6mer Seed Toxicity

A tool to determine the toxicity of any siRNA, shRNA or miRNA with known 6mer seed sequence.

Data is loading...

To search for miRNAs either type the miRNA accession number (MIMAT#) or the exact name of the miRNA arm.
  • For instance "miR-34a" will not yield a result.
  • You can either search for "miR-34a-5p" or "miR-34a-3p". Dashes and capitalization are not relevant (i.e. "mir34a5p" will also work).
We are currently working on a greatly improved miRNA search functionality. Watch this space.
Info

This site allows to determine the activity of any siRNA, shRNA, or miRNA to be toxic through its 6mer seed sequence in human (HeyA8 - ovarian and H460 - lung) and mouse (M565 - liver and 3LL - lung) cancer cell lines.

  • miRNAs with low viability (high toxicity,
    red color
    ) will likely be tumor suppressive.
  • miRNAs with high viability (low toxicity,
    green color
    ) can be tumor promoting.

Enter one of 4096 possible 6mers into the search field, any nucleotide sequence of less than 6 nucleotides, or the name of any miRNA or mature miRNA listed at mirbase.org. Use positions 2-7 of the guide/antisense strand of the siRNA duplex as the 6mer.

Click on a miRNA in the results to be taken to the mirbase site describing the miRNA.

  • Mature miRNAs representing the predominant arm are shown in
    dark purple
    .
  • Mature miRNAs representing the lesser expressed arm (the * activity) are shown in
    light purple
    .
  • miRNAs that are highly expressed and processed by Drosha (RISC bound in wild-type but not Drosha k.o. HCT116 cells) have a
    yellow
    outline
    .
    • All other miRNAs are either not processed by Drosha (i.e. miR-320a), miRtrons, or not significantly expressed in HCT116 cells.
  • miRtrons have a
    blue
    outline
    .


References

Gao, Q.Q., Putzbach, W.E., Murmann, A.E., Chen, S., Sarshad, A.A., Peter, J.M., Bartom, E.T., Hafner, M. and Peter, M.E. (2018) 6mer seed toxicity in tumor suppressive microRNAs. Nature Comm, 9:4504.


Version History

Click for detailed changelogs.

Loading...

Acknowledgements

This site was developed by Johannes Peter.

The source code is available on Github.