Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
48 hits were found for GAAGCCAUAGCCAAGGAAG (36 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 | |||||||||||||
NM_000093 | COL5A1 | 7913 | 7931 | a | A | A | G | C | C | A | U | A | G | C | C | g | A | G | G | A | c | u | 79 | 4 | 11 | false | <90% | 8439 | |||
NM_015018 | DOPEY1 | 5916 | 5934 | c | c | A | G | C | C | A | U | A | G | C | C | A | A | G | G | A | c | a | 78 | 4 | 15 | ac | false | <90% | 7918 | ||
NM_015077 | SARM1 | 4905 | 4923 | u | A | g | G | C | C | A | U | A | G | C | C | A | A | G | G | A | u | c | 70 | 4 | 14 | c | false | <90% | 6862 | ||
NM_031956 | TTC29 | 1134 | 1152 | G | A | A | G | C | C | A | U | A | G | C | C | A | A | G | G | u | c | c | 68 | 3 | 16 | ac | false | <90% | 1760 | ||
NM_015475 | FAM98A | 699 | 717 | c | A | A | G | C | C | A | U | A | G | C | C | A | A | u | G | A | A | u | 68 | 3 | 13 | c | false | <90% | 2745 | ||
NM_024054 | C7orf25 | 196 | 214 | a | u | c | G | C | C | A | U | A | G | C | C | A | A | G | G | A | A | c | 62 | 4 | 15 | bc | false | <90% | 1812 | ||
NM_152468 | TMC8 | 277 | 295 | G | A | g | G | C | C | A | U | A | G | C | C | A | A | G | G | c | c | u | 49 | 4 | 13 | c | false | <90% | 2798 | ||
XR_017033 | LOC642395 | 73 | 91 | G | A | A | G | C | C | A | U | A | G | C | C | A | A | G | u | g | u | c | 42 | 4 | 15 | c | false | <90% | 1920 | ||
NM_015841 | ADAR | 1914 | 1932 | G | A | A | G | C | C | A | a | A | G | C | C | A | A | G | G | A | c | a | 30 | 3 | 9 | c | false | <90% | 6505 | ||
NM_001025107 | ADAR | 1806 | 1824 | G | A | A | G | C | C | A | a | A | G | C | C | A | A | G | G | A | c | a | 30 | 3 | 9 | c | false | <90% | 6532 | ||
NM_015840 | ADAR | 1914 | 1932 | G | A | A | G | C | C | A | a | A | G | C | C | A | A | G | G | A | c | a | 30 | 3 | 9 | c | false | <90% | 6562 | ||
NM_001111 | ADAR | 1914 | 1932 | G | A | A | G | C | C | A | a | A | G | C | C | A | A | G | G | A | c | a | 30 | 3 | 9 | c | false | <90% | 6640 | ||
NM_003819 | PABPC4 | 1344 | 1362 | G | g | A | G | C | C | A | a | A | G | C | C | A | A | G | G | A | A | u | 21 | 3 | 10 | bc | false | <90% | 3065 | ||
NM_013992 | PAX8 | 1418 | 1436 | G | A | A | G | C | a | A | U | A | G | C | C | g | A | G | G | A | A | c | 21 | 3 | 6 | false | <90% | 3653 | |||
NM_013953 | PAX8 | 1520 | 1538 | G | A | A | G | C | a | A | U | A | G | C | C | g | A | G | G | A | A | c | 21 | 3 | 6 | false | <90% | 3755 | |||
NM_013951 | PAX8 | 1641 | 1659 | G | A | A | G | C | a | A | U | A | G | C | C | g | A | G | G | A | A | c | 21 | 3 | 6 | false | <90% | 3876 | |||
NM_013952 | PAX8 | 1751 | 1769 | G | A | A | G | C | a | A | U | A | G | C | C | g | A | G | G | A | A | c | 21 | 3 | 6 | false | <90% | 3986 | |||
NM_003466 | PAX8 | 1830 | 1848 | G | A | A | G | C | a | A | U | A | G | C | C | g | A | G | G | A | A | c | 21 | 3 | 6 | false | <90% | 4065 | |||
NM_021076 | NEFH | 2947 | 2965 | G | A | g | G | C | C | A | a | A | G | C | C | A | A | G | G | A | A | G | 18 | 2 | 11 | bc | false | <90% | 3695 | ||
NM_021161 | KCNK10 | 383 | 401 | G | A | A | G | C | a | A | U | A | G | C | C | A | u | G | G | A | A | G | 17 | 2 | 7 | c | false | <90% | 2710 | ||
NM_025132 | WDR19 | 2855 | 2873 | u | A | u | G | C | C | A | a | A | G | C | C | A | A | G | G | A | A | G | 16 | 3 | 11 | bc | false | <90% | 4534 | ||
NM_030623 | SKIP | 1865 | 1883 | G | A | A | G | C | C | A | U | u | G | C | C | A | A | G | G | g | A | u | 11 | 3 | 8 | c | false | <90% | 6824 | ||
NM_002913 | RFC1 | 735 | 753 | G | A | A | G | C | C | A | U | c | G | C | C | A | A | G | c | A | A | u | 8 | 3 | 8 | c | false | <90% | 4925 | ||
NM_001605 | AARS | 2337 | 2355 | G | A | A | G | C | C | A | U | u | G | C | C | A | A | G | G | g | u | a | 8 | 4 | 8 | c | false | <90% | 3344 | ||
NM_003798 | CTNNAL1 | 301 | 319 | G | A | A | G | C | u | A | U | A | G | C | C | A | A | u | G | A | A | a | 7 | 3 | 8 | c | false | <90% | 2445 | ||
NM_020817 | KIAA1407 | 2356 | 2374 | G | A | A | G | C | a | A | U | A | G | C | C | A | A | a | G | A | A | c | 7 | 3 | 8 | c | false | <90% | 3996 | ||
XM_371878 | FLJ14712 | 298 | 316 | G | A | A | G | C | C | A | c | A | G | C | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 3164 | ||
XM_936911 | FLJ14712 | 298 | 316 | G | A | A | G | C | C | A | c | A | G | C | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 3164 | ||
XM_374405 | FLJ14712 | 298 | 316 | G | A | A | G | C | C | A | c | A | G | C | C | A | A | G | a | A | A | u | 6 | 3 | 7 | c | false | <90% | 3164 | ||
XR_019443 | LOC442270 | 75 | 93 | a | c | c | G | C | C | A | U | g | G | C | C | A | A | G | G | A | A | G | 6 | 4 | 10 | bc | false | <90% | 500 | ||
XR_017483 | LOC442270 | 75 | 93 | a | c | c | G | C | C | A | U | g | G | C | C | A | A | G | G | A | A | G | 6 | 4 | 10 | bc | false | <90% | 500 | ||
NM_031481 | SLC25A18 | 389 | 407 | G | g | g | G | C | C | A | g | A | G | C | C | A | A | G | G | A | A | G | 6 | 3 | 11 | bc | false | <90% | 2087 | ||
NM_020927 | KIAA1576 | 92 | 110 | a | g | c | G | C | C | A | U | g | G | C | C | A | A | G | G | A | A | G | 6 | 4 | 10 | bc | false | <90% | 3784 | ||
XM_001126140 | LOC727846 | 838 | 856 | G | A | A | G | C | C | u | U | A | G | C | C | A | A | G | G | g | u | c | 2 | 4 | 9 | c | false | <90% | 1328 | ||
XM_001133726 | LOC731713 | 838 | 856 | G | A | A | G | C | C | u | U | A | G | C | C | A | A | G | G | g | u | c | 2 | 4 | 9 | c | false | <90% | 1328 | ||
NM_004869 | VPS4B | 1593 | 1611 | u | A | A | G | C | C | A | a | A | G | a | C | A | A | G | G | A | A | G | -25 | 3 | 8 | c | false | <90% | 3396 |
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_002664 | PLEK | 1518 | 1536 | C | U | U | C | C | U | U | G | G | C | U | A | a | G | u | C | U | U | g | 59 | 3 | 12 | false | <90% | 2745 | |||
NM_080669 | SLC46A1 | 2026 | 2044 | g | a | U | C | C | U | U | G | G | C | U | A | U | G | G | C | c | U | a | 58 | 4 | 14 | ac | false | <90% | 6505 | ||
NM_005048 | PTHR2 | 683 | 701 | g | U | U | C | C | U | U | G | G | C | U | g | U | G | G | C | U | a | u | 56 | 4 | 10 | false | <90% | 2810 | |||
NM_030641 | APOL6 | 1023 | 1041 | C | U | c | C | C | U | U | G | G | C | U | A | U | G | a | C | U | U | g | 50 | 3 | 11 | c | false | <90% | 10156 | ||
NM_178128 | FADS6 | 1512 | 1530 | C | g | g | C | C | U | U | G | G | C | U | A | U | u | G | C | U | U | C | 49 | 3 | 10 | c | false | <90% | 2052 | ||
NM_022736 | MFSD1 | 178 | 196 | C | U | U | C | C | U | U | G | G | C | U | u | U | G | G | C | a | g | C | 40 | 3 | 11 | false | <90% | 2161 | |||
NM_000120 | EPHX1 | 828 | 846 | C | a | U | C | C | c | U | G | G | C | U | A | U | G | G | C | U | U | C | 25 | 2 | 13 | bc | false | <90% | 1856 | ||
NM_002241 | KCNJ10 | 535 | 553 | C | a | c | C | a | U | U | G | G | C | U | A | U | G | G | C | U | U | C | 17 | 3 | 14 | bc | false | <90% | 4440 | ||
NM_031936 | GPR61 | 829 | 847 | a | g | g | C | C | U | U | G | G | C | c | A | U | G | G | C | U | U | C | 5 | 4 | 8 | c | false | <90% | 2462 | ||
NM_000937 | POLR2A | 6566 | 6584 | C | U | U | C | C | U | U | G | c | C | U | g | U | G | G | C | U | U | g | 1 | 3 | 8 | false | <90% | 6732 | |||
NM_007101 | SARDH | 1468 | 1486 | C | U | U | C | C | U | g | G | G | C | U | g | U | G | G | C | U | U | C | 0 | 2 | 7 | false | <90% | 3363 | |||
NM_006639 | CYSLTR1 | 511 | 529 | C | U | U | C | u | U | U | G | G | C | a | A | U | G | G | C | U | U | u | -17 | 3 | 7 | c | false | <90% | 1537 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2879
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