Automatic recommendation
Not OK - siRNA is not specific
35 hits were found for AGCAGAGGCCAUGGAUAUU (23 guide strand hits and 12 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 | |||||||||||||
XM_001128792 | LOC728748 | 1533 | 1551 | A | u | C | A | G | A | G | G | C | C | A | U | G | G | A | U | A | c | U | 85 | 2 | 15 | ac | false | <90% | 1755 | ||
NM_004705 | PRKRIR | 2964 | 2982 | A | u | C | A | G | A | G | G | C | C | A | U | G | G | A | U | A | c | U | 85 | 2 | 15 | ac | false | <90% | 3202 | ||
XR_016912 | LOC644363 | 3074 | 3092 | A | u | C | A | G | A | G | G | C | C | A | U | G | G | A | U | A | c | U | 85 | 2 | 15 | ac | false | <90% | 3306 | ||
NM_006618 | JARID1B | 821 | 839 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | A | U | U | 80 | 1 | 13 | c | false | <90% | 6393 | ||
NM_024093 | C2orf49 | 662 | 680 | g | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | A | a | c | 70 | 4 | 12 | c | false | <90% | 902 | ||
NM_000613 | HPX | 697 | 715 | g | G | C | A | G | A | G | G | C | C | A | U | G | G | A | c | A | c | a | 64 | 4 | 14 | c | false | <90% | 1389 | ||
XR_015890 | LOC728900 | 724 | 742 | A | G | C | A | G | A | G | G | C | C | A | U | c | G | A | U | g | a | c | 58 | 4 | 12 | false | <90% | 2537 | |||
NM_000918 | P4HB | 722 | 740 | A | G | C | A | G | A | G | G | C | C | A | U | c | G | A | U | g | a | c | 58 | 4 | 12 | false | <90% | 2596 | |||
XR_015513 | LOC729342 | 293 | 311 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | g | a | U | 54 | 3 | 13 | c | false | <90% | 1320 | ||
XR_015144 | LOC730467 | 293 | 311 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | g | a | U | 54 | 3 | 13 | c | false | <90% | 1320 | ||
NM_020784 | KIAA1344 | 3467 | 3485 | A | G | u | A | G | A | G | G | C | C | A | U | G | G | A | U | c | c | U | 54 | 3 | 13 | c | false | <90% | 4552 | ||
XR_017511 | LOC390411 | 183 | 201 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | u | a | c | 49 | 4 | 13 | c | false | <90% | 871 | ||
XR_018240 | LOC390411 | 183 | 201 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | u | a | c | 49 | 4 | 13 | c | false | <90% | 871 | ||
NM_013269 | CLEC2D | 1289 | 1307 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | g | a | c | 49 | 4 | 13 | c | false | <90% | 5167 | ||
NM_001004419 | CLEC2D | 1371 | 1389 | A | G | C | A | G | A | G | G | C | C | A | U | G | a | A | U | g | a | c | 49 | 4 | 13 | c | false | <90% | 5249 | ||
NM_017953 | C1orf181 | 110 | 128 | A | G | C | A | G | A | G | G | C | C | A | a | G | G | A | U | c | g | U | 40 | 3 | 11 | false | <90% | 2821 | |||
NM_015160 | PMPCA | 845 | 863 | c | G | C | A | G | A | G | G | C | C | g | U | G | G | A | U | A | U | U | 36 | 2 | 9 | c | false | <90% | 2097 | ||
NM_004299 | ABCB7 | 475 | 493 | u | G | C | A | a | A | G | G | C | C | A | U | G | a | A | U | A | U | U | 27 | 3 | 8 | c | false | <90% | 2404 | ||
NM_006598 | SLC12A7 | 699 | 717 | u | G | C | A | G | g | G | G | C | C | A | U | G | u | A | U | A | U | U | 15 | 3 | 7 | c | false | <90% | 5316 | ||
XM_495863 | GVIN1 | 1220 | 1238 | u | G | C | A | G | A | G | G | C | C | c | U | G | G | A | c | A | U | U | 10 | 3 | 9 | c | false | <90% | 8820 | ||
XM_940224 | GVIN1 | 1220 | 1238 | u | G | C | A | G | A | G | G | C | C | c | U | G | G | A | c | A | U | U | 10 | 3 | 9 | c | false | <90% | 8820 | ||
NM_173054 | RELN | 8737 | 8755 | u | G | C | A | G | g | G | G | C | C | A | U | G | G | A | g | A | U | U | 8 | 3 | 9 | c | false | <90% | 11558 | ||
NM_005045 | RELN | 8737 | 8755 | u | G | C | A | G | g | G | G | C | C | A | U | G | G | A | g | A | U | U | 8 | 3 | 9 | c | false | <90% | 11564 |
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 | |||||||||||||
XR_019157 | LOC392214 | 537 | 555 | A | A | c | A | U | C | C | A | U | G | G | g | C | U | C | U | G | C | a | 41 | 3 | 8 | false | <90% | 1285 | |||
XR_016410 | LOC392214 | 537 | 555 | A | A | c | A | U | C | C | A | U | G | G | g | C | U | C | U | G | C | a | 41 | 3 | 8 | false | <90% | 1285 | |||
NM_147133 | NFX1 | 2798 | 2816 | A | A | U | c | U | C | C | A | U | G | G | C | C | U | C | U | a | a | g | 32 | 4 | 12 | c | false | <90% | 3200 | ||
NM_002504 | NFX1 | 2798 | 2816 | A | A | U | c | U | C | C | A | U | G | G | C | C | U | C | U | a | a | g | 32 | 4 | 12 | c | false | <90% | 4629 | ||
NM_025243 | SLC19A3 | 611 | 629 | c | A | U | A | U | C | C | u | U | G | G | C | C | U | C | U | G | u | c | 28 | 4 | 9 | c | false | <90% | 3775 | ||
NM_018019 | MED9 | 54 | 72 | c | g | g | A | g | C | C | A | U | G | G | C | C | U | C | U | G | C | U | 15 | 4 | 14 | bc | false | <90% | 2222 | ||
NM_015329 | KIAA0892 | 3503 | 3521 | c | c | g | A | g | C | C | A | U | G | G | C | C | U | C | U | G | C | U | 15 | 4 | 14 | bc | false | <90% | 4853 | ||
NM_145647 | WDR67 | 1798 | 1816 | u | A | U | A | U | g | C | A | U | G | G | C | C | U | C | U | u | C | U | 11 | 3 | 10 | c | false | <90% | 3502 | ||
NM_021961 | TEAD1 | 4427 | 4445 | A | A | U | A | U | C | C | c | U | G | G | C | C | U | C | U | a | C | c | 9 | 3 | 8 | c | false | <90% | 8850 | ||
NM_178457 | C20orf174 | 3222 | 3240 | c | g | U | A | U | C | C | A | U | c | G | C | C | U | C | U | G | C | a | -1 | 4 | 8 | bc | false | <90% | 9404 | ||
NM_032777 | GPR124 | 2457 | 2475 | c | A | U | A | g | C | C | A | U | G | a | C | C | U | C | U | G | C | U | -14 | 3 | 8 | c | false | <90% | 5680 | ||
NM_001039547 | GK5 | 4956 | 4974 | A | A | U | A | U | C | C | c | U | G | a | C | C | U | C | U | G | C | c | -28 | 3 | 7 | c | false | <90% | 9834 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3410
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