shRNA choices

Grey shRNAs are recommended
Light blue indicates preferred values
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Regeneration seed: 1254875022
siRNA sense strand
siRNA loop area
siRNA anti-sense strand
Sticky vector linkers (use yours)
RNA polymerase terminator (use yours)
Strand not transcribed

ID Target Gene(s)
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Target
Loc(s)
Nontarget Gene(s)
(Click for details)
Nontarget
Loc(s)
Target
Temp
Nontarget
Temp
Temp
Diff
3' AT
Count
3' Open
Energy
Min
Range
Multi
Loc
Binding
Energy
Score
(0-6)
shRNA Schematic Drawings (Oligos hidden under URL links)
1 HBV_genome
HBV_genome
150
3332
ENSMUST00000075578
ENST00000289753
674
1525
74.92 60.42
57.50
14.5 1 -13.75 18 2 -46.93 3 5'- GCACCTCTCTTTACGCGGA CTATATGTC TCCGCGTAAAGAGAGGTGCGC -3'-X
3'- CGTGGAGAGAAATGCGCCT GATATACAG AGGCGCATTTCTCTCCACGCG -5'-Y
2 HBV_genome
HBV_genome
282
3464
ENSMUST00000098858
ENST00000326544
215
243
69.45 59.59
57.40
9.86 3 -10.97 17 2 -43.66 2 5'- GAGGACTCTTGGACTCTCA GCCGTGGAT TGAGAGTCCAAGAGTCCTCTT -3'-X
3'- CTCCTGAGAACCTGAGAGT CGGCACCTA ACTCTCAGGTTCTCAGGAGAA -5'-Y
3 HBV_genome
523
ENSMUST00000117706
ENST00000380094
2229
208
74.56 62.73
65.31
9.25 3 -10.86 15 1 -46.48 2 5'- GCATGGACATCGACCCTTA TAGGCGTGG TAAGGGTCGATGTCCATGCCC -3'-X
3'- CGTACCTGTAGCTGGGAAT ATCCGCACC ATTCCCAGCTACAGGTACGGG -5'-Y
4 HBV_genome
736
ENSMUST00000055655
ENST00000406168
847
178
70.02 61.18
62.53
7.48 4 -9.58 18 1 -42.04 3 5'- GGGTGGGTGTTAATTTGGA AGGATATGT TCCAAATTAACACCCACCCAG -3'-X
3'- CCCACCCACAATTAAACCT TCCTATACA AGGTTTAATTGTGGGTGGGTC -5'-Y
5 HBV_genome
737
ENSMUST00000040320
ENST00000321562
3598
2507
67.79 57.68
57.95
9.84 4 -9.58 17 1 -40.89 3 5'- GGTGGGTGTTAATTTGGAA GACGTGGAT TTCCAAATTAACACCCACCCA -3'-X
3'- CCACCCACAATTAAACCTT CTGCACCTA AAGGTTTAATTGTGGGTGGGT -5'-Y
6 HBV_genome
769
ENSMUST00000009538
ENST00000244020
2251
2230
62.69 48.78
47.46
13.9 4 -8.69 16 1 -40.11 4 5'- GAGACCTAGTAGTCAGTTA TGGCGCCGA TAACTGACTACTAGGTCTCTA -3'-X
3'- CTCTGGATCATCAGTCAAT ACCGCGGCT ATTGACTGATGATCCAGAGAT -5'-Y
7 HBV_genome
859
ENSMUST00000053768
ENST00000327134
4098
5540
61.62 50.34
49.28
11.27 4 -10.08 17 1 -35.09 2 5'- GAGAAACAGTTATAGAGTA TTGATATGT TACTCTATAACTGTTTCTCTT -3'-X
3'- CTCTTTGTCAATATCTCAT AACTATACA ATGAGATATTGACAAAGAGAA -5'-Y
8 HBV_genome
956
ENSMUST00000092070
ENST00000405322
400
690
67.61 61.22
58.13
6.39 4 -8.93 18 1 -41.95 3 5'- GGAGACTACTGTTGTTAGA CGGTGGATA TCTAACAACAGTAGTCTCCGG -3'-X
3'- CCTCTGATGACAACAATCT GCCACCTAT AGATTGTTGTCATCAGAGGCC -5'-Y
9 HBV_genome
959
ENSMUST00000041978
ENST00000389652
3005
2227
63.97 49.36
53.79
10.18 3 -11.38 18 1 -40.02 2 5'- GACTACTGTTGTTAGACGA CGTATGTCC TCGTCTAACAACAGTAGTCTC -3'-X
3'- CTGATGACAACAATCTGCT GCATACAGG AGCAGATTGTTGTCATCAGAG -5'-Y
10 HBV_genome
1113
ENSMUST00000041055
ENST00000405303
7434
1286
62.44 50.35
49.83
12.08 4 -10 17 1 -38.36 2 5'- GCTTTATTCTTCTACTGTA CCTATGTCC TACAGTAGAAGAATAAAGCCC -3'-X
3'- CGAAATAAGAAGATGACAT GGATACAGG ATGTCATCTTCTTATTTCGGG -5'-Y
11 HBV_genome
1342
ENSMUST00000119943
ENST00000409406
2684
287
56.23 47.98
48.02
8.2 4 -9.58 16 1 -32.59 2 5'- GTTAATCATTACTTCCAAA CTCTGCGGG TTTGGAAGTAATGATTAACTA -3'-X
3'- CAATTAGTAATGAAGGTTT GAGACGCCC AAACCTTCATTACTAATTGAT -5'-Y
12 HBV_genome
1390
ENSMUST00000066241
ENST00000396128
204
4116
62.37 49.89
53.01
9.36 5 -7.79 18 1 -37.22 2 5'- GCGGGTATATTATATAAGA GAGCGTGGA TCTTATATAATATACCCGCCT -3'-X
3'- CGCCCATATAATATATTCT CTCGCACCT AGAATATATTATATGGGCGGA -5'-Y
13 HBV_genome
1440
ENSMUST00000036732
ENST00000302981
295
759
67.65 52.75
54.45
13.2 3 -11.91 17 1 -42.56 2 5'- GTCACCATATTCTTGGGAA CAGCGGGTA TTCCCAAGAATATGGTGACCC -3'-X
3'- CAGTGGTATAAGAACCCTT GTCGCCCAT AAGGGTTCTTATACCACTGGG -5'-Y
14 HBV_genome
1529
ENSMUST00000120860
ENST00000369473
1986
467
73.84 62.17
62.44
11.4 3 -10.89 16 1 -45.74 2 5'- GATCCAGCCTTCAGAGCAA ACTGGATAT TTGCTCTGAAGGCTGGATCCA -3'-X
3'- CTAGGTCGGAAGTCTCGTT TGACCTATA AACGAGACTTCCGACCTAGGT -5'-Y
15 HBV_genome
1562
ENSMUST00000119407
ENST00000378281
45
175
69.53 58.19
57.90
11.34 3 -12.08 17 1 -42.27 2 5'- GATTGGGACTTCAATCCCA ACTGGATAT TGGGATTGAAGTCCCAATCTG -3'-X
3'- CTAACCCTGAAGTTAGGGT TGACCTATA ACCCTAACTTCAGGGTTAGAC -5'-Y
16 HBV_genome
1793
ENSMUST00000121863
ENST00000203664
1917
873
73.04 65.19
69.49
3.55 4 -9.75 17 1 -45.59 3 5'- GCCATGCAGTGGAATTCCA CATAAATAG TGGAATTCCACTGCATGGCCT -3'-X
3'- CGGTACGTCACCTTAAGGT GTATTTATC ACCTTAAGGTGACGTACCGGA -5'-Y
17 HBV_genome
1910
ENSMUST00000105884
ENST00000395423
584
4014
71.29 61.28
63.96
7.33 3 -9.99 16 1 -44.03 2 5'- GCCTCTCCCTTATCGTCAA TCTAAATAG TTGACGATAAGGGAGAGGCAG -3'-X
3'- CGGAGAGGGAATAGCAGTT AGATTTATC AACTGCTATTCCCTCTCCGTC -5'-Y
18 HBV_genome
1989
ENSMUST00000117217
ENST00000261318
1356
887
72.53 59.54
64.94
7.59 4 -8.85 17 1 -45.06 3 5'- GACCCCTTCTCGTGTTACA GGGTGGATA TGTAACACGAGAAGGGGTCCT -3'-X
3'- CTGGGGAAGAGCACAATGT CCCACCTAT ACATTGTGCTCTTCCCCAGGA -5'-Y
19 HBV_genome
2009
ENSMUST00000106233
ENST00000313080
261
3041
71.08 62.20
66.59
4.48 4 -9.74 18 1 -41.96 3 5'- GCGGGGTTTTTCTTGTTGA CACGGGTAA TCAACAAGAAAAACCCCGCCT -3'-X
3'- CGCCCCAAAAAGAACAACT GTGCCCATT AGTTGTTCTTTTTGGGGCGGA -5'-Y
20 HBV_genome
2012
ENSMUST00000105534
ENST00000311075
362
1669
68.31 55.08
54.26
13.23 4 -9.74 17 1 -38.48 3 5'- GGGTTTTTCTTGTTGACAA GAGCGTGGA TTGTCAACAAGAAAAACCCCG -3'-X
3'- CCCAAAAAGAACAACTGTT CTCGCACCT AACAGTTGTTCTTTTTGGGGC -5'-Y
21 HBV_genome
2269
ENSMUST00000021547
ENST00000270459
5141
1855
72.33 65.61
61.34
6.71 3 -11.1 16 1 -42.69 1 5'- GTTGCCCGTTTGTCCTCTA ATGGCGTGG TAGAGGACAAACGGGCAACAT -3'-X
3'- CAACGGGCAAACAGGAGAT TACCGCACC ATCTCCTGTTTGCCCGTTGTA -5'-Y
22 HBV_genome
2390
ENSMUST00000027226
ENST00000358674
150
652
74.52 58.63
56.84
15.88 3 -11.02 17 1 -42.97 2 5'- GACGGAAATTGCACCTGTA TTGATATGT TACAGGTGCAATTTCCGTCCG -3'-X
3'- CTGCCTTTAACGTGGACAT AACTATACA ATGTCCACGTTAAAGGCAGGC -5'-Y
23 HBV_genome
2462
ENSMUST00000029667
ENST00000281882
3312
218
77.41 65.16
68.42
8.98 2 -13.22 15 1 -48.04 2 5'- GCCCGTTTCTCCTGGCTCA GTGGTAAAT TGAGCCAGGAGAAACGGGCTG -3'-X
3'- CGGGCAAAGAGGACCGAGT CACCATTTA ACTCGGTCCTCTTTGCCCGAC -5'-Y
24 HBV_genome
2622
ENSMUST00000029936
ENST00000266673
2182
2875
61.40 54.29
50.98
7.11 5 -6.4 14 1 -34.84 3 5'- GTCTTTGGGTATACATTTA AAGTAAATA TAAATGTATACCCAAAGACAA -3'-X
3'- CAGAAACCCATATGTAAAT TTCATTTAT ATTTACATATGGGTTTCTGTT -5'-Y
25 HBV_genome
2629
ENSMUST00000041447
ENST00000284061
3988
1910
62.92 49.60
44.64
13.32 3 -12.17 17 1 -37.3 1 5'- GGTATACATTTAAACCCTA ACTGGATAT TAGGGTTTAAATGTATACCCA -3'-X
3'- CCATATGTAAATTTGGGAT TGACCTATA ATCCCAAATTTACATATGGGT -5'-Y
26 HBV_genome
2630
ENSMUST00000041447
ENST00000406025
3988
766
60.31 49.60
46.14
10.71 3 -10.86 16 1 -36.12 1 5'- GTATACATTTAAACCCTAA CAGGTAAAT TTAGGGTTTAAATGTATACCC -3'-X
3'- CATATGTAAATTTGGGATT GTCCATTTA AATCCCAAATTTACATATGGG -5'-Y
27 HBV_genome
2658
ENSMUST00000033664
ENST00000376717
1485
3954
67.85 53.94
58.38
9.46 4 -10.19 16 1 -41.79 2 5'- GAGATGGGGTTACTCTCTA AAGTCCTGC TAGAGAGTAACCCCATCTCTT -3'-X
3'- CTCTACCCCAATGAGAGAT TTCAGGACG ATCTCTCATTGGGGTAGAGAA -5'-Y
28 HBV_genome
2892
ENSMUST00000048229
ENST00000393870
945
2313
73.15 60.17
57.45
12.98 2 -13.5 17 1 -43.38 2 5'- GGCTTTCACTTTCTCGCCA ACTGGATAT TGGCGAGAAAGTGAAAGCCTG -3'-X
3'- CCGAAAGTGAAAGAGCGGT TGACCTATA ACCGCTCTTTCACTTTCGGAC -5'-Y
29 HBV_genome
2893
ENSMUST00000048229
ENST00000389805
945
1681
70.76 60.93
56.94
9.83 2 -12.08 16 1 -42.2 1 5'- GCTTTCACTTTCTCGCCAA CTGGCGTGG TTGGCGAGAAAGTGAAAGCCT -3'-X
3'- CGAAAGTGAAAGAGCGGTT GACCGCACC AACCGCTCTTTCACTTTCGGA -5'-Y
30 HBV_genome
3014
ENSMUST00000078367
ENST00000403066
3519
2336
80.70 70.61
67.29
10.09 1 -15.31 17 1 -50.99 2 5'- GGGGCTTGGTCATGGGCCA TCATAGCTG TGGCCCATGACCAAGCCCCAG -3'-X
3'- CCCCGAACCAGTACCCGGT AGTATCGAC ACCGGGTACTGGTTCGGGGTC -5'-Y
31 HBV_genome
3066
ENSMUST00000001256
ENST00000293861
1785
1037
73.76 58.22
56.28
15.54 2 -12.32 16 1 -45.58 2 5'- GCCGATCCATACTGCGGAA CTATATGTC TTCCGCAGTATGGATCGGCAG -3'-X
3'- CGGCTAGGTATGACGCCTT GATATACAG AAGGCGTCATACCTAGCCGTC -5'-Y

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