Automatic recommendation
Not OK - siRNA is not specific
60 hits were found for GACAAAGAGGCAAGAAAAA (37 guide strand hits and 23 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_016604 | JMJD1B | 1407 | 1425 | a | A | C | A | A | A | G | A | G | G | C | A | g | G | A | A | A | A | A | 87 | 2 | 11 | false | <90% | 6830 | |||
NM_019083 | CCDC76 | 1164 | 1182 | c | A | C | A | A | A | G | A | G | G | C | A | A | G | A | u | A | A | u | 66 | 3 | 14 | c | false | <90% | 3129 | ||
NM_004628 | XPC | 1591 | 1609 | G | u | a | A | A | A | G | A | G | G | C | A | A | G | A | A | A | A | u | 64 | 3 | 15 | bc | false | <90% | 3714 | ||
NM_015441 | OLFML2B | 3042 | 3060 | a | u | g | A | A | A | G | A | G | G | C | A | A | G | A | A | A | g | A | 64 | 4 | 14 | c | false | <90% | 3240 | ||
NM_005596 | NFIB | 2891 | 2909 | G | A | C | A | A | A | G | A | G | G | C | A | g | G | c | A | A | A | u | 59 | 3 | 12 | false | <90% | 8159 | |||
NM_000610 | CD44 | 1139 | 1157 | a | A | C | c | A | A | G | A | G | G | C | A | A | G | A | A | A | c | c | 53 | 4 | 13 | c | false | <90% | 5748 | ||
NM_007256 | SLCO2B1 | 2293 | 2311 | G | A | C | A | A | A | G | A | G | G | C | A | A | G | g | A | c | c | A | 49 | 3 | 14 | c | false | <90% | 4108 | ||
NM_015106 | RAD54L2 | 4281 | 4299 | a | c | a | A | A | A | G | A | G | G | C | A | A | a | A | A | A | A | A | 47 | 4 | 10 | c | false | <90% | 4319 | ||
XR_018416 | LOC648702 | 488 | 506 | c | u | a | A | A | A | G | A | G | G | C | A | A | G | A | A | g | A | A | 43 | 4 | 13 | c | false | <90% | 917 | ||
XR_016613 | LOC644557 | 488 | 506 | c | u | a | A | A | A | G | A | G | G | C | A | A | G | A | A | g | A | A | 43 | 4 | 13 | c | false | <90% | 917 | ||
NM_005039 | PRB1 | 588 | 606 | c | A | C | A | A | g | G | A | G | G | C | A | A | G | A | A | A | c | c | 27 | 4 | 11 | c | false | <90% | 1173 | ||
NM_182628 | CCDC37 | 205 | 223 | G | A | g | A | A | A | c | A | G | G | C | A | A | G | A | A | A | A | A | 14 | 2 | 12 | bc | false | <90% | 2086 | ||
XM_001126353 | ACSM2 | 1005 | 1023 | G | A | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | g | 14 | 3 | 7 | c | false | <90% | 1791 | ||
NM_183245 | INVS | 1668 | 1686 | G | A | C | A | A | A | G | A | G | G | g | A | A | G | A | A | c | A | g | 10 | 3 | 10 | c | false | <90% | 3370 | ||
NM_014425 | INVS | 1668 | 1686 | G | A | C | A | A | A | G | A | G | G | g | A | A | G | A | A | c | A | g | 10 | 3 | 10 | c | false | <90% | 3880 | ||
XM_001129743 | LOC729245 | 293 | 311 | G | A | a | A | A | A | a | A | G | G | C | A | A | G | A | A | A | A | c | 9 | 3 | 11 | bc | false | <90% | 975 | ||
XM_001131277 | LOC731927 | 293 | 311 | G | A | a | A | A | A | a | A | G | G | C | A | A | G | A | A | A | A | c | 9 | 3 | 11 | bc | false | <90% | 975 | ||
NM_033527 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2323 | ||
NM_033532 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2362 | ||
NM_033529 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2409 | ||
NM_033528 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2436 | ||
NM_024011 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2439 | ||
NM_033531 | CDC2L2 | 385 | 403 | u | g | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 2448 | ||
NM_002471 | MYH6 | 1975 | 1993 | G | c | a | A | A | g | G | A | G | G | C | A | A | G | A | A | A | A | A | 5 | 3 | 13 | bc | false | <90% | 5939 | ||
NM_017637 | BNC2 | 9298 | 9316 | a | c | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 12926 | ||
NM_000081 | LYST | 12031 | 12049 | c | c | a | A | A | A | G | A | G | G | a | A | A | G | A | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 13493 | ||
NM_145720 | TIGD4 | 880 | 898 | u | g | g | A | A | A | G | u | G | G | C | A | A | G | A | A | A | A | A | 4 | 4 | 11 | bc | false | <90% | 2451 | ||
NM_014677 | RIMS2 | 3426 | 3444 | a | c | a | A | A | A | G | u | G | G | C | A | A | G | A | A | A | A | A | 4 | 4 | 11 | bc | false | <90% | 4451 | ||
NM_001013680 | LOC401233 | 151 | 169 | c | A | C | A | A | A | G | A | G | G | g | g | A | G | A | A | A | A | A | 2 | 3 | 9 | false | <90% | 2851 | |||
NM_152994 | CCDC128 | 436 | 454 | a | A | C | c | A | c | G | A | G | G | C | A | A | G | A | A | A | A | A | -2 | 3 | 13 | bc | false | <90% | 3155 | ||
NM_001163 | APBA1 | 1511 | 1529 | a | A | u | A | A | A | G | A | G | u | C | A | A | G | A | A | A | A | A | -4 | 3 | 9 | bc | false | <90% | 3778 | ||
NM_002912 | REV3L | 1401 | 1419 | G | A | C | A | A | A | G | A | G | u | C | A | A | G | c | A | A | A | g | -12 | 3 | 9 | c | false | <90% | 10716 | ||
NM_015111 | N4BP3 | 5839 | 5857 | u | A | C | A | A | A | G | u | a | G | C | A | A | G | A | A | A | A | A | -24 | 3 | 10 | bc | false | <90% | 5987 | ||
NM_012115 | CASP8AP2 | 1280 | 1298 | G | A | C | A | A | A | G | A | a | G | a | A | A | G | A | A | A | A | g | -26 | 3 | 8 | c | false | <90% | 6782 | ||
NM_005994 | TBX2 | 3341 | 3359 | G | A | C | A | A | A | a | A | c | G | C | A | A | G | A | A | A | A | c | -31 | 3 | 9 | bc | false | <90% | 3396 | ||
NM_006824 | EBNA1BP2 | 1078 | 1096 | u | A | C | A | A | A | G | A | a | c | C | A | A | G | A | A | A | A | A | -44 | 3 | 9 | bc | false | <90% | 1325 | ||
NM_021218 | C9orf80 | 244 | 262 | G | A | C | A | A | A | G | A | G | a | a | A | A | G | A | A | A | A | c | -49 | 3 | 9 | c | false | <90% | 1532 |
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_004343 | CALR | 1587 | 1605 | c | U | U | U | U | C | U | U | G | C | C | U | C | U | g | U | G | c | C | 70 | 3 | 13 | c | false | <90% | 1899 | ||
XR_017492 | LOC644330 | 1618 | 1636 | c | U | U | U | U | C | U | U | G | C | C | U | C | c | U | U | G | a | a | 70 | 4 | 12 | c | false | <90% | 2146 | ||
NM_133493 | CD109 | 6402 | 6420 | a | U | U | U | U | C | U | U | G | C | C | U | u | U | U | U | u | U | C | 64 | 3 | 11 | false | <90% | 9447 | |||
NR_002723 | GABPAP | 68118 | 68136 | U | U | U | U | U | C | U | U | G | C | C | U | g | U | U | U | c | U | u | 61 | 3 | 12 | false | <90% | 194142 | |||
NM_000809 | GABRA4 | 8008 | 8026 | U | U | U | U | U | C | U | U | G | C | C | U | g | U | U | U | a | c | a | 58 | 4 | 12 | false | <90% | 11143 | |||
NM_022778 | CCDC21 | 3462 | 3480 | U | U | U | U | U | C | U | U | G | C | C | U | C | c | U | g | G | U | u | 49 | 3 | 13 | c | false | <90% | 3961 | ||
NR_003135 | CEP170L | 70623 | 70641 | U | U | U | U | U | C | c | U | G | C | C | U | C | U | U | U | G | U | g | 28 | 2 | 11 | bc | false | <90% | 90477 | ||
NM_001039712 | DEDD | 307 | 325 | g | c | U | U | U | C | U | U | u | C | C | U | C | U | U | U | G | U | u | 21 | 4 | 9 | bc | false | <90% | 2300 | ||
NM_001039711 | DEDD | 336 | 354 | g | c | U | U | U | C | U | U | u | C | C | U | C | U | U | U | G | U | u | 21 | 4 | 9 | bc | false | <90% | 2329 | ||
NM_032998 | DEDD | 369 | 387 | g | c | U | U | U | C | U | U | u | C | C | U | C | U | U | U | G | U | u | 21 | 4 | 9 | bc | false | <90% | 2362 | ||
NM_005788 | PRMT3 | 2377 | 2395 | a | g | U | U | U | C | U | U | c | C | C | U | C | U | U | U | G | U | g | 21 | 4 | 9 | bc | false | <90% | 2630 | ||
NM_004845 | PCYT1B | 4116 | 4134 | U | U | U | U | U | C | U | U | u | C | C | U | C | U | U | U | u | U | C | 16 | 2 | 8 | c | false | <90% | 5447 | ||
NM_147150 | PALM2-AKAP2 | 137 | 155 | U | U | U | U | U | C | U | U | u | C | C | U | C | U | U | U | c | c | C | 13 | 3 | 8 | c | false | <90% | 5180 | ||
NM_007203 | PALM2-AKAP2 | 137 | 155 | U | U | U | U | U | C | U | U | u | C | C | U | C | U | U | U | c | c | C | 13 | 3 | 8 | c | false | <90% | 7522 | ||
NM_020177 | FEM1C | 2780 | 2798 | U | U | U | U | U | C | U | U | G | C | u | U | C | U | U | U | c | U | u | 10 | 3 | 10 | c | false | <90% | 5813 | ||
NM_182749 | N6AMT1 | 4183 | 4201 | U | U | U | U | U | C | c | U | G | C | C | U | C | a | U | U | G | U | u | 9 | 3 | 6 | c | false | <90% | 4799 | ||
NM_013240 | N6AMT1 | 4267 | 4285 | U | U | U | U | U | C | c | U | G | C | C | U | C | a | U | U | G | U | u | 9 | 3 | 6 | c | false | <90% | 4883 | ||
NM_015308 | FNBP4 | 3489 | 3507 | U | U | U | U | U | C | U | g | G | C | C | U | C | U | U | U | u | c | u | 6 | 4 | 8 | c | false | <90% | 3995 | ||
NM_001083910 | SIRPB1 | 1097 | 1115 | a | U | U | c | U | C | U | U | u | C | C | U | C | U | U | U | G | U | C | 1 | 3 | 10 | bc | false | <90% | 1762 | ||
NM_006065 | SIRPB1 | 1748 | 1766 | a | U | U | c | U | C | U | U | u | C | C | U | C | U | U | U | G | U | C | 1 | 3 | 10 | bc | false | <90% | 2413 | ||
NM_018569 | C4orf16 | 2720 | 2738 | U | U | U | U | U | C | U | U | G | g | C | U | u | U | U | U | G | U | u | 1 | 3 | 9 | false | <90% | 2831 | |||
NM_130906 | PPIL3 | 257 | 275 | a | a | U | U | U | C | U | U | G | g | C | U | C | U | U | U | G | U | g | -1 | 4 | 8 | bc | false | <90% | 1114 | ||
NM_131916 | PPIL3 | 763 | 781 | a | a | U | U | U | C | U | U | G | g | C | U | C | U | U | U | G | U | g | -1 | 4 | 8 | bc | false | <90% | 1620 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2021
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