Schema for CenSat Annotation - Centromeric Satellite Annotation |
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Database: hub_567047_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
| field | example | description |
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| chrom | chr1 | Chromosome (or contig, scaffold, etc.) | | chromStart | 116796047 | Start position in chromosome | | chromEnd | 121405145 | End position in chromosome | | name | ct_1_1(p_arm) | Name of item | | score | 100 | Score from 0-1000 | | strand | . | + or - | | thickStart | 116796047 | Start of where display should be thick (start codon) | | thickEnd | 121405145 | End of where display should be thick (stop codon) | | reserved | 224,224,224 | itemRgb | | component | ct_1_1(p_arm) | full component name |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | component |
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| chr1 | 116796047 | 121405145 | ct_1_1(p_arm) | 100 | . | 116796047 | 121405145 | 224,224,224 | ct_1_1(p_arm) |
| chr1 | 121405145 | 121406286 | censat_1_1 | 100 | . | 121405145 | 121406286 | 0,204,204 | censat_1_1(rnd-6_family-4384) |
| chr1 | 121406286 | 121619169 | ct_1_2 | 100 | . | 121406286 | 121619169 | 224,224,224 | ct_1_2 |
| chr1 | 121619169 | 121625213 | hor_1_1(S3C1H2-A,B,C) | 100 | . | 121619169 | 121625213 | 255,146,0 | hor_1_1(S3C1H2-A,B,C) |
| chr1 | 121625213 | 121667941 | hor_1_2(S3C1H2-A,B) | 100 | . | 121625213 | 121667941 | 255,146,0 | hor_1_2(S3C1H2-A,B) |
| chr1 | 121667941 | 121788213 | hor_1_3(S3C1H2-B) | 100 | . | 121667941 | 121788213 | 255,146,0 | hor_1_3(S3C1H2-B) |
| chr1 | 121788213 | 121790362 | ct_1_3 | 100 | . | 121788213 | 121790362 | 224,224,224 | ct_1_3 |
| chr1 | 121790362 | 121796048 | hor_1_4(S3C1H2-A) | 100 | . | 121790362 | 121796048 | 255,146,0 | hor_1_4(S3C1H2-A) |
| chr1 | 121796048 | 126300487 | hor_1_5(S1C1/5/19H1L) | 100 | . | 121796048 | 126300487 | 250,0,0 | hor_1_5(S1C1/5/19H1L) |
| chr1 | 126300487 | 126590802 | hor_1_6(S3C1H2-A) | 100 | . | 126300487 | 126590802 | 255,146,0 | hor_1_6(S3C1H2-A) |
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CenSat Annotation (hub_567047_censat) Track Description
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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
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| | 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
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