Genomic Insertions and Deletions (Indels)

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

Indels are insertions and deletions in the genome; 40% of indels are single nucleotide changes, while 98% consist of changes fewer than 100 bps. Mechanisms for small indel events are replication slippage (as seen in STR regions), recombination, unequal crossing over, and tandem duplication caused by imperfect repair of double strand breaks. Larger indels may be caused by segmental duplications and transposable elements. Humans have an expanded genome compared to great apes due in part to insertions resulting from retrotransposon activity. Indels that are due to repetitive sequence-mediated deletions, and indels that are not associated with repeat sequences, do not differ significantly by species. Retrotransposon-produced insertions are lineage specific and the increased insertions in humans are caused by younger retrotransposons (Alu, L1, LTR), not ancient ones (L2, L3, DNA transposons). Intergenic indels are more common than intragenic indels; intragenic indels account for 0.21% of human sequence uniqueness, whereas intragenic indels account for 1.4%. A recent study identified 844,552 human-specific indels of segments shorter than 100 base pairs, and of genes with known function, those most affected by indels in a human-specific fashion are involved in transcription and translation regulatory activities.

The Human Difference: 

Genome expansion
Increased insertions
Novel insertions and deletions

Related MOCA Topics


  1. Indels in the Evolution of the Human and Chimpanzee Genomes, Wetterbom, Anna, Cavelier Lucia, and Bergström Tomas F. , Handbook of Human Molecular Evolution, Volume 1, p.616-623, (2008)
  2. Human-specific insertions and deletions inferred from mammalian genome sequences., Chen, Feng-Chi, Chen Chueng-Jong, Li Wen-Hsiung, and Chuang Trees-Juen , Genome Res, 01/2007, Volume 17, Issue 1, p.16-22, (2007)
  3. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome., Liu, Ge, Zhao Shaying, Bailey Jeffrey A., S Sahinalp Cenk, Alkan Can, Tuzun Eray, Green Eric D., and Eichler Evan E. , Genome Res, 03/2003, Volume 13, Issue 3, p.358-68, (2003)