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 siAbasic: a comprehensive database for potent siRNA-6Φ sequences without off-target effects, not only gives a list of siRNA-6Φ for repression of specified target mRNAs or target genes, but also designs siRNA-6Φ for any mRNA sequences submitted by users.

siAbasic provides two functionality in two tabs as follows.

  1. "Search siRNA-6Φ in human and mouse" : search pre-designed siRNA-6Φs for RefSeq genes in human and mouse.
  2. "Design siRNA-6Φ in your sequence" : design potent siRNA-6Φ targeting your sequence with default or user-defined parameter.

 As a result, siAbasic will present the list of siRNAs with abasic substitution on the pivot (position 6 of the guide strand of siRNA) and provide the information for each siRNA-6Φ including (1) the accession number of the target mRNA, (2) the gene symbol of the target gene, (3) the gene description for the target gene, (4) the start position and (5) the end position of the siRNA-6Φ on the target mRNA, the sequence of (6) guide strand and (7) passenger strand for siRNA-6Φ duplex, (8) the sequence of the mRNA target region, (9) the sequence of the seed region (base position 2-5), (10) the free energy of seed pairing (kcal mol-1), (11) the free energy of whole length interaction (kcal mol-1), and the (12) GC content of the siRNA-6Φ.

 


Select the organism:

Option 1: Search with Gene Symbol.
Option 2: Search with RefSeq accession number.

STEP 1: Type your own target sequence to design siRNA-6Φ


You can mark unwanted base as 'X'. eg) TATCXXTTAAGGCATXTACT
STEP 2: Choose options for the siRNA-6Φ design

Default Advanced options
Option 1) Enter the number of nucleotides to be excluded for designing
                siRNA-6Φ from both ends of the input sequence
5`end:    3`end:
Option 2) Select the range of free energy from transitional nucleation.
≤ ΔG[2:5] ≤

Option 3) Select the length for contiguous nucleotide and GC stretches
                to be avoided.
For contiguous nucleotide stretches ≥ 
For GC stretches ≥ 
Option 4) Select the range of GC content.
(31.6%)  ≤  GC content  ≤  (52.6%)

 

 

We kindly ask users to cite the following reference if they include siAbasic results in their manuscripts:

JY. Park*, SH. Ahn*, KM. Cho*, DW. Gu, ES. Jang, SW. Chi
siAbasic: a comprehensive database for potent siRNA-6Φ sequences without off-target effects
Database, Volume 2018, 1 January 2018, bay109,
https://doi.org/10.1093/database/bay109

 

Contact at seunghyunahn91@gmail.com

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