Repeat Masker track constructed with the HMMER alignment engine and Dfam_3.1 database.
Color is based on repeat name or family:
| Repeat | Color | Repeat | Color |
|---|---|---|---|
| (CATTC)n | (GAATC)n | ||
| ALR/Alpha | BSR/Beta | ||
| CER | DNA | ||
| GSAT | HSAT | ||
| LINE | Low_complexity | ||
| LSAU | LTR | ||
| RC/Helitron | Retroposon | ||
| RNA | rRNA | ||
| SAR | Satellite/acro | ||
| Satellite/telo | SATR1 | ||
| scRNA | Simple repeat | ||
| SINE | snRNA | ||
| srpRNA | SSTI | ||
| SUBTEL_sa | tRNA | ||
| Unknown |
RepeatMasker with Dfam.
Thanks to Arian Smit, Robert Hubley, and the Dfam project for providing the tools and models used to generate this track.
Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.
Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846
Robert Hubley; Robert D. Finn; Jody Clements; Sean R. Eddy; Thomas A. Jones; Weidong Bao; Arian F.A. Smit; Travis J. Wheeler The Dfam database of repetitive DNA families Nucleic Acids Research (2016) Database Issue 44:D81-89. DOI: 10.1093/nar/gkv1272
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