siRNA Design

Design siRNA

Enter a gene symbol to resolve the MANE Select transcript, or paste a nucleotide sequence. Options follow the siDirect 2.1 workflow: functional rules, seed Tm, then transcript specificity.

FASTA or plain sequenceup to 10,000 nt

Target input

Sequence

Start with a gene symbol to resolve MANE Select (NM_), or retrieve by accession / paste a sequence.

Gene symbol

Accession number

Sequence

>NM_012131.3 Homo sapiens claudin 17 (CLDN17), mRNA
ATGCATTTACAACAGGTACTTCTAGTTAGGCCAAGTTCAGTCACAGCTACTGATTTGGACTAAAACGTTA
TGGGCAGCAGCCAAGGAGAACATCATCAAAGACTTCTCTAGACTCAAAAGGCTTCCACGTTCTACATCTT
GAGCATCTTCTACCACTCCGAATTGAACCAGTCTTCAAAGTAAAGGCAATGGCATTTTATCCCTTGCAAA
TTGCTGGGCTGGTTCTTGGGTTCCTTGGCATGGTGGGGACTCTTGCCACAACCCTTCTGCCTCAGTGGAG
AGTATCAGCTTTTGTTGGCAGCAACATTATTGTCTTTGAGAGGCTCTGGGAAGGGCTCTGGATGAATTGC
ATCCGACAAGCCAGGGTCCGGTTGCAATGCAAGTTCTATAGCTCCTTGTTGGCTCTCCCGCCTGCCCTGG
AAACAGCCCGGGCCCTCATGTGTGTGGCTGTTGCTCTCTCCTTGATCGCCCTGCTTATTGGCATCTGTGG
CATGAAGCAGGTCCAGTGCACAGGCTCTAACGAGAGGGCCAAAGCATACCTTCTGGGAACTTCAGGAGTC
CTCTTCATCCTGACGGGCATCTTCGTTCTGATTCCGGTGAGCTGGACAGCCAATATAATCATCAGAGATT
TCTACAACCCAGCCATCCACATAGGTCAGAAACGAGAGCTGGGAGCAGCACTTTTCCTTGGCTGGGCAAG
CGCTGCTGTCCTCTTCATTGGAGGGGGTCTGCTTTGTGGATTTTGCTGCTGCAACAGAAAGAAGCAAGGG
TACAGATATCCAGTGCCTGGCTACCGTGTGCCACACACAGATAAGCGAAGAAATACGACAATGCTTAGTA
AGACCTCCACCAGTTATGTCTAATGCCTCCTTTTGGCTCCAAGTATGGACTATGGTCAATGTTTTTTATA
AAGTCCTGCTAGAAACTGTAAGTATGTGAGGCAGGAGAACTTGCTTTATGTCTAGATTTACATTGATACG
AAAGTTTCAATTTGTTACTGGTGGTAGGAATGAAAATGACTTACTTGGACATTCTGACTTCAGGTGTATT
AAATGCATTGACTATTGTTGGACCCAATCGCTGCTCCAATTTTCATATTCTAAATTCAAGTATACCCATA
ATCATTAGCAAGTGTACAATGATGGACTACTTATTACTTTTTGACCATCATGTATTATCTGATAAGAATC
TAAAGTTGAAATTGATATTCTATAACAATAAAACATATACCTATTCTAAAA

1,241ntGC 44.6%NM_012131.3 Homo sapiens claudin 17 (CLDN17), mRNA

Functional selection

Efficacy algorithms

Ui-Tei is the primary filter. Reynolds and Amarzguioui can be combined with + (OR) or × (AND).

Combined rule

Ui-Tei + Reynolds + AmarzguiouiUnion — keep candidates that pass any selected algorithmUi-Tei + Reynolds × AmarzguiouiKeep candidates that pass (Ui-Tei or Reynolds) and AmarzguiouiUi-Tei × Reynolds × AmarzguiouiIntersection — keep candidates that pass every selected algorithm

Off-target

Seed-duplex stability

Lower seed Tm reduces miRNA-like off-target silencing on both guide and passenger strands.

Max Tm: °C
Recommended: ≤ 21.5 °C
Seed region: Guide 2–8
Checked strands: Guide and passenger

Specificity

Transcript database

Near-perfect matches are searched on 19-mers from positions 2–20 of both strands.

Specificity check

Hide less-specific siRNAsDefault siDirect filter: at least two mismatches to any non-target transcript.

Show off-target hits within three mismatchesCount 19/19, 18/19, 17/19 and 16/19 hits for each candidate.

Constraints

Other options

Optional range, composition, and motif filters applied after the functional rules.

Target range

–nt

GC content

–%

Avoid contiguous G's or C'sFor chemically synthesized siRNA

nt or more

Avoid contiguous A's or T'sFor shRNA vectors with a pol III promoter

nt or more

Custom pattern

Exclude pattern

Only show siRNAs that match all checked criteriaTurn this off if a strict combination returns no candidates.

Submits through a local proxy to siDirect, then parses HTML into the result JSON.