Enter an accession number and retrieve sequence:
or Paste in a nucleotide sequence: >sample sequence ggctgccaag aacctgcagg aggcagaaga atggtacaaa tccaagtttg ctgacctctc tgaggctgcc aaccggaaca atgacgccct gcgccaggca aagcaggagt ccactgagta ccggagacag gtgcagtccc tcacctgtga agtggatgcc cttaaaggaa ccaatgagtc cctggaacgc cagatgcgtg aaatggaaga gaactttgcc gttgaagctg ctaactacca agacactatt ggccgcctgc aggatgagat tcagaatatg aaggaggaaa tggctcgtca ccttcgtgaa taccaagacc tgctcaatgt taagatggcc cttgacattg agattgccac ctacaggaag ctgctggaag gcgaggagag caggatttct ctgcctcttc caaacttttc ctccctgaac ctgagggaaa ctaatctgga ttcactccct ctggttgata cccactcaaa aaggacactt ctgattaaga cggttgaaac tagagatgga caggttatca acgaaacttc tcagcatcac gatgaccttg aataaaaatt gcacacactc agtgcagcaa tatattacca
Functional siRNA selection algorithm by:
Ui-Tei et al., Nucleic Acids Res 32, 936-948 (2004) Link Reynolds et al., Nat Biotechnol 22, 326-330 (2004) Link Amarzguioui et al., BBRC 316, 1050-1058 (2004) Link
use combined rule: Ui-Tei + Reynolds + Amarzguioui Ui-Tei + Reynolds × Amarzguioui Ui-Tei × Reynolds × Amarzguioui
Minimization of seed-dependent off-target effects
Seed-duplex stability: Max Tm °C (for reducing seed-dependent off-target effect) Ui-Tei et al., Nucleic Acids Res 36, 7100-7109 (2008) Link
Specificity check: none Human (Homo sapiens) transcript, RefSeq release 225 (Jul, 2024) Human (Homo sapiens) transcript, RefSeq release 220 (Sep, 2023) Human (Homo sapiens) transcript, RefSeq release 215 (Nov, 2022) Human (Homo sapiens) transcript, RefSeq release 210 (Jan, 2022) Human (Homo sapiens) transcript, RefSeq release 205 (Mar, 2021) Human (Homo sapiens) transcript, RefSeq release 200 (May, 2020) Mouse (Mus musculus) transcript, RefSeq release 225 (Jul, 2024) Mouse (Mus musculus) transcript, RefSeq release 220 (Sep, 2023) Mouse (Mus musculus) transcript, RefSeq release 215 (Nov, 2022) Mouse (Mus musculus) transcript, RefSeq release 210 (Jan, 2022) Mouse (Mus musculus) transcript, RefSeq release 205 (Mar, 2021) Mouse (Mus musculus) transcript, RefSeq release 200 (May, 2020) Rat (Rattus norvegicus) transcript, RefSeq release 225 (Jul, 2024) Rat (Rattus norvegicus) transcript, RefSeq release 220 (Sep, 2023) Rat (Rattus norvegicus) transcript, RefSeq release 215 (Nov, 2022) Rat (Rattus norvegicus) transcript, RefSeq release 210 (Jan, 2022) Rat (Rattus norvegicus) transcript, RefSeq release 205 (Mar, 2021) Rat (Rattus norvegicus) transcript, RefSeq release 200 (May, 2020) Hide less-specific siRNAs Show number of off-target hits within three mismatches
Other options
Target range: from to
Avoid contiguous G's or C's 4 5 6 7 nt or more (for chemically synthesized siRNA) Avoid contiguous A's or T's 4 5 6 7 nt or more (for shRNA vectors with pol III promoter)
GC content: from % to %
Custom pattern: Exclude pattern:
Only show siRNAs that match all checked criteria
siDirect v2.1 | Last modified on Oct 23, 2024. Previsous version: siDirect v2.0
