Automatic recommendation
Not OK - siRNA is not specific
92 hits were found for CCAAGAGAAAAACUGAAAA (57 guide strand hits and 35 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_013450 | BAZ2B | 4586 | 4604 | g | a | A | A | G | A | G | A | A | A | A | A | C | U | G | A | A | A | A | 86 | 2 | 17 | abc | false | <90% | 8145 | ||
NM_183378 | OVCH1 | 3205 | 3223 | a | a | A | A | G | A | G | A | A | A | A | A | C | U | G | A | A | u | u | 78 | 4 | 15 | ac | false | <90% | 3420 | ||
NM_014721 | PHACTR2 | 844 | 862 | g | C | A | A | G | A | G | A | A | A | A | A | C | U | G | A | c | A | A | 74 | 2 | 15 | ac | false | <90% | 4318 | ||
NR_002723 | GABPAP | 110750 | 110768 | g | C | A | A | G | A | G | A | A | A | A | A | a | a | G | A | A | A | A | 68 | 3 | 11 | false | <90% | 194142 | |||
NM_021179 | C1orf114 | 1213 | 1231 | a | a | g | A | G | A | G | A | A | A | A | A | C | U | G | A | A | A | A | 67 | 3 | 16 | bc | false | <90% | 1866 | ||
NM_018051 | WDR60 | 1359 | 1377 | u | C | A | A | G | A | G | A | A | A | A | A | C | U | G | g | A | A | g | 66 | 3 | 14 | c | false | <90% | 3784 | ||
NM_017738 | C9orf39 | 471 | 489 | g | a | A | A | G | A | G | A | A | A | A | A | C | a | G | A | A | A | u | 62 | 4 | 11 | c | false | <90% | 5522 | ||
NM_001429 | EP300 | 4097 | 4115 | C | C | A | A | G | A | G | A | A | A | A | A | a | U | G | A | c | A | c | 61 | 3 | 12 | false | <90% | 8765 | |||
XM_938194 | LOC127602 | 2740 | 2758 | u | C | A | A | G | A | G | A | A | A | A | A | u | U | G | g | A | A | A | 61 | 3 | 11 | false | <90% | 13621 | |||
XM_059166 | LOC127602 | 2740 | 2758 | u | C | A | A | G | A | G | A | A | A | A | A | u | U | G | g | A | A | A | 61 | 3 | 11 | false | <90% | 13622 | |||
NM_003579 | RAD54L | 693 | 711 | C | C | A | A | G | A | G | A | A | A | A | c | C | U | G | A | A | g | g | 58 | 3 | 11 | false | <90% | 3107 | |||
NM_001259 | CDK6 | 10302 | 10320 | C | C | A | A | G | A | G | A | A | A | A | A | C | U | a | A | u | c | A | 49 | 3 | 14 | c | false | <90% | 11611 | ||
NM_005511 | MLANA | 317 | 335 | u | C | A | A | G | A | G | A | A | A | A | A | C | U | G | u | g | A | A | 48 | 3 | 14 | c | false | <90% | 1524 | ||
NM_020164 | ASPH | 340 | 358 | C | C | A | A | G | A | G | A | A | A | A | A | C | U | a | A | g | g | c | 44 | 4 | 14 | c | false | <90% | 1254 | ||
NM_032467 | ASPH | 365 | 383 | C | C | A | A | G | A | G | A | A | A | A | A | C | U | a | A | g | g | c | 44 | 4 | 14 | c | false | <90% | 1279 | ||
NM_014799 | HEPH | 3850 | 3868 | C | C | A | A | G | A | G | A | A | A | A | A | C | U | c | A | u | u | g | 44 | 4 | 14 | c | false | <90% | 4231 | ||
NM_138737 | HEPH | 3882 | 3900 | C | C | A | A | G | A | G | A | A | A | A | A | C | U | c | A | u | u | g | 44 | 4 | 14 | c | false | <90% | 4279 | ||
NM_052952 | DIRC1 | 739 | 757 | u | u | c | A | G | A | G | A | A | A | A | A | C | U | G | g | A | A | A | 40 | 4 | 12 | c | false | <90% | 1454 | ||
NM_000059 | BRCA2 | 4165 | 4183 | a | C | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | A | 36 | 2 | 9 | c | false | <90% | 11386 | ||
NM_018177 | N4BP2 | 2540 | 2558 | g | g | A | A | c | A | G | A | A | A | A | A | C | U | G | A | A | A | A | 35 | 3 | 14 | bc | false | <90% | 6616 | ||
NM_024996 | GFM1 | 2727 | 2745 | C | a | u | A | G | A | G | A | A | A | A | g | C | U | G | A | A | A | A | 35 | 3 | 8 | false | <90% | 3468 | |||
XM_001126918 | LOC653695 | 5 | 23 | C | C | A | A | G | A | G | A | A | A | g | A | C | U | G | A | A | g | g | 31 | 3 | 10 | c | false | <90% | 222 | ||
XM_929021 | LOC653695 | 5 | 23 | C | C | A | A | G | A | G | A | A | A | g | A | C | U | G | A | A | g | g | 31 | 3 | 10 | c | false | <90% | 222 | ||
NM_020810 | TRMT5 | 4268 | 4286 | C | C | A | A | G | A | G | A | A | A | g | A | C | U | G | A | A | g | g | 31 | 3 | 10 | c | false | <90% | 5302 | ||
NM_173156 | SMG7 | 1888 | 1906 | a | C | A | A | G | A | G | g | A | A | A | A | C | U | G | A | A | A | c | 30 | 3 | 10 | bc | false | <90% | 5846 | ||
NM_198535 | ZNF699 | 557 | 575 | u | C | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | g | u | 29 | 4 | 9 | c | false | <90% | 2094 | ||
NR_003377 | LOC728939 | 1840 | 1858 | a | C | A | A | G | A | G | A | g | A | A | A | g | U | G | A | A | A | A | 27 | 3 | 7 | false | <90% | 18232 | |||
NM_015288 | PHF15 | 6071 | 6089 | a | C | A | A | G | A | G | A | A | A | u | A | u | U | G | A | A | A | A | 26 | 3 | 9 | false | <90% | 6463 | |||
NM_207407 | TMPRSS11F | 474 | 492 | u | C | A | A | G | A | a | A | A | A | A | A | u | U | G | A | A | A | A | 21 | 3 | 6 | false | <90% | 2077 | |||
NM_001761 | CCNF | 3189 | 3207 | a | C | A | A | a | A | G | A | A | A | A | A | C | U | u | A | A | A | A | 21 | 3 | 9 | c | false | <90% | 4287 | ||
NM_014803 | ZNF518 | 1728 | 1746 | g | C | A | A | a | A | G | A | A | A | A | A | C | U | G | g | A | A | A | 20 | 3 | 10 | c | false | <90% | 8296 | ||
XR_016710 | LOC644817 | 453 | 471 | u | u | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | g | 20 | 4 | 8 | c | false | <90% | 1369 | ||
XR_018100 | LOC642180 | 453 | 471 | u | u | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | g | 20 | 4 | 8 | c | false | <90% | 1369 | ||
NM_003576 | STK24 | 644 | 662 | u | u | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | g | 20 | 4 | 8 | c | false | <90% | 4539 | ||
NM_001032296 | STK24 | 729 | 747 | u | u | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | g | 20 | 4 | 8 | c | false | <90% | 4624 | ||
NM_004999 | MYO6 | 3638 | 3656 | a | g | A | A | G | A | G | A | A | A | u | A | C | U | G | A | A | A | c | 20 | 4 | 8 | c | false | <90% | 8662 | ||
NR_003366 | ANKRD20B | 48356 | 48374 | g | a | A | A | G | g | G | A | A | A | A | A | C | U | G | A | A | A | c | 18 | 4 | 12 | bc | false | <90% | 96524 | ||
XR_017609 | LOC645292 | 877 | 895 | u | a | A | A | G | A | a | A | A | A | A | A | C | U | G | A | A | A | u | 15 | 4 | 11 | bc | false | <90% | 2325 | ||
XR_015985 | LOC731809 | 877 | 895 | u | a | A | A | G | A | a | A | A | A | A | A | C | U | G | A | A | A | u | 15 | 4 | 11 | bc | false | <90% | 2325 | ||
NM_014779 | TSC22D2 | 2711 | 2729 | u | u | A | A | G | A | a | A | A | A | A | A | C | U | G | A | A | A | g | 15 | 4 | 11 | bc | false | <90% | 3901 | ||
NM_152569 | C9orf66 | 1558 | 1576 | u | C | A | A | G | A | u | A | A | A | A | A | C | a | G | A | A | A | A | 12 | 3 | 6 | c | false | <90% | 2279 | ||
NM_001042599 | ERBB4 | 1564 | 1582 | a | C | A | A | c | A | G | A | A | A | A | g | C | U | G | A | A | A | A | 12 | 3 | 7 | false | <90% | 11893 | |||
NM_005235 | ERBB4 | 1564 | 1582 | a | C | A | A | c | A | G | A | A | A | A | g | C | U | G | A | A | A | A | 12 | 3 | 7 | false | <90% | 11941 | |||
NM_000104 | CYP1B1 | 3826 | 3844 | a | a | g | A | G | A | G | A | A | A | c | A | C | U | G | A | A | A | A | 5 | 4 | 8 | c | false | <90% | 5128 | ||
NM_015659 | RSL1D1 | 4113 | 4131 | g | g | c | A | G | A | G | c | A | A | A | A | C | U | G | A | A | A | A | 4 | 4 | 11 | bc | false | <90% | 5137 | ||
NM_007187 | WBP4 | 1183 | 1201 | a | a | A | A | G | A | G | A | A | g | A | A | C | U | G | A | A | A | A | 3 | 3 | 9 | bc | false | <90% | 2354 | ||
NM_176815 | DHFRL1 | 1156 | 1174 | a | a | c | A | G | u | G | A | A | A | A | A | C | U | G | A | A | A | A | 3 | 4 | 13 | bc | false | <90% | 3770 | ||
NM_017542 | POGK | 1294 | 1312 | g | g | c | A | G | g | G | A | A | A | A | A | C | U | G | A | A | A | A | 3 | 4 | 13 | bc | false | <90% | 3852 | ||
XR_015213 | LOC730656 | 1691 | 1709 | C | C | A | A | G | A | u | A | A | A | A | g | C | U | G | A | A | A | u | -5 | 3 | 6 | false | <90% | 2712 | |||
XR_015618 | LOC729665 | 1691 | 1709 | C | C | A | A | G | A | u | A | A | A | A | g | C | U | G | A | A | A | u | -5 | 3 | 6 | false | <90% | 2712 | |||
NM_001033873 | LOC57228 | 218 | 236 | C | C | A | A | G | A | G | A | A | g | A | A | C | U | G | A | u | g | A | -8 | 3 | 9 | c | false | <90% | 1076 | ||
NM_020467 | LOC57228 | 206 | 224 | C | C | A | A | G | A | G | A | A | g | A | A | C | U | G | A | u | g | A | -8 | 3 | 9 | c | false | <90% | 1076 | ||
NM_001031628 | LOC57228 | 229 | 247 | C | C | A | A | G | A | G | A | A | g | A | A | C | U | G | A | u | g | A | -8 | 3 | 9 | c | false | <90% | 1087 | ||
NM_004815 | ARHGAP29 | 2501 | 2519 | a | C | A | A | a | A | u | A | A | A | A | A | C | U | G | A | A | A | A | -19 | 3 | 12 | bc | false | <90% | 9121 | ||
NM_145018 | FLJ25416 | 2913 | 2931 | C | C | A | A | G | A | a | A | g | A | A | A | C | U | G | A | A | A | c | -31 | 3 | 9 | bc | false | <90% | 3545 | ||
NM_018087 | TMEM48 | 2435 | 2453 | u | C | A | A | c | A | G | A | A | u | A | A | C | U | G | A | A | A | A | -36 | 3 | 9 | bc | false | <90% | 2541 | ||
NM_014223 | NFYC | 540 | 558 | C | C | A | A | G | A | G | A | u | g | A | A | C | U | G | A | A | A | c | -47 | 3 | 8 | bc | false | <90% | 1965 |
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_199131 | VAX1 | 2915 | 2933 | c | U | U | U | C | A | G | U | U | U | U | U | u | U | C | U | U | u | c | 79 | 4 | 11 | false | <90% | 4493 | |||
NM_000147 | FUCA1 | 1492 | 1510 | g | c | U | U | C | A | G | U | U | U | U | U | C | U | C | U | U | a | u | 78 | 4 | 15 | ac | false | <90% | 2095 | ||
XM_001126647 | MLKL | 85 | 103 | c | U | U | U | C | A | G | U | U | U | U | U | C | U | C | U | a | a | a | 66 | 4 | 15 | ac | false | <90% | 1832 | ||
NM_018046 | AGGF1 | 3529 | 3547 | U | g | U | U | C | A | G | U | U | U | U | U | C | U | C | U | c | a | G | 62 | 3 | 14 | ac | false | <90% | 4480 | ||
NM_004845 | PCYT1B | 4877 | 4895 | a | U | U | U | C | A | G | U | U | U | U | g | C | U | C | U | U | a | G | 61 | 3 | 10 | false | <90% | 5447 | |||
NM_005669 | REEP5 | 1864 | 1882 | U | c | U | U | C | A | G | U | U | U | U | U | C | U | C | U | g | G | c | 60 | 3 | 14 | ac | false | <90% | 3116 | ||
NM_032973 | PCDH11Y | 5247 | 5265 | U | U | U | U | C | A | G | U | U | U | U | U | u | U | g | U | U | G | u | 59 | 3 | 12 | false | <90% | 9056 | |||
NM_032969 | PCDH11X | 5349 | 5367 | U | U | U | U | C | A | G | U | U | U | U | U | u | U | g | U | U | G | u | 59 | 3 | 12 | false | <90% | 9146 | |||
NM_032968 | PCDH11X | 5379 | 5397 | U | U | U | U | C | A | G | U | U | U | U | U | u | U | g | U | U | G | u | 59 | 3 | 12 | false | <90% | 9176 | |||
NM_079422 | MYL1 | 679 | 697 | U | c | U | U | C | A | G | U | U | U | U | U | C | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 862 | ||
NM_079420 | MYL1 | 869 | 887 | U | c | U | U | C | A | G | U | U | U | U | U | C | U | C | U | g | a | a | 57 | 4 | 14 | ac | false | <90% | 1052 | ||
NM_181762 | UBE2A | 779 | 797 | g | c | U | U | C | A | G | U | U | U | U | U | C | U | g | U | U | G | u | 56 | 4 | 12 | c | false | <90% | 1709 | ||
NM_003336 | UBE2A | 869 | 887 | g | c | U | U | C | A | G | U | U | U | U | U | C | U | g | U | U | G | u | 56 | 4 | 12 | c | false | <90% | 1799 | ||
NM_181777 | UBE2A | 1714 | 1732 | g | c | U | U | C | A | G | U | U | U | U | U | C | U | g | U | U | G | u | 56 | 4 | 12 | c | false | <90% | 2678 | ||
NM_002711 | PPP1R3A | 3475 | 3493 | a | g | U | g | C | A | G | U | U | U | U | U | C | U | C | U | U | G | a | 44 | 4 | 14 | bc | false | <90% | 6779 | ||
NR_003135 | CEP170L | 32294 | 32312 | U | U | U | U | C | A | G | U | U | U | U | U | C | U | C | c | a | a | a | 42 | 4 | 15 | c | false | <90% | 90477 | ||
NM_005653 | TFCP2 | 1357 | 1375 | a | U | a | g | C | A | G | U | U | U | U | U | C | U | C | U | U | G | G | 41 | 3 | 15 | bc | false | <90% | 2393 | ||
NM_000788 | DCK | 1628 | 1646 | U | U | U | U | a | A | G | U | U | U | U | U | C | U | C | U | U | u | u | 40 | 3 | 12 | c | false | <90% | 2460 | ||
NM_016166 | PIAS1 | 2223 | 2241 | U | U | U | U | C | A | G | U | U | U | U | a | C | U | u | U | U | G | u | 36 | 3 | 11 | false | <90% | 2309 | |||
XM_938514 | PRPF40A | 3739 | 3757 | a | a | U | U | C | A | G | U | c | U | U | U | C | U | C | U | U | G | c | 21 | 4 | 9 | bc | false | <90% | 7651 | ||
XM_371575 | PRPF40A | 4368 | 4386 | a | a | U | U | C | A | G | U | c | U | U | U | C | U | C | U | U | G | c | 21 | 4 | 9 | bc | false | <90% | 8280 | ||
NM_004398 | DDX10 | 276 | 294 | U | U | U | U | C | A | G | a | U | U | U | U | C | c | C | U | U | G | u | 13 | 3 | 7 | c | false | <90% | 3204 | ||
NM_007037 | ADAMTS8 | 263 | 281 | U | U | U | U | C | A | G | U | U | U | c | U | C | U | C | U | c | u | G | 12 | 3 | 10 | c | false | <90% | 4028 | ||
NM_013449 | BAZ2A | 6484 | 6502 | U | U | U | U | C | A | G | a | U | U | U | U | C | U | C | U | c | a | u | 6 | 4 | 8 | c | false | <90% | 8934 | ||
NM_014023 | WDR37 | 3495 | 3513 | g | c | c | U | C | A | c | U | U | U | U | U | C | U | C | U | U | G | G | 0 | 4 | 12 | bc | false | <90% | 4611 | ||
NM_005798 | TRIM13 | 4371 | 4389 | U | U | U | g | C | A | G | U | a | U | U | U | C | U | C | U | U | G | u | -1 | 3 | 9 | bc | false | <90% | 6776 | ||
NM_052811 | TRIM13 | 4456 | 4474 | U | U | U | g | C | A | G | U | a | U | U | U | C | U | C | U | U | G | u | -1 | 3 | 9 | bc | false | <90% | 6861 | ||
NM_001007278 | TRIM13 | 4570 | 4588 | U | U | U | g | C | A | G | U | a | U | U | U | C | U | C | U | U | G | u | -1 | 3 | 9 | bc | false | <90% | 6975 | ||
NM_213590 | TRIM13 | 4906 | 4924 | U | U | U | g | C | A | G | U | a | U | U | U | C | U | C | U | U | G | u | -1 | 3 | 9 | bc | false | <90% | 7311 | ||
NM_007250 | KLF8 | 2297 | 2315 | U | U | U | c | C | A | a | U | U | U | U | U | C | U | C | U | U | G | u | -8 | 3 | 11 | bc | false | <90% | 2559 | ||
XM_001133722 | LOC731797 | 1152 | 1170 | U | U | U | U | C | A | G | c | a | U | U | U | C | U | C | U | U | G | G | -22 | 2 | 10 | bc | false | <90% | 1278 | ||
XM_934714 | RAPGEF2 | 454 | 472 | U | U | U | U | C | u | u | U | U | U | U | U | C | U | C | U | U | G | G | -29 | 2 | 12 | bc | false | <90% | 5309 | ||
XM_944403 | RAPGEF2 | 454 | 472 | U | U | U | U | C | u | u | U | U | U | U | U | C | U | C | U | U | G | G | -29 | 2 | 12 | bc | false | <90% | 7645 | ||
XM_376350 | RAPGEF2 | 454 | 472 | U | U | U | U | C | u | u | U | U | U | U | U | C | U | C | U | U | G | G | -29 | 2 | 12 | bc | false | <90% | 7647 | ||
XM_001128998 | BRUNOL4 | 3614 | 3632 | U | U | U | U | C | u | u | U | U | U | U | U | C | U | C | U | U | G | a | -34 | 3 | 11 | bc | false | <90% | 3825 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2372
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