ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome.
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.
Burn Research, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA.
Damian
D
Kao
Karen
K
Hsu
Sophia
S
Chiu
Vince
V
Tu
Alex
A
Chew
Kang-Hoon
KH
Lee
Young-Kwan
YK
Lee
Deug-Nam
DN
Kwon
David G
DG
Greenhalgh
Kiho
K
Cho
D000818:Animals; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry; D030541:Databases, Genetic; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics*; D016678:Genome; D051379:Mice; D008810:Mice, Inbred C57BL; D016366:Open Reading Frames; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011995:Recombination, Genetic; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D020079:Terminal Repeat Sequences; D014158:Transcription, Genetic
D017931:DNA Primers