Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
46 hits were found for GAAGCAGGAAUACCAAGAG (31 guide strand hits and 15 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_001271 | CHD2 | 4127 | 4145 | a | A | u | G | C | A | G | G | A | A | U | A | C | g | A | A | G | A | G | 58 | 3 | 10 | c | false | <90% | 9374 | ||
NM_133378 | TTN | 13911 | 13929 | G | A | u | G | C | A | G | G | A | A | U | A | C | a | A | A | G | A | u | 55 | 3 | 10 | c | false | <90% | 101519 | ||
XR_017059 | LOC646048 | 817 | 835 | c | A | A | G | C | A | G | G | A | A | U | A | C | g | A | g | G | A | G | 52 | 3 | 12 | c | false | <90% | 931 | ||
XR_019608 | LOC646048 | 817 | 835 | c | A | A | G | C | A | G | G | A | A | U | A | C | g | A | g | G | A | G | 52 | 3 | 12 | c | false | <90% | 931 | ||
NM_001005736 | LYST | 6467 | 6485 | u | u | u | G | C | A | G | G | A | A | U | A | C | a | A | A | G | A | G | 47 | 4 | 10 | c | false | <90% | 7069 | ||
NM_000081 | LYST | 6091 | 6109 | u | u | u | G | C | A | G | G | A | A | U | A | C | a | A | A | G | A | G | 47 | 4 | 10 | c | false | <90% | 13493 | ||
NM_001079818 | ITGA6 | 632 | 650 | G | A | A | G | C | A | G | G | A | A | U | c | C | C | g | A | G | A | c | 36 | 3 | 11 | false | <90% | 5680 | |||
NM_000210 | ITGA6 | 632 | 650 | G | A | A | G | C | A | G | G | A | A | U | c | C | C | g | A | G | A | c | 36 | 3 | 11 | false | <90% | 5810 | |||
NM_058172 | ANTXR2 | 2011 | 2029 | G | A | A | G | C | A | G | G | A | A | g | A | C | C | A | A | G | A | a | 33 | 2 | 10 | c | false | <90% | 3881 | ||
NM_001310 | CREBL2 | 587 | 605 | c | A | A | G | C | A | G | G | c | A | U | A | C | C | A | A | G | g | c | 30 | 4 | 8 | c | false | <90% | 3748 | ||
NM_177550 | SLC13A5 | 594 | 612 | G | c | A | G | C | A | G | G | A | A | g | A | C | C | A | A | G | A | G | 27 | 2 | 8 | c | false | <90% | 3248 | ||
NM_015590 | GPATCH4 | 1173 | 1191 | G | A | A | G | C | A | G | G | A | A | a | A | g | C | A | A | G | A | a | 23 | 3 | 10 | false | <90% | 1906 | |||
NM_182679 | GPATCH4 | 1247 | 1265 | G | A | A | G | C | A | G | G | A | A | a | A | g | C | A | A | G | A | a | 23 | 3 | 10 | false | <90% | 1980 | |||
XM_938923 | LOC649851 | 20 | 38 | c | c | A | G | C | A | G | G | A | A | g | A | C | C | A | A | G | A | a | 20 | 4 | 8 | c | false | <90% | 387 | ||
NM_002477 | MYL5 | 110 | 128 | c | c | A | G | C | A | G | G | A | A | g | A | C | C | A | A | G | A | a | 20 | 4 | 8 | c | false | <90% | 661 | ||
NM_015192 | PLCB1 | 3441 | 3459 | G | g | A | G | C | A | a | G | A | A | U | A | C | C | A | A | G | A | c | 17 | 3 | 11 | bc | false | <90% | 6705 | ||
NM_182734 | PLCB1 | 3559 | 3577 | G | g | A | G | C | A | a | G | A | A | U | A | C | C | A | A | G | A | c | 17 | 3 | 11 | bc | false | <90% | 6823 | ||
XM_937424 | LOC653978 | 156 | 174 | G | A | A | c | a | A | G | G | A | A | U | A | C | C | A | A | G | A | G | 11 | 2 | 14 | bc | false | <90% | 525 | ||
NM_138800 | TRIM43 | 739 | 757 | G | A | A | c | a | A | G | G | A | A | U | A | C | C | A | A | G | A | G | 11 | 2 | 14 | bc | false | <90% | 1642 | ||
XR_017562 | LOC643445 | 737 | 755 | G | A | A | c | a | A | G | G | A | A | U | A | C | C | A | A | G | A | G | 11 | 2 | 14 | bc | false | <90% | 1670 | ||
XM_926437 | LOC653192 | 739 | 757 | G | A | A | c | a | A | G | G | A | A | U | A | C | C | A | A | G | A | G | 11 | 2 | 14 | bc | false | <90% | 1674 | ||
NM_022444 | SLC13A1 | 1024 | 1042 | u | A | A | G | C | A | a | G | A | A | U | A | C | C | A | A | a | A | G | 8 | 3 | 9 | c | false | <90% | 3811 | ||
NM_176815 | DHFRL1 | 1974 | 1992 | G | A | A | G | C | A | G | G | A | A | a | A | C | C | A | A | u | u | c | 7 | 4 | 10 | c | false | <90% | 3770 | ||
NM_000791 | DHFR | 2303 | 2321 | G | A | A | G | C | A | G | G | A | A | a | A | C | C | A | A | u | u | a | 7 | 4 | 10 | c | false | <90% | 3932 | ||
NM_001858 | COL19A1 | 994 | 1012 | G | A | A | G | C | A | G | G | A | u | U | A | C | C | A | g | G | A | G | -8 | 2 | 9 | c | false | <90% | 8725 | ||
NM_014943 | ZHX2 | 4156 | 4174 | a | A | A | G | a | A | G | G | A | A | a | A | C | C | A | A | G | A | G | -14 | 3 | 8 | c | false | <90% | 4373 | ||
XR_016641 | LOC392545 | 81 | 99 | u | A | A | G | a | A | G | a | A | A | U | A | C | C | A | A | G | A | G | -15 | 3 | 11 | bc | false | <90% | 629 | ||
XR_018699 | LOC392545 | 81 | 99 | u | A | A | G | a | A | G | a | A | A | U | A | C | C | A | A | G | A | G | -15 | 3 | 11 | bc | false | <90% | 629 | ||
XR_018199 | LOC648160 | 1064 | 1082 | c | A | A | G | C | A | a | a | A | A | U | A | C | C | A | A | G | A | G | -30 | 3 | 11 | bc | false | <90% | 1118 | ||
XR_016844 | LOC643309 | 1064 | 1082 | c | A | A | G | C | A | a | a | A | A | U | A | C | C | A | A | G | A | G | -30 | 3 | 11 | bc | false | <90% | 1118 | ||
NM_020937 | FANCM | 3932 | 3950 | c | A | A | G | C | A | c | u | A | A | U | A | C | C | A | A | G | A | G | -30 | 3 | 11 | bc | false | <90% | 7143 |
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_194314 | ZBTB41 | 7965 | 7983 | u | g | C | U | U | G | G | U | A | U | U | C | C | U | G | C | U | U | g | 81 | 3 | 16 | abc | false | <90% | 8474 | ||
NM_001001921 | OR5AS1 | 82 | 100 | u | U | C | U | U | G | G | U | A | U | U | C | C | U | u | C | U | g | g | 65 | 4 | 13 | c | false | <90% | 975 | ||
NM_017758 | ALKBH5 | 1603 | 1621 | u | U | C | U | U | G | G | U | A | U | U | C | C | U | c | C | U | g | g | 65 | 4 | 13 | c | false | <90% | 2992 | ||
NM_021156 | TXNDC13 | 672 | 690 | C | U | C | U | U | G | G | a | A | U | U | C | C | U | G | C | U | U | g | 32 | 2 | 10 | bc | false | <90% | 2368 | ||
NM_001037234 | TMEM75 | 904 | 922 | u | U | C | U | U | u | G | U | A | U | U | C | C | U | G | u | U | U | C | 8 | 3 | 9 | c | false | <90% | 2165 | ||
XR_019475 | LOC651980 | 565 | 583 | C | U | C | U | U | G | G | U | g | U | U | C | C | U | G | C | a | c | a | 8 | 4 | 8 | c | false | <90% | 596 | ||
XR_017618 | LOC647039 | 565 | 583 | C | U | C | U | U | G | G | U | g | U | U | C | C | U | G | C | a | c | a | 8 | 4 | 8 | c | false | <90% | 596 | ||
NM_014875 | KIF14 | 485 | 503 | u | U | C | U | U | G | a | U | A | U | U | C | C | U | u | C | U | U | C | 6 | 3 | 7 | c | false | <90% | 6586 | ||
NM_001040440 | CCDC112 | 1970 | 1988 | u | c | a | U | U | a | G | U | A | U | U | C | C | U | G | C | U | U | C | 3 | 4 | 13 | bc | false | <90% | 2506 | ||
NM_152549 | CCDC112 | 2016 | 2034 | u | c | a | U | U | a | G | U | A | U | U | C | C | U | G | C | U | U | C | 3 | 4 | 13 | bc | false | <90% | 2552 | ||
NR_003265 | SDHALP2 | 23096 | 23114 | u | U | C | U | U | G | G | U | A | U | g | g | C | U | G | C | U | U | C | 2 | 3 | 9 | false | <90% | 30843 | |||
NR_003264 | SDHALP1 | 22273 | 22291 | u | U | C | U | U | G | G | U | A | U | g | g | C | U | G | C | U | U | C | 2 | 3 | 9 | false | <90% | 30398 | |||
NM_009589 | ARSD | 803 | 821 | C | U | C | U | U | G | G | U | A | c | U | C | C | U | c | C | U | U | C | -7 | 2 | 9 | c | false | <90% | 2236 | ||
NM_001669 | ARSD | 803 | 821 | C | U | C | U | U | G | G | U | A | c | U | C | C | U | c | C | U | U | C | -7 | 2 | 9 | c | false | <90% | 5159 | ||
NM_133457 | EMID2 | 2829 | 2847 | C | U | C | U | U | G | G | U | A | c | U | C | C | U | G | u | U | U | g | -13 | 3 | 9 | c | false | <90% | 3034 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3225
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