Description

Repetitive genomic elements including Transposable Element (TE) families, Satellite, Short Tandem Repeats, and low complexity DNA as annotated by RepeatMasker. These tracks were constructed with the NCBI BLAST-derived search engine RMBlast and Dfam 3.3 database (plus T2T-CHM13-derived entries submitted to the Dfam 3.6 data release in April 2022, and HG002 chrY-derived entries not yet submitted).

Individual tracks are identified using the three main components of the analysis, the version of RepeatMasker, the search engine used, and finally the repeat library version.

RepeatMasker version April 01 2021 open-4.1.2-p1
Search Engine: RMBlast (-e ncbi) [ 2.10.0+ (March 2020) ]
RepeatMasker Database: Dfam_3.3 (plus T2T-CHM13-derived entries submitted to the Dfam 3.6 data release in April 2022, and HG002 chrY-derived entries not yet submitted)

Display Conventions and Configuration

The following table lists the repeat class colors:

Color	Repeat Class
	SINE - Short Interspersed Nuclear Element
	LINE - Long Interspersed Nuclear Element
	LTR - Long Terminal Repeat
	DNA - DNA Transposon
	Simple - Single Nucleotide Stretches and Tandem Repeats
	Low_complexity - Low Complexity DNA
	Satellite - Satellite Repeats
	RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
	Other - Other Repeats (including class RC - Rolling Circle)
	Unknown - Unknown Classification

A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.

Methods

The RepeatMasker (www.repeatmasker.org) tool was used to generate the datasets found on this track hub.

References

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

For the discovery of the additional T2T-CHM13-derived repeats included in this track, as well as the methods (and scripts) for masking the assembly with these T2T-CHM13-derived repeats and previously known repeats:

Hoyt SJ, et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements. bioRxiv. 2022 Apr 1.

Hoyt SJ, et al. From telomere to telomere: the transcriptional and epigenetic state of human repeat elements analysis code: T2T-CHM13. bioRxiv. 2022 Apr 1.

Dfam is described in:

Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res. 2013 Jan;41(Database issue):D70-82. PMID: 23203985; PMC: PMC3531169

Repbase Update is described in:

Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846