Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
60 hits were found for GCCUCAUCUUCUUAUUGGU (12 guide strand hits and 48 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_001042536 | INSC | 1797 | 1815 | u | C | C | U | C | A | U | C | U | U | C | U | U | A | U | U | u | a | U | 71 | 3 | 15 | ac | false | <90% | 2894 | ||
NM_001031853 | INSC | 1873 | 1891 | u | C | C | U | C | A | U | C | U | U | C | U | U | A | U | U | u | a | U | 71 | 3 | 15 | ac | false | <90% | 2970 | ||
NM_005972 | PPYR1 | 1321 | 1339 | a | C | C | U | C | A | U | C | U | U | C | U | U | A | g | U | G | u | g | 65 | 4 | 13 | c | false | <90% | 1956 | ||
NM_003830 | SIGLEC5 | 1506 | 1524 | G | C | C | U | C | A | U | C | U | U | C | U | U | u | U | U | a | a | U | 54 | 3 | 13 | c | false | <90% | 2130 | ||
XR_017856 | LOC441233 | 2256 | 2274 | u | C | C | U | u | A | U | C | U | U | C | U | U | A | U | U | G | u | U | 43 | 3 | 12 | c | false | <90% | 2539 | ||
XR_017940 | LOC441233 | 2256 | 2274 | u | C | C | U | u | A | U | C | U | U | C | U | U | A | U | U | G | u | U | 43 | 3 | 12 | c | false | <90% | 2539 | ||
NM_024746 | KIAA1822L | 141 | 159 | G | C | C | U | C | A | U | a | U | U | C | U | U | g | U | U | G | G | g | 13 | 3 | 7 | c | false | <90% | 2582 | ||
XM_936336 | SYNPO2 | 3380 | 3398 | G | C | C | U | C | A | U | C | a | U | C | U | U | A | U | U | u | u | g | 8 | 4 | 8 | c | false | <90% | 7050 | ||
NM_133477 | SYNPO2 | 3380 | 3398 | G | C | C | U | C | A | U | C | a | U | C | U | U | A | U | U | u | u | g | 8 | 4 | 8 | c | false | <90% | 7318 | ||
XM_942780 | SYNPO2 | 3376 | 3394 | G | C | C | U | C | A | U | C | a | U | C | U | U | A | U | U | u | u | g | 8 | 4 | 8 | c | false | <90% | 9946 | ||
NM_004727 | SLC24A1 | 358 | 376 | G | C | C | U | C | c | U | C | U | U | C | U | U | A | c | U | G | G | g | 7 | 3 | 8 | c | false | <90% | 5768 | ||
NM_152890 | COL24A1 | 2904 | 2922 | G | C | C | U | C | A | U | g | g | U | C | U | U | A | U | U | G | G | U | -22 | 2 | 10 | bc | false | <90% | 6500 |
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_003411 | ZFY | 1673 | 1691 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | a | A | G | u | u | 67 | 3 | 14 | c | false | <90% | 4556 | ||
NM_002690 | POLB | 947 | 965 | u | u | C | A | A | U | A | A | G | A | A | u | A | U | G | A | G | G | g | 47 | 4 | 9 | false | <90% | 1259 | |||
NM_018453 | EAPP | 802 | 820 | g | u | C | c | A | U | A | A | G | A | A | G | A | U | G | A | G | G | u | 44 | 4 | 14 | bc | false | <90% | 1363 | ||
NM_014309 | RBM9 | 936 | 954 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6948 | ||
NM_001082579 | RBM9 | 890 | 908 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6954 | ||
NM_001082577 | RBM9 | 933 | 951 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6957 | ||
NM_001082578 | RBM9 | 893 | 911 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6957 | ||
NM_001082576 | RBM9 | 933 | 951 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6985 | ||
NM_001031695 | RBM9 | 933 | 951 | A | C | C | A | A | U | A | A | G | A | A | G | A | U | G | g | u | c | a | 42 | 4 | 15 | c | false | <90% | 6997 | ||
NM_178135 | HSD17B13 | 797 | 815 | A | C | C | A | A | U | A | A | G | A | A | a | A | U | G | A | u | u | u | 35 | 4 | 11 | false | <90% | 2377 | |||
NM_001014797 | KCNMA1 | 9482 | 9500 | u | a | u | A | A | U | A | A | G | A | A | c | A | U | G | A | G | G | C | 33 | 4 | 8 | false | <90% | 11993 | |||
NM_000335 | SCN5A | 3367 | 3385 | A | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 31 | 2 | 12 | bc | false | <90% | 8501 | ||
NM_198056 | SCN5A | 3367 | 3385 | A | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 31 | 2 | 12 | bc | false | <90% | 8504 | ||
NM_001001575 | PDE9A | 247 | 265 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1675 | ||
NM_001001569 | PDE9A | 291 | 309 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1719 | ||
NM_001001572 | PDE9A | 302 | 320 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1730 | ||
NM_001001577 | PDE9A | 325 | 343 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1753 | ||
NM_001001568 | PDE9A | 346 | 364 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1774 | ||
NM_001001579 | PDE9A | 362 | 380 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1790 | ||
NM_001001578 | PDE9A | 369 | 387 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1797 | ||
NM_001001574 | PDE9A | 417 | 435 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1845 | ||
NM_001001571 | PDE9A | 424 | 442 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1852 | ||
NM_001001584 | PDE9A | 424 | 442 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1852 | ||
NM_001001573 | PDE9A | 482 | 500 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1910 | ||
NM_001001567 | PDE9A | 495 | 513 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1923 | ||
NM_001001570 | PDE9A | 516 | 534 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1944 | ||
NM_001001581 | PDE9A | 526 | 544 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1954 | ||
NM_001001585 | PDE9A | 549 | 567 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 1977 | ||
NM_001001583 | PDE9A | 597 | 615 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 2025 | ||
NM_001001582 | PDE9A | 604 | 622 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 2032 | ||
NM_002606 | PDE9A | 675 | 693 | g | a | C | A | u | U | A | A | G | A | A | G | A | U | G | A | G | G | g | 30 | 4 | 13 | bc | false | <90% | 2103 | ||
NM_024781 | CCDC102B | 823 | 841 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | A | G | c | u | 29 | 3 | 11 | c | false | <90% | 2015 | ||
NM_004316 | ASCL1 | 1007 | 1025 | g | C | C | A | A | c | A | A | G | A | A | G | A | U | G | A | G | u | a | 27 | 4 | 11 | c | false | <90% | 2482 | ||
NM_013449 | BAZ2A | 2332 | 2350 | A | g | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | C | 25 | 2 | 13 | bc | false | <90% | 8934 | ||
NM_015693 | INTU | 137 | 155 | c | a | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 18 | 4 | 12 | bc | false | <90% | 3238 | ||
NM_080629 | COL11A1 | 1116 | 1134 | u | u | C | A | A | a | A | A | G | A | A | G | A | U | G | A | G | G | a | 18 | 4 | 12 | bc | false | <90% | 7327 | ||
NM_015169 | RRS1 | 966 | 984 | A | C | C | A | A | U | A | A | G | c | A | G | A | U | G | A | G | G | g | 12 | 2 | 9 | bc | false | <90% | 1724 | ||
NM_147233 | NCOA1 | 4931 | 4949 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6892 | ||
NM_003743 | NCOA1 | 4934 | 4952 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6895 | ||
NM_147223 | NCOA1 | 4991 | 5009 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6952 | ||
NM_198503 | KCNT2 | 2004 | 2022 | A | C | C | A | A | U | c | A | G | A | A | G | A | U | G | A | a | a | C | 7 | 3 | 9 | c | false | <90% | 5909 | ||
NM_003898 | SYNJ2 | 1879 | 1897 | A | C | C | A | A | c | A | A | G | A | A | G | A | U | G | u | G | G | g | 5 | 3 | 9 | c | false | <90% | 6738 | ||
NM_194301 | GARNL1 | 7425 | 7443 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | g | G | G | a | 5 | 3 | 9 | c | false | <90% | 7851 | ||
NM_014990 | GARNL1 | 7456 | 7474 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | g | G | G | a | 5 | 3 | 9 | c | false | <90% | 7882 | ||
NM_014959 | CARD8 | 2317 | 2335 | A | C | C | A | A | a | A | A | G | A | A | a | A | U | G | A | G | G | g | -2 | 3 | 6 | false | <90% | 5059 | |||
NM_182483 | NSFL1C | 1092 | 1110 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3451 | ||
NM_018839 | NSFL1C | 1190 | 1208 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3551 | ||
NM_016143 | NSFL1C | 1190 | 1208 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3644 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1887
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