Description page for dbRIP track hub

Data Overview

Retrotransposons, also generally termed Mobile Elements (MEs), constitute ~50% of the human genome with millions of copies classified into the LTR and non-LTR families. Non-LTR retrotransposons can be further classified into LINE, SINE, SVA, and retro-genes (processed pseudogenes). Endogenous retrovirus (ERV), L1 and Alu are the main representive subfamilies of LTRs, LINEs, and SINEs. MEs play important in genome evolution and gene functions via variety of mechanisms.

Due to past and ongoing retrotransposition activities, many retrotransposns occurred as insertions uniquely present in the human genomes (human-specific MEs (HS-MEs)) or polymorphic (for their presence and absence) among human individuals (polymorphic MEs). dbRIP serves to provide a comphrehensive documentation of human-specific and polymorphic retrotransposon insertions with detailed sequence characterization and allele frequency (for polymorphic MEs).

dbRIP Track Hub is a composite track consisting the follow specific tracks:

  • Polymorphic Alu (dbRIP_Alu)
  • Polymorphic L1 (dbRIP_L1)
  • Polymorphic SVA (dbRIP_SVA)
  • Polymorphic Retrogenes (dbRIP_PPG)
  • Polymorphic ERV (dbRIP_ERV)
  • Human-specific MEs (dbRIP_HS-ME)

    dbRIP tracks are currently available for hg19 and hg38. A more advanced search interface of the data is available at here.

    Methods

    Please refer to the relevant publications listed in the citations.

    Credits and Citations

    dbRIP:

  • Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans.Hum Mutat 27(4):323-329, 2006; PubMed ID: 16511833.
  • Liang P and Wang T. Database documentation of retrotransposon insertion polymorphisms. Front Biosci (Elite Ed) 4,1542-1555, 2012.
  • Dahi Z, et al. Complete sequence characterization and allele frequency analysis for 6000 polymorphic mobile element insertions in human. (Manuscript in preparation)

    HS-MEs:

  • Tang W, Mun S, Joshi A, Han K, Liang P. Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. (manuscript under review with DNA Research)