TranspoGene and microTranspoGene: Transposed elements influence on the transcriptome of seven vertebrates and invertebrates

Asaf Levy, Noa Sela, Gil Ast*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

62 Scopus citations

Abstract

Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as microRNAs. We have constructed the TranspoGene database, which covers TEs located inside protein-coding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TEs were classified according to location within the gene: proximal promoter TEs, exonized TEs (insertion within an intron that led to exon creation), exonic TEs (insertion into an existing exon) or intronic TEs. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. In addition, we created microTranspoGene: a database of human, mouse, zebrafish and nematode TE-derived microRNAs. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. Publicly available query interfaces to TranspoGene and microTranspoGene are available at http://transpogene.tau.ac.il/ and http://microtranspogene.tau.ac.il, respectively. The entire database can be downloaded as flat files.

Original languageAmerican English
Pages (from-to)D47-D52
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 2008
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Cooperation Program in Cancer Research of the Deutsches Krebsforschungs-zentrum (DKFZ) and Israel’s Ministry of Science and Technology (MOST), by a grant from the Israel Science Foundation (1449/04 and 40/05), GIF, ICA through the Ber-Lehmsdorf Memorial Fund and DIP. N.S. is funded in part by EURASNET. Fan Hsu from the UCSC genome browser team kindly supplied us the high-quality known genes tables of human and mouse. Glen Borchert and Beverly Davidson from Iowa University kindly supplied us with part of the data used for microTranspoGene. We would like to thank Amiel Dror for his help in graphical design. We also wish to thank Itay Menachem, the head of the Life Sciences IT Unit, and the Unix system specialist Hila Afargan, for their assistance in the infrastructure design and implementation of the needed system that enables us to run TranspoGene. Funding to pay the Open Access publication charges for this article was provided by EURASNET.

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