Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
39 hits were found for GGCAAAGCCAUCCCCAUUG (27 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_001001670 | FLJ46321 | 4579 | 4597 | G | u | C | A | A | A | G | C | C | A | U | C | C | C | C | A | a | U | c | 60 | 3 | 14 | ac | false | <90% | 4828 | ||
XR_018260 | LOC138972 | 295 | 313 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 1048 | ||
XR_016778 | LOC138972 | 295 | 313 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 1048 | ||
NM_001077685 | CTGLF4 | 892 | 910 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 2420 | ||
NM_001077686 | CTGLF5 | 892 | 910 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 2420 | ||
NM_133446 | CTGLF1 | 892 | 910 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 2420 | ||
XM_370567 | KIAA1975 | 1556 | 1574 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3182 | ||
XM_937229 | KIAA1975 | 1556 | 1574 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3182 | ||
XM_001127181 | LOC728005 | 1742 | 1760 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3293 | ||
XM_001132582 | LOC729092 | 1743 | 1761 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3295 | ||
XR_016668 | LOC653234 | 2008 | 2026 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3558 | ||
XR_015281 | LOC728127 | 2272 | 2290 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3817 | ||
XR_015233 | LOC642517 | 2272 | 2290 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 3817 | ||
XM_001132574 | LOC729092 | 2934 | 2952 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 4402 | ||
XM_001132585 | LOC729092 | 2865 | 2883 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 4417 | ||
XM_001127197 | LOC728005 | 2905 | 2923 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 4456 | ||
XM_001132588 | LOC729092 | 2934 | 2952 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 4486 | ||
XM_001127212 | LOC728005 | 2974 | 2992 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 4525 | ||
XM_001127140 | LOC728005 | 5624 | 5642 | G | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 43 | 2 | 13 | bc | false | <90% | 7115 | ||
XR_016708 | LOC653259 | 2985 | 3003 | a | G | C | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 41 | 3 | 13 | bc | false | <90% | 4536 | ||
NM_018018 | SLC38A4 | 2416 | 2434 | G | G | C | A | A | A | G | C | u | A | U | C | a | C | C | A | U | U | u | 24 | 3 | 8 | false | <90% | 3961 | |||
NM_001077665 | CTGLF3 | 892 | 910 | G | G | u | A | g | A | G | C | C | A | U | C | C | C | C | A | U | U | a | 23 | 3 | 13 | bc | false | <90% | 2429 | ||
NM_001004713 | OR1I1 | 265 | 283 | a | G | C | A | g | A | G | C | C | A | U | C | C | C | C | u | U | U | G | 20 | 3 | 10 | c | false | <90% | 1068 | ||
NM_000690 | ALDH2 | 913 | 931 | G | G | g | A | A | A | a | C | C | A | U | C | C | C | C | A | U | U | G | 14 | 2 | 12 | bc | false | <90% | 2445 | ||
XR_016143 | LOC642317 | 886 | 904 | G | G | C | A | A | A | G | u | C | A | U | C | C | C | C | A | c | a | c | 6 | 4 | 8 | c | false | <90% | 1242 | ||
NM_001949 | E2F3 | 2697 | 2715 | G | a | g | A | A | A | G | a | C | A | U | C | C | C | C | A | U | U | G | 6 | 3 | 11 | bc | false | <90% | 4744 | ||
NM_030791 | SGPP1 | 728 | 746 | G | G | C | A | c | c | G | C | C | A | U | C | C | C | C | A | U | U | u | -19 | 3 | 12 | bc | false | <90% | 3323 |
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_002901 | RCN1 | 334 | 352 | u | g | A | U | G | G | G | G | A | U | G | G | C | U | U | U | G | u | C | 83 | 3 | 15 | ac | false | <90% | 2104 | ||
NM_014246 | CELSR1 | 10018 | 10036 | a | g | g | U | G | G | G | G | A | U | G | G | C | U | U | U | G | u | C | 64 | 4 | 14 | c | false | <90% | 11389 | ||
NM_030805 | LMAN2L | 401 | 419 | g | c | A | U | G | G | G | G | A | U | G | G | C | U | U | g | G | C | a | 55 | 4 | 13 | c | false | <90% | 2412 | ||
XM_939887 | HNRPA1P4 | 610 | 628 | C | A | A | U | G | G | G | G | A | U | G | G | C | U | a | U | a | a | u | 44 | 4 | 14 | c | false | <90% | 1574 | ||
XM_372050 | HNRPA1P4 | 610 | 628 | C | A | A | U | G | G | G | G | A | U | G | G | C | U | a | U | a | a | u | 44 | 4 | 14 | c | false | <90% | 1574 | ||
NM_005656 | TMPRSS2 | 1647 | 1665 | C | A | A | U | G | G | G | G | c | U | G | G | u | U | U | U | G | C | u | 24 | 3 | 8 | false | <90% | 3226 | |||
NM_018682 | MLL5 | 3969 | 3987 | C | A | A | U | G | G | u | G | A | U | G | G | C | U | g | U | G | C | C | 9 | 2 | 7 | c | false | <90% | 6725 | ||
NM_182931 | MLL5 | 4117 | 4135 | C | A | A | U | G | G | u | G | A | U | G | G | C | U | g | U | G | C | C | 9 | 2 | 7 | c | false | <90% | 6873 | ||
NM_020960 | GPR107 | 6294 | 6312 | g | A | A | U | G | G | G | c | A | U | G | G | C | U | U | g | G | C | C | 9 | 3 | 7 | c | false | <90% | 6895 | ||
XM_941785 | LOC652355 | 477 | 495 | g | A | c | U | G | G | G | G | A | a | G | G | C | U | U | U | G | C | C | -4 | 3 | 9 | bc | false | <90% | 1269 | ||
NM_000615 | NCAM1 | 5089 | 5107 | u | A | A | U | G | u | c | G | A | U | G | G | C | U | U | U | G | C | C | -31 | 3 | 12 | bc | false | <90% | 5951 | ||
NM_181351 | NCAM1 | 5119 | 5137 | u | A | A | U | G | u | c | G | A | U | G | G | C | U | U | U | G | C | C | -31 | 3 | 12 | bc | false | <90% | 5981 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2097
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