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)
Colors
| 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 |
+The raw data can be explored interactively with the +Table Browser or the +Data Integrator. The data can also be +accessed from scripts through our REST +API, where the track name is censat.
++For automated analysis, the data may be downloaded from our +download server as a +bigBed file. The file for this track is called censat.bb. Individual regions or the whole +genome annotation can be obtained using our tool bigBedToBed, which can be compiled from +the source code or downloaded as a precompiled binary for your system. Instructions for downloading +source code and binaries can be found +here. +The tool can also be used to obtain only features within a given range, for example:
+bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/censat/censat.bb -chrom=chr6 -start=0 -end=1000000 stdout ++Please refer to our +mailing +list archives for questions, or our +Data Access FAQ for more +information.
+Karen Miga <khmiga@ucsc.edu>, Nicolas Altemose, Ivan A. Alexandrov
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ et al. Complete genomic and epigenetic maps of human centromeres. Science. 2022 Apr;376(6588):eabl4178. PMID: 35357911; PMC: PMC9233505