Pyknons

If you use any of the below please cite: Tsirigos A. and I. Rigoutsos, Human and mouse introns are linked to the same processes and functions through each genome’s most frequent non-conserved motifs Nucl Acids Res, 2008 Jun;36(10):3484-93. doi: 10.1093/nar/gkn155. Epub 2008 May 1

 
From this page you can obtain access to the list of human and mouse pyknons that are described in “Human and mouse introns are linked to the same processes and functions through each genome‚Äôs most frequent non-conserved motifs”1 (Click to download the paper). These pyknons are a superset of the pyknons that are described in the original publication 2 (Click to download the paper).

There are several download and browsing options:

  1. the tab-separated file of the human pyknons as a single compressed file (635 Mbytes) can de downloaded by clicking the button below.
    480 Downloads
  2. the tab-separated file of the human pyknons in pieces that are 29 Mbytes each (un-compressed plain text) can be found in this directory.
  3. the tab-separated file of the human pyknons in order of chromosomal location can be found in this directory.
  4. the tab-separated file of the mouse pyknons as a single compressed file (367 Mbytes). Click on the button below to download.
    424 Downloads
  5. the tab-separated file of the mouse pyknons in pieces that are 29 Mbytes each (un-compressed plain text) can be found in this directory.
  6. the tab-separated file of the mouse pyknons in order of chromosomal location can be found in this directory.

Pyknon Naming and File Structure

In order to standardize their nomenclature and subsequent use, we have established a notation that includes an abbreviation of the corresponding organism’s name, and an eight-digit number that is unique for each pyknon sequence e.g. HSA-PYKNON-00013431. Each list of pyknons is tab-delimited and sorted in increasing order of the 8-digit number in the pyknon’s label. The columns of each file have as follows:
Column 1: pyknon name
Column 2: chromosome
Column 3: strand
Column 4: “from” coordinate (all-inclusive)
Column 5: “to” coordinate (all-inclusive)
Column 6: the actual pyknon sequence (listed always in 5′->3′ direction)

So a typical line of the file looks like:

      HSA-PYKNON-00013431     8       +       90647806        90647821        CAGGTGAGGAAACTGA

Notes

  1. Depending on your usage of pyknons you may need to take into account the sense or the antisense sequence of the pyknon, or both, into consideration (columns 3 and 6).
  2. In the files that we make available you will find that we have enumerated for each pyknon all of its genomic instances.

References

  1. Tsirigos A. and I. Rigoutsos, Human and mouse introns are linked to the same processes and functions through each genome’s most frequent non-conserved motifs Nucl Acids Res, 2008 Jun;36(10):3484-93. doi: 10.1093/nar/gkn155. Epub 2008 May 1.
  2. Rigoutsos I. et al., Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes Proc Natl Acad Sci USA, 2006 Apr 25;103(17):6605-10. Epub 2006 Apr 24.

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