% | 7084 | ||
NM_001042540 | NCBP2 | 930 | 948 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 2016 | ||
NM_145312 | ZNF485 | 1892 | 1910 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | u | c | c | 8 | 4 | 8 | c | false | <90% | 2070 | ||
XM_943043 | LOC653904 | 1920 | 1938 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 2090 | ||
NM_007362 | NCBP2 | 1089 | 1107 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 2175 | ||
NM_001039755 | FLJ44124 | 2695 | 2713 | G | G | C | A | A | C | A | U | g | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 3013 | ||
NM_032485 | MCM8 | 3218 | 3236 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 3704 | ||
NM_182802 | MCM8 | 3224 | 3242 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 3710 | ||
NM_004323 | BAG1 | 2460 | 2478 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 3885 | ||
NM_017656 | ZNF562 | 5477 | 5495 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 5539 | ||
NM_020546 | ADCY2 | 6360 | 6378 | G | G | C | A | A | C | A | U | a | G | C | A | A | G | A | C | c | c | c | 8 | 4 | 8 | c | false | <90% | 6553 |
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_007107 | SSR3 | 846 | 864 | A | A | U | G | U | C | U | U | G | C | A | A | U | G | U | g | c | u | g | 42 | 4 | 15 | c | false | <90% | 3067 | ||
NM_005599 | NHLH2 | 240 | 258 | A | A | U | u | U | C | U | U | G | C | A | A | U | G | U | U | u | g | a | 32 | 4 | 12 | c | false | <90% | 2518 | ||
NM_177405 | CECR1 | 1755 | 1773 | A | g | U | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 27 | 2 | 8 | c | false | <90% | 3071 | ||
NM_017424 | CECR1 | 2613 | 2631 | A | g | U | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 27 | 2 | 8 | c | false | <90% | 3947 | ||
NM_007334 | KLRD1 | 1226 | 1244 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 1271 | ||
XM_942121 | LOC645843 | 860 | 878 | A | A | U | G | U | C | U | U | G | C | u | A | U | a | U | U | G | C | C | 19 | 2 | 10 | c | false | <90% | 1296 | ||
XM_930419 | LOC645843 | 860 | 878 | A | A | U | G | U | C | U | U | G | C | u | A | U | a | U | U | G | C | C | 19 | 2 | 10 | c | false | <90% | 1296 | ||
NM_002262 | KLRD1 | 1319 | 1337 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 1364 | ||
NM_153018 | ZFP3 | 2863 | 2881 | A | A | a | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 5011 | ||
NM_014897 | ZNF652 | 3821 | 3839 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 5428 | ||
XM_371664 | KIAA1257 | 2601 | 2619 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 6094 | ||
XM_939875 | KIAA1257 | 2601 | 2619 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 6095 | ||
NM_015077 | SARM1 | 5899 | 5917 | A | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 19 | 2 | 8 | c | false | <90% | 6862 | ||
NM_201550 | LRRC10 | 1968 | 1986 | g | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 17 | 3 | 8 | c | false | <90% | 2649 | ||
NM_145305 | SLC25A43 | 2017 | 2035 | g | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 17 | 3 | 8 | c | false | <90% | 2788 | ||
NM_015291 | DNAJC16 | 4694 | 4712 | g | A | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 17 | 3 | 8 | c | false | <90% | 6035 | ||
XM_377476 | MGC57346 | 968 | 986 | A | g | g | G | U | C | U | U | G | C | c | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 1879 | ||
NM_175900 | C16orf54 | 2269 | 2287 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 2581 | ||
XM_001128758 | LOC728070 | 2285 | 2303 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 2601 | ||
NM_001056 | SULT1C2 | 2526 | 2544 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 2799 | ||
NM_176825 | SULT1C2 | 2559 | 2577 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 2832 | ||
NM_173473 | C10orf104 | 1666 | 1684 | A | u | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 3277 | ||
NM_198584 | CA13 | 1202 | 1220 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 3564 | ||
NM_172069 | PLEKHH2 | 5446 | 5464 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 7027 | ||
NM_173598 | KSR2 | 8589 | 8607 | A | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 7 | 3 | 8 | c | false | <90% | 16655 | ||
NM_001002033 | HN1 | 349 | 367 | g | g | g | G | U | C | U | U | G | C | c | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 1696 | ||
NM_203294 | TRIM7 | 2136 | 2154 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2592 | ||
NM_203295 | TRIM7 | 2204 | 2222 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2660 | ||
NM_003333 | UBA52 | 1916 | 1934 | g | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2801 | ||
NM_015243 | VPS13B | 2635 | 2653 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2822 | ||
NM_001033930 | UBA52 | 1938 | 1956 | g | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2823 | ||
NM_203293 | TRIM7 | 2406 | 2424 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2862 | ||
NM_203296 | TRIM7 | 2413 | 2431 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 2869 | ||
NM_203297 | TRIM7 | 2570 | 2588 | u | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 3026 | ||
NM_004360 | CDH1 | 3685 | 3703 | g | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 4828 | ||
NM_080876 | DUSP19 | 2399 | 2417 | g | g | a | G | U | C | U | U | G | C | c | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 5183 | ||
NM_001029864 | KIAA1755 | 4781 | 4799 | g | g | g | G | U | C | U | U | G | C | u | A | U | G | U | U | G | C | C | 5 | 4 | 8 | c | false | <90% | 6412 | ||
NM_000362 | TIMP3 | 5404 | 5422 | A | u | U | G | U | C | U | U | G | u | A | A | U | G | U | U | G | C | a | 0 | 3 | 8 | bc | false | <90% | 5496 | ||
NM_005907 | MAN1A1 | 2788 | 2806 | A | A | U | G | U | u | U | U | G | C | c | A | U | G | U | U | G | C | a | -29 | 3 | 7 | c | false | <90% | 4139 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2080
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