Description

This track displays conserved non-exonic elements that have been deposited by mobile elements (repeats), a process termed "exaptation" (Gould et al., 1982). These regions were identified during a genome-wide survey (Lowe et al., 2007) with the expectation that regions of this type may act as distal transcriptional regulators for nearby genes. A previous case study experimentally verified an exapted mobile element acting as a distal enhancer (Bejerano et al. , 2006).

Methods

All regions were identified as having originated as mobile element insertions by RepeatMasker (Smit et al.). A subset of elements that have clear repeat homology can be identified by very significant BLASTZ (Schwartz et al., 2003) alignments to consensus sequences in RepBase (Jurka et al., 2000).

This dataset is from a genome-wide survey of mobile elements being exapted as conserved non-exonic sequence; a full explanation of methods can be found in Lowe et al., 2007.

References

Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006 May 4;441(7089):87-90.

Gould SJ, Vrba ES. Exaptation; a missing term in the science of form. Paleobiology. 1982 Jan 1;8(1):4-15.

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

Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A. 2007 May 8;104(19):8005-10. Epub 2007 Apr 26.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and Miller W. Human-Mouse Alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7.

Smit AFA et al. www.repeatmasker.org