Search for reagents
The reagent identifier search on the GenomeRNAi home page will only identify exact matches in the database (no wild-card use). (Another option to show the reagent information is to search for a specific gene and choose a reagent in the 'Reagents' tab.)
In the example shown below, GenomeRNAi was queried for the reagent BKN22805:
<p>The resulting page is subdivided in four tabs: 'Reagent info', 'Gene(s)', 'Phenotypes' and 'Genome browser'. </p> <p>Detailed information about the reagent is displayed in the 'Reagent info' tab. Besides the full sequence and sequence length the primers and primer parameters (such as length, melting temperature and percent GC content) are listed as well as predicted sequence specificity ('Reagent quality' and 'Intended targets') and predicted efficiency. Information marked with an asterix is generated by <a href="http://www.nextrnai.org/" target="_blank">NEXT-RNAi</a>.</p>
'siRNAs [19nt]' is the number of all possible 19 nt siRNAs obtained from the dsRNA sequence (with an off-set of 1).
'On-target' is the number of siRNAs mapping only to the transcripts of the intended target gene.
'Off-target' is the number of siRNAs with mappings to transcripts of multiple target genes.
'No target' is the number of siRNAs with no transcript-target at all (e.g. for intron-spanning designs). BKN22805 has no predicted off-target to unintended transcripts.
<p>The predicted efficiency ('Efficiency[%]') is calculated for each 19 nt siRNA according to the rules defined in <a href="http://www.ncbi.nlm.nih.gov/pubmed/17540034" target="_blank">Shah et al.</a> and averaged over all siRNAs. It is on a scale from 0% to 100% and is basically a weighted scoring of overall 12 parameters (such as GC content, asymmetry between 3' and 5' end certain base preferences).</p>
The 'Intended targets' table lists the primary target gene, all annotated splice variants and the number of siRNAs targeting each transcript. BKN22805 targets the transcript FBtr0080051 with all 316 siRNAs.
In case transcripts of other genes are targeted an additional table ('Off-targets') is displayed. An example is shown below for BKN21751 targeting Drosophila wls (CG6210, FBgn0036141, Entrez Gene ID 39259). This dsRNA has one perfect 19 nt match to the two splice forms of CG13366 (FBgn0025633, Entrez Gene ID 31004).
The other outputs ('Gene(s)', 'Phenotypes' and 'Genome browser' tabs) are analogous to the outputs described for gene searches.
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