Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
58 hits were found for GGGAAAGAAAGAGAAUUAA (43 guide strand hits and 15 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_014648 | DZIP3 | 619 | 637 | a | G | G | A | A | A | G | A | A | A | G | A | G | g | A | U | U | A | u | 73 | 3 | 12 | c | false | <90% | 5319 | ||
NM_016323 | HERC5 | 1275 | 1293 | G | a | u | A | A | A | G | A | A | A | G | A | G | A | A | U | U | c | A | 66 | 3 | 14 | c | false | <90% | 3525 | ||
NM_018156 | VPS13D | 9510 | 9528 | u | a | u | A | A | A | G | A | A | A | G | A | G | A | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 16266 | ||
NM_015378 | VPS13D | 9585 | 9603 | u | a | u | A | A | A | G | A | A | A | G | A | G | A | A | U | U | A | u | 62 | 4 | 15 | bc | false | <90% | 16341 | ||
NM_020664 | DECR2 | 1544 | 1562 | G | G | a | A | A | A | G | A | A | A | G | A | G | g | A | U | U | A | A | 60 | 2 | 10 | c | false | <90% | 1599 | ||
NM_001080 | ALDH5A1 | 3996 | 4014 | u | G | G | g | A | A | G | A | A | A | G | A | G | A | A | U | U | A | u | 56 | 3 | 14 | bc | false | <90% | 5131 | ||
NM_170740 | ALDH5A1 | 4035 | 4053 | u | G | G | g | A | A | G | A | A | A | G | A | G | A | A | U | U | A | u | 56 | 3 | 14 | bc | false | <90% | 5170 | ||
XM_939699 | C20orf82 | 1865 | 1883 | c | a | G | A | A | A | G | A | A | A | G | A | G | A | c | U | U | A | g | 56 | 4 | 12 | c | false | <90% | 2587 | ||
XM_097736 | C20orf82 | 1865 | 1883 | c | a | G | A | A | A | G | A | A | A | G | A | G | A | c | U | U | A | g | 56 | 4 | 12 | c | false | <90% | 2587 | ||
NM_016216 | DBR1 | 1695 | 1713 | a | a | c | A | A | A | G | A | A | A | G | A | a | A | A | U | U | A | A | 56 | 4 | 9 | false | <90% | 2667 | |||
NM_001031617 | COX19 | 3588 | 3606 | a | a | a | A | A | A | G | A | A | A | G | A | a | A | A | U | U | A | A | 56 | 4 | 9 | false | <90% | 4896 | |||
NM_053042 | KIAA1729 | 344 | 362 | u | a | u | A | A | A | G | A | A | A | G | A | u | A | A | U | U | A | A | 56 | 4 | 9 | false | <90% | 6936 | |||
XM_938247 | LOC649181 | 41 | 59 | G | G | a | A | A | A | G | A | A | A | G | A | G | A | g | U | U | A | A | 55 | 2 | 11 | c | false | <90% | 288 | ||
NM_052937 | PCMTD1 | 924 | 942 | G | G | a | A | A | A | G | A | A | A | G | A | G | A | g | U | U | A | A | 55 | 2 | 11 | c | false | <90% | 3967 | ||
NM_014721 | PHACTR2 | 2352 | 2370 | c | a | G | A | A | A | G | A | A | A | G | A | G | A | A | a | U | A | u | 55 | 4 | 13 | c | false | <90% | 4318 | ||
NM_139245 | PPM1L | 811 | 829 | a | G | G | A | A | A | G | A | A | A | G | A | G | g | A | U | a | A | A | 54 | 3 | 12 | c | false | <90% | 3056 | ||
NM_005867 | DSCR4 | 569 | 587 | G | G | G | A | A | A | G | A | A | A | G | A | G | c | u | U | U | A | u | 50 | 3 | 13 | c | false | <90% | 1102 | ||
NM_018193 | KIAA1794 | 2595 | 2613 | G | G | G | A | A | A | G | A | A | A | G | A | G | A | A | a | g | g | A | 47 | 3 | 15 | c | false | <90% | 4569 | ||
NM_002454 | MTRR | 2185 | 2203 | a | u | u | A | A | A | G | A | A | A | G | A | G | g | A | U | U | A | A | 47 | 4 | 10 | c | false | <90% | 3259 | ||
NM_024010 | MTRR | 2217 | 2235 | a | u | u | A | A | A | G | A | A | A | G | A | G | g | A | U | U | A | A | 47 | 4 | 10 | c | false | <90% | 3291 | ||
NM_198564 | FLJ44290 | 566 | 584 | G | G | G | A | A | A | G | A | A | A | G | A | G | A | A | g | a | A | c | 45 | 3 | 15 | c | false | <90% | 2048 | ||
NM_012255 | XRN2 | 1354 | 1372 | a | a | a | A | A | A | G | A | A | A | G | A | G | A | A | U | g | A | A | 43 | 4 | 13 | c | false | <90% | 3449 | ||
NM_138357 | CCDC109A | 2236 | 2254 | u | u | G | A | g | A | G | A | A | A | G | A | G | A | A | U | U | A | A | 35 | 3 | 14 | bc | false | <90% | 2978 | ||
NM_024989 | PGAP1 | 4683 | 4701 | a | G | G | A | A | A | G | A | g | A | G | A | G | A | A | U | U | u | A | 35 | 3 | 8 | c | false | <90% | 11113 | ||
NM_015678 | NBEA | 3131 | 3149 | G | G | G | A | A | A | G | A | A | A | G | g | G | A | A | U | g | u | g | 35 | 4 | 11 | false | <90% | 10812 | |||
NM_005502 | ABCA1 | 6003 | 6021 | G | G | G | A | A | A | G | A | c | A | G | A | G | A | A | U | U | c | u | 32 | 3 | 8 | c | false | <90% | 10412 | ||
NM_152336 | AGBL1 | 1152 | 1170 | G | G | G | c | A | A | G | A | A | A | G | A | G | A | A | U | a | u | g | 32 | 4 | 12 | c | false | <90% | 3493 | ||
NM_014429 | MORC1 | 1083 | 1101 | G | a | G | A | A | A | c | A | A | A | G | A | G | A | A | U | U | A | A | 22 | 2 | 12 | bc | false | <90% | 3765 | ||
NM_018472 | FAM45B | 146 | 164 | G | G | G | A | A | g | G | A | A | A | G | A | a | A | A | U | U | A | c | 21 | 3 | 6 | false | <90% | 1624 | |||
XM_001131039 | LOC730914 | 115 | 133 | G | G | G | A | g | A | G | A | A | A | G | A | G | A | A | U | g | A | u | 20 | 3 | 11 | c | false | <90% | 551 | ||
XM_001132596 | LOC729051 | 115 | 133 | G | G | G | A | g | A | G | A | A | A | G | A | G | A | A | U | g | A | u | 20 | 3 | 11 | c | false | <90% | 551 | ||
NM_016518 | PIPOX | 611 | 629 | G | G | G | A | A | u | G | A | A | A | G | A | G | A | A | U | c | A | A | 13 | 2 | 10 | c | false | <90% | 2412 | ||
XM_001129482 | STARD9 | 5655 | 5673 | u | G | G | A | A | A | G | A | A | A | c | A | G | A | A | U | a | A | A | 13 | 3 | 9 | c | false | <90% | 15083 | ||
XM_001129290 | STARD9 | 5655 | 5673 | u | G | G | A | A | A | G | A | A | A | c | A | G | A | A | U | a | A | A | 13 | 3 | 9 | c | false | <90% | 15083 | ||
NM_000916 | OXTR | 2407 | 2425 | G | G | G | A | A | A | G | A | A | A | a | A | G | A | A | a | U | A | A | 12 | 2 | 10 | c | false | <90% | 4361 | ||
NM_003135 | SRP19 | 498 | 516 | a | G | G | A | A | A | G | A | A | A | a | A | G | A | A | g | U | A | A | 10 | 3 | 9 | c | false | <90% | 894 | ||
NM_002759 | EIF2AK2 | 1234 | 1252 | u | u | u | A | A | A | G | A | A | A | u | A | G | A | A | U | U | A | A | 5 | 4 | 8 | c | false | <90% | 2808 | ||
NM_175061 | JAZF1 | 1066 | 1084 | u | u | u | A | A | A | G | A | A | A | a | A | G | A | A | U | U | A | A | 5 | 4 | 8 | c | false | <90% | 3210 | ||
NM_014813 | LRIG2 | 863 | 881 | u | u | a | A | A | A | G | A | A | A | c | A | G | A | A | U | U | A | A | 5 | 4 | 8 | c | false | <90% | 4015 | ||
NM_052832 | SLC26A7 | 3666 | 3684 | u | a | a | A | A | u | G | A | A | A | G | A | G | A | A | U | U | A | A | 3 | 4 | 13 | bc | false | <90% | 5280 | ||
NM_000348 | SRD5A2 | 1712 | 1730 | G | u | a | A | A | A | c | A | A | A | G | A | G | A | A | U | U | A | A | 2 | 3 | 12 | bc | false | <90% | 2446 | ||
NR_003370 | LOC730092 | 12407 | 12425 | a | G | G | c | A | A | G | A | A | A | a | A | G | A | A | U | U | A | A | 0 | 3 | 8 | c | false | <90% | 26557 | ||
NM_005188 | CBL | 1963 | 1981 | u | G | G | A | c | A | G | g | A | A | G | A | G | A | A | U | U | A | A | -15 | 3 | 11 | bc | false | <90% | 11242 |
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_004232 | SOCS6 | 4814 | 4832 | c | U | A | A | U | U | C | U | C | U | U | U | C | U | g | U | C | u | a | 65 | 4 | 13 | c | false | <90% | 5846 | ||
NM_016507 | CRKRS | 2987 | 3005 | a | g | A | A | U | U | C | U | C | U | U | U | C | a | U | U | C | C | u | 62 | 4 | 11 | c | false | <90% | 5515 | ||
NM_001023587 | ABCC5 | 1626 | 1644 | U | U | A | A | U | U | C | U | C | U | U | U | C | c | U | U | a | g | C | 54 | 3 | 13 | c | false | <90% | 2007 | ||
NM_002025 | AFF2 | 8439 | 8457 | U | U | A | A | U | U | C | U | C | U | U | U | C | c | a | U | C | C | u | 50 | 3 | 13 | c | false | <90% | 13746 | ||
NM_016206 | VGLL3 | 2211 | 2229 | c | U | A | A | U | U | C | U | C | U | U | U | C | U | a | g | C | C | C | 47 | 3 | 13 | c | false | <90% | 10396 | ||
NM_017811 | UBE2R2 | 1838 | 1856 | U | g | A | A | U | U | C | U | g | U | U | U | C | U | U | U | C | C | u | 23 | 3 | 9 | bc | false | <90% | 4457 | ||
NM_001014979 | LOC90835 | 973 | 991 | c | c | A | A | U | U | C | g | C | U | U | U | C | U | U | U | C | C | g | 19 | 4 | 10 | bc | false | <90% | 1844 | ||
XR_018653 | LOC643329 | 1612 | 1630 | a | a | A | A | U | c | C | U | C | U | U | U | C | U | U | U | C | C | u | 18 | 4 | 12 | bc | false | <90% | 1892 | ||
XR_016332 | LOC643329 | 1612 | 1630 | a | a | A | A | U | c | C | U | C | U | U | U | C | U | U | U | C | C | u | 18 | 4 | 12 | bc | false | <90% | 2003 | ||
NM_001039573 | SEC14L1 | 2767 | 2785 | U | U | A | A | U | U | C | a | C | U | U | U | C | c | U | U | C | C | u | 13 | 3 | 7 | c | false | <90% | 2933 | ||
NM_019117 | KLHL4 | 4580 | 4598 | U | U | A | A | U | U | C | U | u | U | U | U | C | U | U | U | a | u | a | 8 | 4 | 8 | c | false | <90% | 5762 | ||
NM_173082 | SHPRH | 5983 | 6001 | U | g | g | A | U | U | C | U | u | U | U | U | C | U | U | U | C | C | C | 8 | 3 | 10 | bc | false | <90% | 7000 | ||
NM_001042683 | SHPRH | 6330 | 6348 | U | g | g | A | U | U | C | U | u | U | U | U | C | U | U | U | C | C | C | 8 | 3 | 10 | bc | false | <90% | 7347 | ||
NM_001004759 | OR51T1 | 38 | 56 | U | U | A | A | U | U | a | U | u | U | U | U | C | U | U | U | C | C | u | -31 | 3 | 9 | bc | false | <90% | 1065 | ||
NM_001012418 | LOC340156 | 4657 | 4675 | U | U | A | A | U | U | u | g | C | U | U | U | C | U | U | U | C | C | u | -33 | 3 | 10 | bc | false | <90% | 5768 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3268
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