Description

Centromeric and Sub-telomeric Satellite annotation

Overview of types of Annotations

Alpha Satellite

  • "active(NSFx)" - active alpha Satellite dimeric array, identified as longest dimeric array
  • "dimeric(NSFx)" - dimer repeats, summarized from superfamily annotations NSF1-6
  • "dhor(NSF6)" - diverged HOR repeats of New world monkey superfamily 6
  • "mon" - non dimeric alpha Satellites
  • "mixedAlpha(SFx, SFy) - regions that can't clearly be resolved as dominant SF

    • Other Satellite Annotations

  • "hsat1A" - RepeatMasker SAR annotation
  • "hsat1B - RepeatMasker HSATI annotation
  • "gsat(gsattype)" - RepeatMasker GSat Annotations
  • "HSat2" - Annotated with Nick Altemose' perl script here
  • "HSat3" - Annotated with Nick Altemose' perl script here and Tandem Repeat Finder
  • "pentameric" - GGCAA pentameric repeat satellite annotated with Tandem Repeat Finder

    • Composite Satellite Annotations

  • "bSat(monomerTypes)" - RepeatMasker annotations, monomers include BSR, BSAT, LSAU
  • "cenSat(monomerTypes)" - RepeatMasker annotations - other satellites enriched in centromere, includes CER, SATR, SST1, ACRO, HSAT4/5, and TAF11
  • "subTerm(marmoSat)" - Sub terminal satellite repeats - marmoset specific

    • Other Annotations

  • "ct" - Centromere transition region, see schema below for definition
  • "GAP" - regions of N's annotated using Seqtk gap
  • "rDNA" - rDNA annotation

    • Display Conventions and Configuration

    Colors

    Annotation Color
    Active αSat dimer (hor ... L) dark red
    Mixed αSat (SFx, SFy) red
    Inactive αSat dimer (hor) dark orange
    Divergent αSat (dhor) light orange
    Monomeric αSat (mon) peach/yellow
    Classical Human Satellite 1A (hsat1A) light green
    Classical Human Satellite 1B (hsat1B) dark green
    Classical Human Satellite 2 (HSat2) light blue
    Classical Human Satellite 3 (HSat3) dark blue
    Classical Human Satellite 2/3 (HSat2_3) gray blue
    Pentameric Satellite navy blue
    Beta Satellite (bsat) pink
    Gamma Satellite (gsat) purple
    Other centromeric satellites (censat, COMP) teal
    Subterminal satellites (subTerm) yellow
    Centromeric transition regions (ct) grey
    rDNA dark purple
    GAP black

    Credits

    Satellite Annotations generated by Hailey Loucks.
    Please contact with questions at hloucks@ucsc.edu

    References

    https://github.com/altemose/chm13_hsat