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.
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.
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.
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.