CenSat Annotation Track Settings
Centromeric Satellite Annotation   (All Mapping and Sequencing tracks)

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Centromeric and Pericentromeric Satellite Annotation (cenSat)


Satellite array annotations are defined by intersecting information across alpha HOR annotation track, repeatmasker tracks, and human satellite annotation tracks. The broad definition of “peri/centromeric regions” on each chromosome includes the satellite-rich regions and 5 Mb of sequence on the p-arm and q-arm. Although the distal ends of acrocentric short arms are not truly pericentromeric, the vast majority of satellite DNAs present in these arms are highly enriched in peri/centromeric regions on other chromosomes (e.g. HSat1-3, Beta satellites (βSat), Alpha satellites (αSat)). Therefore, acrocentric short arms are included in the cenSat annotation track in their entirety. The Y chromosome peri/centromeric region includes 5 Mb to either side of the active αSat Higher Order Repeat (HOR) array, but we have included satellite array annotations across the entire chromosome. NB: Satellite array annotations typically merge across inserted transposons. Strand information is not included (all annotations are set to + strand)

Display Conventions and Configuration


Active αSat HOR (hor ... L) red
Inactive αSat HOR (hor) orange
Divergent αSat HOR (dhor) dark red
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) blue
Beta Satellite (bsat) pink
Gamma Satellite (gsat) purple
Other centromeric satellites (censat) teal
Centromeric transition regions (ct) grey


Karen Miga<khmiga@ucsc.edu>, Nicolas Altemose, Ivan A. Alexandrov


N. Altemose, G. A. Logsdon, A. V. Bzikadze, P. Sidhwani, S. A. Langley, G. V. Caldas, S. J. Hoyt, L. Uralsky, F. D. Ryabov, C. J. Shew, M. E. G. Sauria, M. Borchers, A. Gershman, A. Mikheenko, V. A. Shepelev, T. Dvorkina, O. Kunyavskaya, M. R. Vollger, A. Rhie, A. M. McCartney, M. Asri, R. Lorig-Roach, K. Shafin, J. K. Lucas, S. Aganezov, D. Olson, L. Gomes de Lima, T. Potapova, G. A. Hartley, M. Haukness, P. Kerpedjiev, F. Gusev, K. Tigyi, S. Brooks, A. Young, S. Nurk, S. Koren, S. R. Salama, B. Paten, E. I. Rogaev, A. Streets, G. H. Karpen, A. F. Dernburg, B. A. Sullivan, A. F. Straight, T. J. Wheeler, J. L. Gerton, E. E. Eichler, A. M. Phillippy, W. Timp, M. Y. Dennis, R. J. O’Neill, J. M. Zook, M. C. Schatz, P. A. Pevzner, M. Diekhans, C. H. Langley, I. A. Alexandrov, K. H. Miga, Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178 (2022). https://doi.org/10.1126/science.abl4178