Genomic Segmental Duplications/Low Copy Repeats

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Human Uniqueness Compared to "Great Apes": 
Absolute Difference
MOCA Domain: 

Segmental duplications (SDs) are sequences of DNA that exist in two or more genomic locations, occurring in tandem or interspersed in multiple locations, and are classically >1kb in size. They occur commonly in pericentromeric, subtelomeric, and interstitial regions and account for ~5% of the human genome. LCRs are often used synonymously with SDs, although it has also been argued that SDs should encompass high copy repeats, in which case LCRs would be considered a subset of SDs. SDs that are lineage-specific most commonly occur in regions containing ancestral duplications. These duplications produce regions of genomic instability and are associated with copy number differences and with inversions and other chromosomal rearrangements. Humans have an increased proportion of interstitial duplications (occurring in euchromatic regions), which account for the majority of human-specific SDs, and which allow for the creation of novel genes during chromosomal rearrangement. Evidence suggests that more recent duplications transpose closer to the centromere, and included among human-specific SDs is a pericentromeric region of chromosome 22 originally from chromosome 14 that was duplicated and transposed to this novel site. Multiple duplication cores (ancestral duplication centers from which further duplication has occurred in humans) exist that have been found to contain genes with novel human-specific changes.

The Human Difference: 

Interstitial duplication expansion
Novel duplications
Novel duplication transposition
Novel genes


  1. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution, Jiang, Z., Tang H., Ventura M., Cardone M. F., Marques-Bonet T., She X., Pevzner P. A., and Eichler E. E. , Nat Genet, 11/2007, Volume 39, Issue 11, p.1361 - 1368, (2007)
  2. Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization., Goidts, V., Armengol L., Schempp W., Conroy J., Nowak N., Müller S., Cooper D. N., Estivill X., Enard W., Szamalek J. M., et al. , Hum Genet, 03/2006, Volume 119, Issue 1-2, p.185-98, (2006)
  3. Primate segmental duplications: crucibles of evolution, diversity and disease., Bailey, Jeffrey A., and Eichler Evan E. , Nat Rev Genet, 2006 Jul, Volume 7, Issue 7, p.552-64, (2006)
  4. Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications., Horvath, J E., Gulden C L., Bailey J A., Yohn C, McPherson J D., Prescott A, Roe B A., de Jong P J., Ventura M, Misceo D, et al. , Mol Biol Evol, 2003 Sep, Volume 20, Issue 9, p.1463-79, (2003)
  5. Human-Specific Duplication and Mosaic Transcripts: The Recent Paralogous Structure of Chromosome 22, Bailey, J. A., Yavor A. M., Viggiano L., Misceo D., Horvath J. E., Archidiacono N., Schwartz S., Rocchi M., and Eichler E. E. , American Journal of Human Genetics, 01/2002, Volume 70, Issue 1, p.83 - 100, (2002)
  6. Segmental duplications and the evolution of the primate genome., Samonte, Rhea Vallente, and Eichler Evan E. , Nat Rev Genet, 2002 Jan, Volume 3, Issue 1, p.65-72, (2002)