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) (Click for details)	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