Description
Centromeric and Pericentromeric Satellite Annotation (cenSat)
Methods
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
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 |
Data Access
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/hs1/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.
Credits
Karen Miga
<khmiga@ucsc.edu>,
Nicolas Altemose, Ivan A. Alexandrov
References
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