LINE Repeating Elements by RepeatMasker (CR1AVI)
 
Item: CR1AVI
Score: 0
Position: CM032354.1:51926196-51926280
Genomic Size: 85
Strand: +
View DNA for this feature (GCA_019023105.1/black-throated flowerpiercer)

Smith Waterman alignment score292
Base mismatches in parts per thousand259
Bases deleted in parts per thousand36
Bases inserted in parts per thousand47
-#bases after match in genomic sequence-103847954
Class of repeatLINE
Family of repeatCR1
Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence629
End in repeat sequence712
-#bases after match (if strand is +) or start (if strand is -) in repeat sequence-9
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Description

This track shows the Repeat Masker annotations on the 24 Jun 2021 Diglossa brunneiventris/GCA_019023105.1_LSU_DiBr_2.0 genome assembly.

This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below.

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:

  • Short interspersed nuclear elements (SINE), which include ALUs
  • Long interspersed nuclear elements (LINE)
  • Long terminal repeat elements (LTR), which include retroposons
  • DNA repeat elements (DNA)
  • Simple repeats (micro-satellites)
  • Low complexity repeats
  • Satellite repeats
  • RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
  • Other repeats, which includes class RC (Rolling Circle)
  • Unknown

The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading.

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

UCSC has used the most current versions of the RepeatMasker software and repeat libraries available to generate these data. Note that these versions may be newer than those that are publicly available on the Internet.

Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information.

Class profiles

  • 257,341 - Simple
  • 135,794 - LINE
  • 52,938 - Low_complexity
  • 19,165 - LTR
  • 16,953 - DNA
  • 5,441 - SINE
  • 2,536 - Other
  • 1,731 - RNA
  • 12 - Satellite

Detail class profiles

  • 257,341 - Simple_repeat
  • 135,794 - LINE
  • 52,938 - Low_complexity
  • 19,008 - LTR
  • 15,149 - DNA
  • 5,441 - SINE
  • 2,288 - Unknown
  • 1,804 - DNA?
  • 1,372 - tRNA
  • 263 - rRNA
  • 176 - Unspecified
  • 157 - LTR?
  • 91 - snRNA
  • 46 - RC
  • 18 - RC?
  • 12 - Satellite
  • 8 - ARTEFACT
  • 5 - scRNA

Credits

Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track.

References

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

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