Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
87 hits were found for UCUGUGCCUUCUCAUCUGC (24 guide strand hits and 63 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_001040429 | PCDH17 | 6385 | 6403 | U | u | U | G | U | G | C | C | U | U | C | U | C | u | U | C | U | G | g | 64 | 3 | 11 | c | false | <90% | 8009 | ||
NM_025090 | USP36 | 4498 | 4516 | g | C | U | G | U | G | C | C | U | U | C | U | C | A | U | g | U | u | u | 64 | 4 | 14 | c | false | <90% | 5234 | ||
NM_003627 | SLC43A1 | 1348 | 1366 | g | u | U | G | U | G | C | C | U | U | C | U | C | A | c | C | U | G | C | 61 | 3 | 12 | c | false | <90% | 2525 | ||
NM_198141 | GANC | 4218 | 4236 | U | C | U | G | U | G | C | C | U | U | C | U | g | A | U | C | c | c | u | 58 | 4 | 12 | false | <90% | 4603 | |||
NM_001029884 | PLEKHG1 | 3694 | 3712 | U | C | U | G | U | G | C | C | U | U | C | U | C | u | U | C | a | a | a | 49 | 4 | 13 | c | false | <90% | 7237 | ||
NM_182918 | ERG | 1501 | 1519 | c | a | U | a | U | G | C | C | U | U | C | U | C | A | U | C | U | G | g | 44 | 4 | 14 | bc | false | <90% | 3055 | ||
NM_004449 | ERG | 1543 | 1561 | c | a | U | a | U | G | C | C | U | U | C | U | C | A | U | C | U | G | g | 44 | 4 | 14 | bc | false | <90% | 3097 | ||
NM_033405 | PRIC285 | 5689 | 5707 | U | C | U | G | U | G | C | C | U | U | C | c | C | c | U | C | U | G | u | 41 | 3 | 11 | false | <90% | 7507 | |||
NM_001037335 | PRIC285 | 8181 | 8199 | U | C | U | G | U | G | C | C | U | U | C | c | C | c | U | C | U | G | u | 41 | 3 | 11 | false | <90% | 10013 | |||
NM_017559 | FNDC8 | 342 | 360 | U | C | U | c | U | G | C | C | U | U | C | U | C | A | U | C | c | a | C | 37 | 3 | 12 | c | false | <90% | 1369 | ||
XM_001131346 | LOC731941 | 1147 | 1165 | U | C | U | u | U | G | C | C | U | U | C | U | C | A | U | C | a | a | g | 32 | 4 | 12 | c | false | <90% | 2044 | ||
XR_017956 | C6orf59 | 1131 | 1149 | g | C | U | c | U | G | C | C | U | U | C | c | C | A | U | C | U | G | C | 27 | 3 | 7 | false | <90% | 1848 | |||
XR_017853 | C6orf59 | 1131 | 1149 | g | C | U | c | U | G | C | C | U | U | C | c | C | A | U | C | U | G | C | 27 | 3 | 7 | false | <90% | 1848 | |||
NM_001004739 | OR5L2 | 87 | 105 | g | C | U | G | U | u | C | C | U | U | C | U | C | A | U | C | U | a | u | 27 | 4 | 11 | c | false | <90% | 936 | ||
NM_001004738 | OR5L1 | 87 | 105 | g | C | U | G | U | u | C | C | U | U | C | U | C | A | U | C | U | a | u | 27 | 4 | 11 | c | false | <90% | 936 | ||
XM_932037 | KIAA1833 | 1623 | 1641 | c | C | U | G | g | G | C | C | U | U | C | U | C | A | U | C | g | G | C | 23 | 3 | 11 | c | false | <90% | 3808 | ||
XM_001126242 | LOC727957 | 3087 | 3105 | c | C | U | G | g | G | C | C | U | U | C | U | C | A | U | C | g | G | C | 23 | 3 | 11 | c | false | <90% | 5308 | ||
XM_941317 | KIAA1833 | 3087 | 3105 | c | C | U | G | g | G | C | C | U | U | C | U | C | A | U | C | g | G | C | 23 | 3 | 11 | c | false | <90% | 5308 | ||
NM_001077701 | MIER1 | 2005 | 2023 | U | C | U | G | U | a | C | C | U | U | C | U | C | A | U | u | U | G | a | 5 | 3 | 9 | c | false | <90% | 5407 | ||
NM_001077700 | MIER1 | 2086 | 2104 | U | C | U | G | U | a | C | C | U | U | C | U | C | A | U | u | U | G | a | 5 | 3 | 9 | c | false | <90% | 5488 | ||
NM_020948 | MIER1 | 2161 | 2179 | U | C | U | G | U | a | C | C | U | U | C | U | C | A | U | u | U | G | a | 5 | 3 | 9 | c | false | <90% | 5563 | ||
NM_001665 | RHOG | 177 | 195 | g | a | c | G | U | G | C | C | U | g | C | U | C | A | U | C | U | G | C | -15 | 4 | 9 | bc | false | <90% | 1286 | ||
XM_001130886 | FLJ37034 | 915 | 933 | c | C | U | G | c | G | C | C | U | g | C | U | C | A | U | C | U | G | C | -36 | 3 | 9 | bc | false | <90% | 2982 | ||
XM_001127207 | FLJ37034 | 915 | 933 | c | C | U | G | c | G | C | C | U | g | C | U | C | A | U | C | U | G | C | -36 | 3 | 9 | bc | false | <90% | 2983 |
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_016831 | PER3 | 3001 | 3019 | u | C | A | G | A | U | G | A | G | A | A | G | G | a | A | C | A | c | g | 70 | 4 | 12 | c | false | <90% | 6203 | ||
NM_023037 | FRY | 5860 | 5878 | a | C | A | G | A | U | G | A | G | A | A | G | G | C | A | a | A | c | A | 69 | 3 | 14 | c | false | <90% | 10718 | ||
NM_145309 | LRRC51 | 821 | 839 | G | C | A | G | A | U | G | A | G | A | A | G | u | C | A | C | u | u | A | 63 | 3 | 12 | false | <90% | 2130 | |||
NM_182914 | SYNE2 | 12615 | 12633 | G | g | A | G | A | U | G | A | G | A | A | G | G | C | A | g | A | G | c | 57 | 3 | 13 | c | false | <90% | 21882 | ||
NM_015180 | SYNE2 | 12615 | 12633 | G | g | A | G | A | U | G | A | G | A | A | G | G | C | A | g | A | G | c | 57 | 3 | 13 | c | false | <90% | 21816 | ||
NM_001042437 | ST3GAL5 | 151 | 169 | c | a | A | G | A | U | G | A | G | A | A | G | G | C | c | C | A | G | c | 56 | 4 | 12 | c | false | <90% | 2262 | ||
NM_003896 | ST3GAL5 | 296 | 314 | c | a | A | G | A | U | G | A | G | A | A | G | G | C | c | C | A | G | c | 56 | 4 | 12 | c | false | <90% | 2397 | ||
XM_001126439 | LOC730489 | 404 | 422 | u | C | A | G | A | U | G | A | G | A | A | c | u | C | A | C | A | G | A | 53 | 3 | 10 | false | <90% | 543 | |||
XM_001132973 | LOC729112 | 404 | 422 | u | C | A | G | A | U | G | A | G | A | A | c | u | C | A | C | A | G | A | 53 | 3 | 10 | false | <90% | 543 | |||
NM_198267 | ING3 | 360 | 378 | G | C | A | G | A | U | G | A | G | A | A | G | G | u | u | C | A | G | u | 50 | 3 | 13 | c | false | <90% | 1240 | ||
NM_019071 | ING3 | 360 | 378 | G | C | A | G | A | U | G | A | G | A | A | G | G | u | u | C | A | G | u | 50 | 3 | 13 | c | false | <90% | 2221 | ||
NM_172349 | NSD1 | 739 | 757 | G | C | A | G | A | U | G | A | G | A | A | G | G | a | A | a | A | G | c | 49 | 3 | 13 | c | false | <90% | 7693 | ||
NM_022455 | NSD1 | 1504 | 1522 | G | C | A | G | A | U | G | A | G | A | A | G | G | a | A | a | A | G | c | 49 | 3 | 13 | c | false | <90% | 8458 | ||
NM_002912 | REV3L | 7459 | 7477 | G | C | u | G | A | U | G | A | G | A | A | G | G | C | A | C | u | u | u | 49 | 4 | 13 | c | false | <90% | 10716 | ||
XM_001128037 | LOC728654 | 93 | 111 | G | a | A | a | A | U | G | A | G | A | A | G | G | C | A | C | A | G | c | 46 | 3 | 14 | bc | false | <90% | 584 | ||
XM_001129553 | LOC731413 | 93 | 111 | G | a | A | a | A | U | G | A | G | A | A | G | G | C | A | C | A | G | c | 46 | 3 | 14 | bc | false | <90% | 584 | ||
XR_016959 | LOC391472 | 1137 | 1155 | G | a | g | G | A | U | G | A | G | A | A | G | G | C | A | C | u | G | A | 45 | 3 | 13 | c | false | <90% | 1421 | ||
XR_018191 | LOC647702 | 1137 | 1155 | G | a | g | G | A | U | G | A | G | A | A | G | G | C | A | C | u | G | A | 45 | 3 | 13 | c | false | <90% | 1421 | ||
XM_936222 | LOC653877 | 7927 | 7945 | G | C | A | G | A | U | G | A | G | A | A | G | G | C | g | g | A | G | u | 44 | 3 | 14 | c | false | <90% | 8800 | ||
NM_014503 | UTP20 | 7939 | 7957 | G | C | A | G | A | U | G | A | G | A | A | G | G | C | g | g | A | G | u | 44 | 3 | 14 | c | false | <90% | 9029 | ||
NM_001216 | CA9 | 1338 | 1356 | G | C | A | G | A | U | G | A | G | A | A | G | G | C | A | g | c | a | c | 42 | 4 | 15 | c | false | <90% | 1552 | ||
NM_020748 | INTS2 | 1084 | 1102 | G | C | A | G | A | U | G | A | G | A | A | G | G | C | A | g | c | u | u | 42 | 4 | 15 | c | false | <90% | 5894 | ||
XM_001132803 | LOC730175 | 158 | 176 | a | u | u | G | A | U | G | A | G | A | A | G | G | C | A | g | A | G | A | 40 | 4 | 12 | c | false | <90% | 216 | ||
XM_001131623 | LOC732020 | 158 | 176 | a | u | u | G | A | U | G | A | G | A | A | G | G | C | A | g | A | G | A | 40 | 4 | 12 | c | false | <90% | 216 | ||
XM_001128866 | LOC728903 | 156 | 174 | a | C | A | G | A | U | G | A | G | A | A | a | G | C | u | C | A | G | A | 39 | 3 | 10 | false | <90% | 1479 | |||
XM_001128879 | LOC728903 | 199 | 217 | a | C | A | G | A | U | G | A | G | A | A | a | G | C | u | C | A | G | A | 39 | 3 | 10 | false | <90% | 2561 | |||
NM_001486 | GCKR | 1756 | 1774 | G | C | A | c | A | U | G | A | G | A | A | G | G | a | A | C | A | G | g | 38 | 3 | 9 | c | false | <90% | 2197 | ||
NM_015075 | IQSEC2 | 669 | 687 | G | a | g | u | A | U | G | A | G | A | A | G | G | C | A | C | A | G | A | 32 | 3 | 15 | bc | false | <90% | 5248 | ||
NM_004178 | TARBP2 | 1254 | 1272 | G | a | A | G | c | U | G | A | G | A | A | G | G | C | A | C | A | G | g | 32 | 3 | 13 | bc | false | <90% | 1448 | ||
NM_134324 | TARBP2 | 1294 | 1312 | G | a | A | G | c | U | G | A | G | A | A | G | G | C | A | C | A | G | g | 32 | 3 | 13 | bc | false | <90% | 1488 | ||
NM_134323 | TARBP2 | 1719 | 1737 | G | a | A | G | c | U | G | A | G | A | A | G | G | C | A | C | A | G | g | 32 | 3 | 13 | bc | false | <90% | 1888 | ||
XM_928235 | FLJ12688 | 932 | 950 | a | C | A | G | A | U | G | u | G | A | A | G | a | C | A | C | A | G | A | 25 | 3 | 6 | false | <90% | 1839 | |||
XM_940431 | FLJ12688 | 932 | 950 | a | C | A | G | A | U | G | u | G | A | A | G | a | C | A | C | A | G | A | 25 | 3 | 6 | false | <90% | 1839 | |||
NM_198460 | GBP6 | 1582 | 1600 | G | C | A | G | c | U | G | A | G | A | A | G | G | a | A | C | A | G | g | 24 | 3 | 8 | c | false | <90% | 3047 | ||
NM_001159 | AOX1 | 1082 | 1100 | c | C | A | G | A | g | G | A | G | A | A | G | a | C | A | C | A | G | A | 24 | 3 | 6 | false | <90% | 4949 | |||
NM_052941 | GBP4 | 1579 | 1597 | G | C | A | G | c | U | G | A | G | A | A | G | G | a | A | C | A | G | g | 24 | 3 | 8 | c | false | <90% | 5454 | ||
NM_001559 | IL12RB2 | 2681 | 2699 | G | C | A | G | A | g | G | A | G | A | A | G | a | C | A | C | A | G | c | 21 | 3 | 6 | false | <90% | 4040 | |||
NM_005335 | HCLS1 | 809 | 827 | G | a | A | G | A | g | G | A | G | A | A | G | G | C | A | C | A | G | c | 20 | 3 | 12 | bc | false | <90% | 2029 | ||
NM_001025158 | CD74 | 856 | 874 | c | g | A | G | A | U | G | g | G | A | A | G | G | C | A | C | A | G | g | 19 | 4 | 10 | bc | false | <90% | 1155 | ||
NM_004355 | CD74 | 1031 | 1049 | c | g | A | G | A | U | G | g | G | A | A | G | G | C | A | C | A | G | g | 19 | 4 | 10 | bc | false | <90% | 1327 | ||
NM_001025159 | CD74 | 1223 | 1241 | c | g | A | G | A | U | G | g | G | A | A | G | G | C | A | C | A | G | g | 19 | 4 | 10 | bc | false | <90% | 1519 | ||
NM_002693 | POLG | 3214 | 3232 | G | C | A | G | c | U | G | A | G | A | A | G | G | C | c | C | A | G | c | 18 | 3 | 9 | c | false | <90% | 4465 | ||
NM_194286 | KIAA1853 | 741 | 759 | c | a | A | G | A | a | G | A | G | A | A | G | G | C | A | C | A | G | c | 18 | 4 | 12 | bc | false | <90% | 8382 | ||
NM_001007232 | INCA | 374 | 392 | c | C | A | G | A | U | G | A | u | A | A | a | G | C | A | C | A | G | A | 4 | 3 | 7 | false | <90% | 466 | |||
XM_932515 | MIA3 | 2461 | 2479 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 6531 | |||
XM_943832 | MIA3 | 2461 | 2479 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 6531 | |||
NM_198551 | MIA3 | 2459 | 2477 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 8123 | |||
XM_943873 | MIA3 | 2461 | 2479 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 9239 | |||
XM_371369 | MIA3 | 2461 | 2479 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 9416 | |||
XM_496436 | MIA3 | 2461 | 2479 | G | C | A | G | A | U | a | A | G | A | A | a | G | C | A | C | A | G | A | 0 | 2 | 7 | false | <90% | 10108 | |||
NM_003939 | BTRC | 4574 | 4592 | G | C | A | G | A | U | G | A | G | g | A | G | G | u | A | C | A | G | A | -2 | 2 | 9 | c | false | <90% | 6038 | ||
NM_033637 | BTRC | 4682 | 4700 | G | C | A | G | A | U | G | A | G | g | A | G | G | u | A | C | A | G | A | -2 | 2 | 9 | c | false | <90% | 6146 | ||
XM_001127513 | LOC730581 | 427 | 445 | G | C | A | G | u | U | G | g | G | A | A | G | G | C | A | C | A | G | c | -18 | 3 | 10 | bc | false | <90% | 3853 | ||
XM_001128488 | LOC728254 | 427 | 445 | G | C | A | G | u | U | G | g | G | A | A | G | G | C | A | C | A | G | c | -18 | 3 | 10 | bc | false | <90% | 3853 | ||
NM_178857 | RP1L1 | 6407 | 6425 | G | C | A | G | A | a | G | A | G | g | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 7978 | ||
NM_201378 | PLEC1 | 6319 | 6337 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14626 | ||
NM_201381 | PLEC1 | 6339 | 6357 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14646 | ||
NM_201382 | PLEC1 | 6368 | 6386 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14675 | ||
NM_201383 | PLEC1 | 6382 | 6400 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14689 | ||
NM_201379 | PLEC1 | 6444 | 6462 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14751 | ||
NM_000445 | PLEC1 | 6448 | 6466 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14755 | ||
NM_201384 | PLEC1 | 6490 | 6508 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 14797 | ||
NM_201380 | PLEC1 | 6942 | 6960 | G | C | A | G | A | g | G | A | G | c | A | G | G | C | A | C | A | G | g | -51 | 3 | 8 | bc | false | <90% | 15249 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3104
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