siRNA Scan
Enter your sequences in
FASTA
format:
Specify the following parameters for siRNA
:
Length of siRNA (nt):
18
19
20
21
22
23
24
25
26
27
28
29
The 5' terminal base of antisense strand is A or U
Minimum A/U bp in 7 terminal bases of antisense
3
4
5
The 5' terminal base of sense strand is G or C
GC content (%):
from
to
Avoid 4 or more Gs or Cs in a row:
Avoid 9 G/C in a row:
Mismatch allowed in BLAST search:
Specify dataset:
---------------Plant---------------
Arabidopsis thaliana mRNA (from TIGR Ath1 5)
Allium_cepa (Onion) V 2 release on 7/17/2008
Arabidopsis thaliana TAIR9 V 9 release on 6/19/2009
Arabidopsis thaliana DFCI Gene Index V 15 release on 4/23/2010
Aquilegia DFCI Gene Index (AQGI) V 2.1 release on 7/23/2008
Beta_vulgaris (Beet) DFCI Gene Index (BVGI) V 3 release on 6/17/2010
Brassica napus (oilseed_rape) DFCI Gene Index (BNGI) V 3 release on 9/12/2007
Brassica napus (oilseed_rape) DFCI Gene Index (BNGI) V 4 release on 3/19/2010
Capsicum_annuum (Pepper) DFCI Gene Index (CAGI) V 4 release on 6/2/2009
Carica_papaya (Papaya) DFCI Gene Index (CAPAGI) V 1 release on 6/28/2010
Chlamydomonas reinhardtii DFCI Gene Index (CHRGI) V 7 release on 4/23/2010
Chlorella_NC64A.best_transcripts V 1 release on 6/13/2008
Chlorella_NC64A_ESTclusters V 1 release on 6/13/2008
Citrus_clementina (Clementine) DFCI Gene Index (CICLGI) V 2 release on 6/2/2009
Citrus_sinensis (Orange) DFCI Gene Index (CSGI) V 1 release on 7/1/2008
Coffea_canephora (coffee) DFCI Gene Index (COCAGI) V 2 release on 4/23/2010
Ectocarpus_siliculosus (Brown algae) DFCI Gene Index (BAGI) V 1 release on 6/28/2010
Euphorbia_esula (Leafy_spurge) DFCI Gene Index (EUESGI) V 1 release on 7/10/2008
Festuca_arundinacea (tall_fescue) DFCI Gene Index (FAGI) V 3 release on 4/23/2010
Festuca_pratensis (Meadow_ryegrass) DFCI Gene Index(MRGI) V 1 release on 6/28/2010
Glycine max (soybean) DFCI Gene Index (GMGI) V 14 release on 6/2/2009
Glycine max (soybean) DFCI Gene Index (GMGI) V 15 release on 4/23/2010
Gossypium (cotton) DFCI Gene Index (CGI) V 9 release on 12/29/2008
Gossypium (cotton) DFCI Gene Index (CGI) V 10 release on 6/2/2009
Gossypium (cotton) DFCI Gene Index (CGI) V 10.1 release on 3/19/2010
Gossypium_raimondii (Cotton_raimondii) DFCI Gene Index (GORAGI) V 1 release on 7/10/2008
Helianthus_annuus (Sunflower) DFCI Gene Index (HAGI) V 6 release on 6/2/2009
Hordeum vulgare (barley) DFCI Gene Index (HVGI) V 11 release on 4/23/2010
Ipomoea_nil (Morning_glory) DFCI Gene Index (IPNIGI) V 1 release on 7/1/2008
Lactuca_sativa (Lettuce) DFCI Gene Index (LSGI) V 3 release on 7/16/2008
Lactuca_serriola (Prickly_lettuce) DFCI Gene Index (LASEGI) V 1 release on 7/1/2008
Lycopersicon esculentum (tomato) SGN unigene V 1 release on 6/17/2009
Lycopersicon esculentum (tomato) DFCI Gene Index (LGI) V 13 release on 4/23/2010
Lotus japonicus (lotus) DFCI Gene Index (LJGI) V 6 release on 7/9/2010
Malus_x_domestica (Apple) DFCI Gene Index (MDGI) V 3 release on 4/23/2010
Manihot_esculenta (Cassava) DFCI Gene Index (MAESGI) V 1 release on 6/28/2010
Medicago truncatula DFCI Gene index (MTGI) V 9 release on 7/17/2008
Medicago truncatula DFCI Gene index (MTGI) V 10 release on 4/23/2020
Mesembryanthemum_crystallinum (Ice plant) DFCI Gene Index (MCGI) V 5 release on 7/1/2008
Mimulus_guttatus (Spotted_monkey_flower) DFCI Gene Index (MIGUGI) V 1 release on 6/28/2010
Nicotiana benthamiana DFCI Gene Index (NBGI) V 4 release on 4/23/2010
Nicotiana tabacum (tobacco) DFCI Gene Index (NTGI) V 6 release on 4/23/2010
Nicotiana tabacum (tobacco) SGN unigene V 2 release on 9/10/2009
Oryza sativa (rice) DFCI Gene index (OGI) V 17 release on 9/28/2006
Oryza sativa (rice) DFCI Gene index (OGI) V 18 release on 4/23/2010
Panicum_virgatum (Switchgrass) DFCI Gene Index (PAVIGI) V 1 release on 6/10/2009
Petunia_hybrida (Petunia) DFCI Gene Index (PHGI) V 2.1 release on 4/23/2010
Phaseolus_coccineus (Scarlet_bean) DFCI Gene Index (PCGI) V 1 release on 6/2/2009
Phaseolus_vulgaris (Bean) DFCI Gene index (PHVGI) V 3.1 release on 4/23/2010
Physcomitrella patens (moss) JGI Gene Transcripts V 1.1 release on 4/1/2008
Physcomitrella_patens (Moss) DFCI Gene Index (PPSPGI) V 1 release on 7/10/2008
Picea (Spruce) DFCI Gene Index (SGI) V 4 release on 3/19/2010
Pinus (Pine) DFGI Gene Index (PGI) V 8 release on 4/23/2020
Populus trichocarpa (poplar) JGI Gene Transcripts V 1.1 release on 2/3/2010
Populus trichocarpa (poplar) DFCI Gene Index (PPLGI) V 5 release on 4/23/2010
Populus trichocarpa (poplar) Genome Assembly V 1 release on 2/3/2010
Populus trichocarpa (poplar) JGI Gene Transcripts V 2 release on 1/26/2010
Quercus (Oak) DFCI Gene Index (OGI) V 1 release on 8/5/2010
Raphanus_sativus (Radish) DFCI Gene Index (RSGI) V 1 release on 6/28/2010
Saccharum_officinarum (Sugarcane) DFCI Gene Index (SOGI) V 3 release on 4/22/2010
Secale_cereale (Rye) DFCI Gene Index (RYEGI) V 4 release on 7/15/2008
Selaginella_moellendorffii (Club_mosses) DFCI Gene Index (CMGI) V 1 release on 6/28/2010
Solanum_melongena (Eggplant) DFCI Gene Index (SOMEGI) V 1 release on 6/28/2010
Solanum tuberosum (potato) DFCI Gene Index (STGI) V 13 release on 7/7/2010
Sorghum_bicolor (Sorghum) DFCI Gene Index (SBGI) V 9 release on 7/25/2008
Striga_hermonthica (Purple_witchweed) DFCI (SHGI) V 1 release on 6/28/2010
Theobroma_cacao (Cocoa) DFCI Gene Index (TCAGI) V 3 release on 6/21/2009
Triphysaria DFCI Gene Index (TRIPHGI) V 1 release on 8/15/2008
Triphysaria_versicolor DFCI Gene Index (TVERGI) V 2 release on 7/1/2008
Triticum aestivum (wheat) DFCI Gene Index (TAGI) V 12 release on 4/23/2010
Vigna_unguiculata (Cowpea) DFCI Gene Index (VUGI) V 1 release on 6/28/2010
Volvox_carteri_f._nagariensis (Green_algae) DFCI Gene Index (VCGI) V 7 release on 4/23/2008
Volvox_carteri_f._nagariensis (Green_algae) DFCI Gene Index (VCGI) V 1 release on 8/6/2010
Zea mays (maize) DFCI Gene Index (ZMGI) V 19 release on 8/12/2010
---------------Animal---------------
Astatotilapia burtoni tgi v1 release on 5/20/2004
Amblyomma variegatum tgi v1 release on 6/10/2002
Aedes aegypti tgi v4 release on 08/26/04
Atlantic salmon tgi v2.1 release on 06/29/04
Brugia malayi tgi v5 release on 01/28/05
Catfish tgi v6 release on 02/14/05
Cattle tgi v11 release on 10/05/04
Caenorhabditis elegans tgi v9 release on 10/06/04
C. elegans confirmed genes genome v142 release on May 8 2005
Dog tgi v6 release on 02/11/05
Chicken tgi v10 release on 02/15/05
Ciona intestinalis tgi v4 release on 10/04/04
Drosophila tgi v10 release on 10/04/04
Drosophila melanogaster genome mRNA release genome v5.6 release on Mar 10 2008
Fugu tgi v1 release on 5/12/2004
Haplochromis chilotes tgi v1 release on 5/20/2004
Haplochromis sp. red tail sheller tgi v1 release on 5/20/2004
Honey bee tgi v4 release on 5/4/2004
Human tgi v16 release on 02/25/05
Human Genome mRNA genome v0 release on Oct 18 2010
Mosquito tgi v8 release on 02/10/05
Mouse tgi v15 release on 02/25/05
Mouse Genome mRNA genome v0 release on Oct 18 2010
Oryzias latipes tgi v5 release on 5/17/2004
Onchocerca volvulus tgi v4 release on 01/28/05
Pig tgi v11 release on 02/11/05
Rat tgi v13 release on 10/05/04
Rhipicephalus appendiculatus tgi v1 release on 12/12/2003
Rainbow Trout tgi v4 release on 5/17/2004
Schistosoma mansoni tgi v5 release on 11/7/2003
Frog (Xenopus laevis) tgi v8 release on 5/12/2004
Zebrafish tgi v16 release on 10/05/04
----------------Virus------------------------
All viral nt sequences from GenBank(as of 5/4/2004)
Viruses (GenBank RefSeq Viral1)
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Update: 10/20/2010