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

Levy A, Sela N, Ast G - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Biochemistry, Tel-Aviv University Medical School, Tel Aviv 69978, Israel.

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.

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The TranspoGene results table generated after a search for human Alu exonizations in the RefSeq mRNA accession NM_000284. The original single result row was spilt into four vertical rows for a better view.
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Figure 1: The TranspoGene results table generated after a search for human Alu exonizations in the RefSeq mRNA accession NM_000284. The original single result row was spilt into four vertical rows for a better view.

Mentions: The TranspoGene website is user-friendly and allows easy searching of the database. Through the TranspoGene webpage (available at http://transpogene.tau.ac.il) the user initially selects genomic area of interest: gene name, protein/mRNA accession from RefSeq or Swiss-Prot, or absolute genomic positions in a specific organism. The user can also insert a list of gene names, possibly from different organisms. The MySQL wildcard sign (%) can be also used for searching genes with similar names. Afterwards the user selects the TE family of interest, where multiple selection of TE families within an organism and/or between organisms is enabled. Finally the TE type according to location in the gene is selected: intronic TE, exonized TE, TE in proximal promoter or exonic TE (multiple types can be selected). The result of the query is provided both in a table format and in a file ready for download. An example for the result of TranspoGene search is given in Figure 1. The results contain links to RefSeq (31), Swiss-Prot (40), OMIM (35) and to the UCSC genome browser (41) in order to provide further information about the relevant transcript, protein, disease and genomic region, respectively. To detect mutations that accumulated in a given TE, the user can view the alignment file of the TE sequence to its consensus sequence, through a link given in the query results table. For exonized TEs, the overlap between the exon and its overlapping TE is emphasized by use of different colors. The microTranspoGene webpage (http://microtranspogene.tau.ac.il/) allows selection of either microRNA precursors structurally derived from TEs or human microRNA genes transcribed by RNA polymerase III using Alu promoters/terminators. It allows searching for a specific microRNA precursor in the database, selection of all relevant microRNAs of a specific species or all microRNA precursors in the database from all organisms. Supplementary Figure 1 demonstrates partial microTranspoGene results for searching human microRNA precursors structurally derived from TEs. The entire database can be downloaded as flat files from the download link.Figure 1.


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

Levy A, Sela N, Ast G - Nucleic Acids Res. (2007)

The TranspoGene results table generated after a search for human Alu exonizations in the RefSeq mRNA accession NM_000284. The original single result row was spilt into four vertical rows for a better view.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238949&req=5

Figure 1: The TranspoGene results table generated after a search for human Alu exonizations in the RefSeq mRNA accession NM_000284. The original single result row was spilt into four vertical rows for a better view.
Mentions: The TranspoGene website is user-friendly and allows easy searching of the database. Through the TranspoGene webpage (available at http://transpogene.tau.ac.il) the user initially selects genomic area of interest: gene name, protein/mRNA accession from RefSeq or Swiss-Prot, or absolute genomic positions in a specific organism. The user can also insert a list of gene names, possibly from different organisms. The MySQL wildcard sign (%) can be also used for searching genes with similar names. Afterwards the user selects the TE family of interest, where multiple selection of TE families within an organism and/or between organisms is enabled. Finally the TE type according to location in the gene is selected: intronic TE, exonized TE, TE in proximal promoter or exonic TE (multiple types can be selected). The result of the query is provided both in a table format and in a file ready for download. An example for the result of TranspoGene search is given in Figure 1. The results contain links to RefSeq (31), Swiss-Prot (40), OMIM (35) and to the UCSC genome browser (41) in order to provide further information about the relevant transcript, protein, disease and genomic region, respectively. To detect mutations that accumulated in a given TE, the user can view the alignment file of the TE sequence to its consensus sequence, through a link given in the query results table. For exonized TEs, the overlap between the exon and its overlapping TE is emphasized by use of different colors. The microTranspoGene webpage (http://microtranspogene.tau.ac.il/) allows selection of either microRNA precursors structurally derived from TEs or human microRNA genes transcribed by RNA polymerase III using Alu promoters/terminators. It allows searching for a specific microRNA precursor in the database, selection of all relevant microRNAs of a specific species or all microRNA precursors in the database from all organisms. Supplementary Figure 1 demonstrates partial microTranspoGene results for searching human microRNA precursors structurally derived from TEs. The entire database can be downloaded as flat files from the download link.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Biochemistry, Tel-Aviv University Medical School, Tel Aviv 69978, Israel.

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.

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