ERE database: A database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome

Damian Kao, Karen Hsu, Sophia Chiu, Vince Tu, Alex Chew, Kang Hoon Lee, Young Kwan Lee, Deug Nam Kwon, David G Greenhalgh, Kiho Cho

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.

Original languageEnglish (US)
Pages (from-to)157-161
Number of pages5
JournalGenomics
Volume100
Issue number3
DOIs
StatePublished - Sep 2012

Fingerprint

Endogenous Retroviruses
Terminal Repeat Sequences
Inbred C57BL Mouse
Database Management Systems
Genome
Databases
Tropism
DNA Transposable Elements
Internet
Genetic Recombination
Binding Sites

Keywords

  • Database
  • Endogenous retrovirus
  • Mouse genome
  • Murine lukemia virus
  • Retroelement
  • Solo long terminal repeat

ASJC Scopus subject areas

  • Genetics

Cite this

ERE database : A database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome. / Kao, Damian; Hsu, Karen; Chiu, Sophia; Tu, Vince; Chew, Alex; Lee, Kang Hoon; Lee, Young Kwan; Kwon, Deug Nam; Greenhalgh, David G; Cho, Kiho.

In: Genomics, Vol. 100, No. 3, 09.2012, p. 157-161.

Research output: Contribution to journalArticle

Kao, Damian ; Hsu, Karen ; Chiu, Sophia ; Tu, Vince ; Chew, Alex ; Lee, Kang Hoon ; Lee, Young Kwan ; Kwon, Deug Nam ; Greenhalgh, David G ; Cho, Kiho. / ERE database : A database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome. In: Genomics. 2012 ; Vol. 100, No. 3. pp. 157-161.
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