Schema for CenSat Annotation - Centromeric Satellite Annotation
  Database: hs1    Primary Table: hub_567047_censat Data last updated: 2022-03-30
Big Bed File Download: /gbdb/hs1/censat/censat.bb
Item Count: 2,523
The data is stored in the binary BigBed format.

Format description: Centromeric and Pericentromeric Satellite Annotation
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart116796047Start position in chromosome
chromEnd121405145End position in chromosome
namect_1_1(p_arm)Name of item
score100Score from 0-1000
strand.+ or -
thickStart116796047Start of where display should be thick (start codon)
thickEnd121405145End of where display should be thick (stop codon)
reserved224,224,224itemRgb
componentct_1_1(p_arm)full component name

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedcomponent
chr1116796047121405145ct_1_1(p_arm)100.116796047121405145224,224,224ct_1_1(p_arm)
chr1121405145121406286censat_1_1100.1214051451214062860,204,204censat_1_1(rnd-6_family-4384)
chr1121406286121619169ct_1_2100.121406286121619169224,224,224ct_1_2
chr1121619169121625213hor_1_1(S3C1H2-A,B,C)100.121619169121625213255,146,0hor_1_1(S3C1H2-A,B,C)
chr1121625213121667941hor_1_2(S3C1H2-A,B)100.121625213121667941255,146,0hor_1_2(S3C1H2-A,B)
chr1121667941121788213hor_1_3(S3C1H2-B)100.121667941121788213255,146,0hor_1_3(S3C1H2-B)
chr1121788213121790362ct_1_3100.121788213121790362224,224,224ct_1_3
chr1121790362121796048hor_1_4(S3C1H2-A)100.121790362121796048255,146,0hor_1_4(S3C1H2-A)
chr1121796048126300487hor_1_5(S1C1/5/19H1L)100.121796048126300487250,0,0hor_1_5(S1C1/5/19H1L)
chr1126300487126590802hor_1_6(S3C1H2-A)100.126300487126590802255,146,0hor_1_6(S3C1H2-A)

CenSat Annotation (hub_567047_censat) Track Description
 

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

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