Difference between revisions of "FlyBase:Natural Transposon Report"
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Symbol || style="width: 80%;" | The valid symbol that is used in FlyBase for the natural transposon. | + | |'''Symbol''' || style="width: 80%;" | The valid symbol that is used in FlyBase for the natural transposon. |
The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the natural transposon symbol is used throughout FlyBase. For D.melanogaster natural transposons, the species prefix is only displayed in the '''GENERAL INFORMATION''' section at the top of a Report. | The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the natural transposon symbol is used throughout FlyBase. For D.melanogaster natural transposons, the species prefix is only displayed in the '''GENERAL INFORMATION''' section at the top of a Report. | ||
|- | |- | ||
| − | |Species || The organism that the natural transposon originates from, with the initial letter of the genus and the full species name listed. | + | |'''Species''' || The organism that the natural transposon originates from, with the initial letter of the genus and the full species name listed. |
|- | |- | ||
| − | |Name || The valid full name that is used in FlyBase for the natural transposon. | + | |'''Name''' || The valid full name that is used in FlyBase for the natural transposon. |
|- | |- | ||
| − | |FlyBase ID || The '''Primary''' FlyBase identifier number of the natural transposon, used to uniquely identify it in the database. | + | |'''FlyBase ID''' || The '''Primary''' FlyBase identifier number of the natural transposon, used to uniquely identify it in the database. |
A natural transposon may also have any number of '''Secondary''' FlyBase identifier numbers, which are listed in the '''SECONDARY FLYBASE IDs''' section of the '''Natural Transposon Report'''. | A natural transposon may also have any number of '''Secondary''' FlyBase identifier numbers, which are listed in the '''SECONDARY FLYBASE IDs''' section of the '''Natural Transposon Report'''. | ||
|- | |- | ||
| − | |Feature type || A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the element. | + | |'''Feature type''' || A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the element. |
|- | |- | ||
| − | |Created/Updated || The date that the natural transposon was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the natural transposon report was last updated. The dates are in the format: year-mm-dd. | + | |'''Created/Updated''' || The date that the natural transposon was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the natural transposon report was last updated. The dates are in the format: year-mm-dd. |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Complete element (bp) || style="width: 80%;" | The reported total length, in nucleotides, of the natural transposon. | + | |'''Complete element (bp)''' || style="width: 80%;" | The reported total length, in nucleotides, of the natural transposon. |
|- | |- | ||
| − | |Terminal repeat (bp) | + | |'''Terminal repeat (bp) ''' || The reported length, in nucleotides, of the terminal repeat of the natural transposon. |
|- | |- | ||
| − | |Reference sequence || A link to a file of 'canonical' sequences of the transposable elements from Drosophila. | + | |'''Reference sequence''' || A link to a file of 'canonical' sequences of the transposable elements from Drosophila. |
|- | |- | ||
| − | |Component genes || This field lists the symbol(s) of the genes encoded by the natural transposon. | + | |'''Component genes''' || This field lists the symbol(s) of the genes encoded by the natural transposon. |
Clicking on the symbol will take you to the relevant '''Gene Report'''. | Clicking on the symbol will take you to the relevant '''Gene Report'''. | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Transposon type || style="width: 80%;" | A list of controlled vocabulary terms from the Sequence Ontology (SO), which describe the class of the natural transposon. | + | |'''Transposon type''' || style="width: 80%;" | A list of controlled vocabulary terms from the Sequence Ontology (SO), which describe the class of the natural transposon. |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Copy number and comments || style="width: 80%;" | The number of copies of the natural transposon in the genome, as reported in the literature. | + | |'''Copy number and comments''' || style="width: 80%;" | The number of copies of the natural transposon in the genome, as reported in the literature. |
|- | |- | ||
| − | |Search for || Links to find Insertions in the sequenced genome and in other genomes | + | |'''Search for''' || Links to find Insertions in the sequenced genome and in other genomes |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Size (bp) || style="width: 80%;" | The reported length, in nucleotides, of the target site duplication of the natural transposon. | + | |'''Size (bp)''' || style="width: 80%;" | The reported length, in nucleotides, of the target site duplication of the natural transposon. |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Curated drosophilid orthologs || style="width: 80%;" | A list of natural transposons that have been reported in the literature to be orthologs of the natural transposon. | + | |'''Curated drosophilid orthologs''' || style="width: 80%;" | A list of natural transposons that have been reported in the literature to be orthologs of the natural transposon. |
Clicking on a natural transposon symbol will take you to the relevant '''Natural Transposon Report'''. | Clicking on a natural transposon symbol will take you to the relevant '''Natural Transposon Report'''. | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Etymology || style="width: 80%;" | The explanation behind the natural transposon name as reported by the authors. | + | |'''Etymology''' || style="width: 80%;" | The explanation behind the natural transposon name as reported by the authors. |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Symbol Synonym || style="width: 80%;" | A list of symbols that have been used in the literature, or by FlyBase, to describe the natural transposon. | + | |'''Symbol Synonym''' || style="width: 80%;" | A list of symbols that have been used in the literature, or by FlyBase, to describe the natural transposon. |
|- | |- | ||
| − | |Name Synonym || A list of names that have been used in the literature, or by FlyBase, to describe the natural transposon. | + | |'''Name Synonym''' || A list of names that have been used in the literature, or by FlyBase, to describe the natural transposon. |
|} | |} | ||
Revision as of 15:58, 18 May 2015
Last Updated: 20 August 2007
This is a field-by-field guide to the information provided in the Natural Transposon Report.
General Information
| Symbol | The valid symbol that is used in FlyBase for the natural transposon.
The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the natural transposon symbol is used throughout FlyBase. For D.melanogaster natural transposons, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a Report. |
| Species | The organism that the natural transposon originates from, with the initial letter of the genus and the full species name listed. |
| Name | The valid full name that is used in FlyBase for the natural transposon. |
| FlyBase ID | The Primary FlyBase identifier number of the natural transposon, used to uniquely identify it in the database.
A natural transposon may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Natural Transposon Report. |
| Feature type | A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the element. |
| Created/Updated | The date that the natural transposon was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the natural transposon report was last updated. The dates are in the format: year-mm-dd. |
Sequences & Components
| Complete element (bp) | The reported total length, in nucleotides, of the natural transposon. |
| Terminal repeat (bp) | The reported length, in nucleotides, of the terminal repeat of the natural transposon. |
| Reference sequence | A link to a file of 'canonical' sequences of the transposable elements from Drosophila. |
| Component genes | This field lists the symbol(s) of the genes encoded by the natural transposon.
Clicking on the symbol will take you to the relevant Gene Report. |
Sequence Accessions
This section contains accession numbers from the following databases:
|DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section (This database is only listed if an accession number exists)
Sequence Ontology (SO)
| Transposon type | A list of controlled vocabulary terms from the Sequence Ontology (SO), which describe the class of the natural transposon. |
Insertions & Copy Number
| Copy number and comments | The number of copies of the natural transposon in the genome, as reported in the literature. |
| Search for | Links to find Insertions in the sequenced genome and in other genomes |
Target Site Duplication
| Size (bp) | The reported length, in nucleotides, of the target site duplication of the natural transposon. |
Orthologs
| Curated drosophilid orthologs | A list of natural transposons that have been reported in the literature to be orthologs of the natural transposon.
Clicking on a natural transposon symbol will take you to the relevant Natural Transposon Report. |
Comments
Free text comments about the natural transposon.
Other Information
| Etymology | The explanation behind the natural transposon name as reported by the authors. |
External Crossreferences
A complete list of links to external databases for the natural transposon. These links may also be present in other sections of the Natural Transposon Report, where appropriate.
The SEQUENCE CROSSREFERENCES section contains accession numbers from the following databases:
DDBJ/EMBL/GenBank - the nucleic acid sequence databases of Japan, the U.S., and Europe UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section (This database is only listed if an accession number exists) The OTHER CROSSREFERENCES section contains accession numbers from other databases listed as FlyBase curated links
Synonyms & Secondary IDs
Reported As
| Symbol Synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the natural transposon. |
| Name Synonym | A list of names that have been used in the literature, or by FlyBase, to describe the natural transposon. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the natural transposon.
References
A list of publications that discuss the natural transposon, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Natural Transposon Report.