Difference between revisions of "FlyBase:Insertion Report"
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The insertion report is used to present data on insertions of transgenic constructs, insertions of natural transposons in the sequenced strain, and insertions of natural transposons in strains other than the sequenced strain. | The insertion report is used to present data on insertions of transgenic constructs, insertions of natural transposons in the sequenced strain, and insertions of natural transposons in strains other than the sequenced strain. | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |'''Inserted element''' || style="width: 80%;" | This field | + | |'''Inserted element''' || style="width: 80%;" | This field contains the transposable-element based transgenic construct inserted or the natural transposon class inserted. Clicking on the symbol will take you to the relevant Recombinant Construct Report or Natural Transposon Report as appropriate. Detailed information is to be found in the '''Inserted Element''' section, below. |
|- | |- | ||
|'''Affected gene(s)''' || Gene(s) reported to be affected by the insertion (hyperlinked to the relevant Gene Report); the insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression. This field includes both genes within the genomic region surrounding the insertion and also genes carried in the inserted element. Detailed information is to be found in the '''Affected Gene(s)''' section, below. | |'''Affected gene(s)''' || Gene(s) reported to be affected by the insertion (hyperlinked to the relevant Gene Report); the insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression. This field includes both genes within the genomic region surrounding the insertion and also genes carried in the inserted element. Detailed information is to be found in the '''Affected Gene(s)''' section, below. | ||
|- | |- | ||
| − | |''' | + | |'''Associated allele(s)''' || Allele(s) created by the presence of the insertion (hyperlinked to the relevant Allele Report). This field includes both alleles of genes within the genomic region surrounding the insertion and also alleles carried in the inserted element. Detailed information is to be found in the '''Alleles and Phenotypes''' section, below. |
|- | |- | ||
|'''LINE ID''' || The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated. Additional information is to be found in the '''Data on Genetic Line''' section, below. | |'''LINE ID''' || The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated. Additional information is to be found in the '''Data on Genetic Line''' section, below. | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |''' | + | |'''Chromosomal location''' || style="width: 80%;" | The chromosome arm on which the insertion is located, followed by cytological location in parentheses. See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated. See the '''Detailed Mapping Data''' section, below, for sources of these data. |
|- | |- | ||
|'''Sequence location''' || Site of insertion on the genomic sequence, if mapped to the sequenced strain. If the precise point of insertion is not known, this value may be a range. Includes orientation of the inserted element relative to the conventional representation of the chromosome arm (if also reported), indicated in brackets. See the '''Detailed Mapping Data''' section, below, for source of this data. | |'''Sequence location''' || Site of insertion on the genomic sequence, if mapped to the sequenced strain. If the precise point of insertion is not known, this value may be a range. Includes orientation of the inserted element relative to the conventional representation of the chromosome arm (if also reported), indicated in brackets. See the '''Detailed Mapping Data''' section, below, for source of this data. | ||
|- | |- | ||
| − | |''' | + | |'''Target / Docking site''' || For insertion progenitors of the type "Replacement descendant of (target)", defined as "progenitor replaced at original location, recombination event (target)", the insertion progenitor is also indicated in this field. See the section below "Progenitor(s) within the Genome". |
| + | |- | ||
| + | |'''Genomic Maps (JBrowse)''' || A JBrowse thumbnail graphic showing the location of the insertion in the genome. The insertion of interest is highlighted in yellow. This map is present only for insertions for which the site of insertion has been mapped to the sequenced genome. Insertions are indicated by blue triangles (which indicate orientation of the insertion) or diamonds (if orientation is not known). See also the JBrowse evidence tiers help document. | ||
| − | The " | + | The "JBrowse" links go to a fully interactive JBrowse views of the same region. |
|} | |} | ||
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|'''Orientation''' || Orientation of the inserted element (using conventional representation of the element's 5' and 3' ends) relative to the conventional representation of the chromosome. Orientation information appears here in some cases where it has been reported without sequence location. | |'''Orientation''' || Orientation of the inserted element (using conventional representation of the element's 5' and 3' ends) relative to the conventional representation of the chromosome. Orientation information appears here in some cases where it has been reported without sequence location. | ||
|- | |- | ||
| − | |'''Cytological location (computed by FlyBase)''' || Inferred cytological location based on reported sequence location (marked as "inferred by FlyBase from sequence location"); or on report of affected gene for which sequence or cytological location is known (marked as "near gene of known cytology"). | + | |'''Cytological location (computed by FlyBase)''' || Inferred cytological location based on reported sequence location (marked as "inferred by FlyBase from sequence location"); or on report of affected gene for which sequence or cytological location is known (marked as "near gene of known cytology"). For more information see [[FlyBase:Computed cytological data | Computed cytological data]]. |
|- | |- | ||
|'''Cytological location (reported)''' || Cytological location as reported; marked as "reported as inferred from sequence location" or "in situ hybridization reported". | |'''Cytological location (reported)''' || Cytological location as reported; marked as "reported as inferred from sequence location" or "in situ hybridization reported". | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |'''Construct''' || style="width: 80%;" | This field | + | |'''Construct''' || style="width: 80%;" | This field contains the transposable-element based transgenic construct inserted or the natural transposon class inserted. Clicking on the symbol will take you to the relevant Recombinant Construct Report or Natural Transposon Report as appropriate. |
|- | |- | ||
|'''Location-dependent role''' || Description of function(s) contained within the inserted element that impact the genomic region of an insertion, or genes within that region. Examples include enhancer trap, gene trap, mobile activating element, deletion generation component. | |'''Location-dependent role''' || Description of function(s) contained within the inserted element that impact the genomic region of an insertion, or genes within that region. Examples include enhancer trap, gene trap, mobile activating element, deletion generation component. | ||
|- | |- | ||
| − | |'''Size''' || Size of the inserted element, in kilobases | + | |'''Size (Kb)''' || Size of the inserted element, in kilobases, if known. Refer to the relevant Recombinant Construct Report or Natural Transposon Report for details and attribution(s). |
|- | |- | ||
| − | |''' | + | |'''Component Allele(s)''' || Alleles curated by FlyBase describing components of the inserted element (hyperlinked to the relevant Allele Report). |
|- | |- | ||
|'''Molecular map''' || If available, map generated by FlyBase of the inserted element, based on compiled sequence data curated by FlyBase. Refer to the relevant Recombinant Construct Report for compiled sequence data and attribution(s). | |'''Molecular map''' || If available, map generated by FlyBase of the inserted element, based on compiled sequence data curated by FlyBase. Refer to the relevant Recombinant Construct Report for compiled sequence data and attribution(s). | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |'''Insertion may affect gene''' || style="width: 80%;" | Gene(s) reported as affected by the insertion (hyperlinked to the relevant Gene Report). The insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression, or may be related by other specified criteria | + | |'''Insertion may affect gene''' || style="width: 80%;" | Gene(s) reported as affected by the insertion (hyperlinked to the relevant Gene Report). The insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression, or may be related by other specified criteria. |
|} | |} | ||
==Alleles and Phenotypes== | ==Alleles and Phenotypes== | ||
| − | This section | + | This section lists alleles associated with the insertion with links to any phenotypic data annotated to those alleles. It includes alleles of genes within the genomic region surrounding the insertion as well as alleles carried in the inserted element. |
{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |''' | + | |'''Allele''' || style="width: 80%;" | Allele associated with the insertion (hyperlinked to the relevant Allele Report). |
| − | |||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| − | |''' | + | |'''Reference(s)''' || A list of the references associated with the given allele (each hyperlinked to the relevant Reference Report). |
|- | |- | ||
| − | |''' | + | |'''Phenotypic Data''' || Buttons that link to the 'Phenotypic Class', 'Phenotype Manifest in' or 'Detailed Description' section of the given allele. |
|} | |} | ||
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|'''Reflects expression of''' || If the reporter is described as reflecting the normal expression of an endogeneous gene, the gene is listed, using the FlyBase gene symbol (hyperlinked to the relevant Gene Report). If the expression pattern is described as reflecting a part of the normal expression pattern of that gene, the gene symbol is followed by the term "subset". | |'''Reflects expression of''' || If the reporter is described as reflecting the normal expression of an endogeneous gene, the gene is listed, using the FlyBase gene symbol (hyperlinked to the relevant Gene Report). If the expression pattern is described as reflecting a part of the normal expression pattern of that gene, the gene symbol is followed by the term "subset". | ||
|- | |- | ||
| − | |'''Reporter construct used in assay''' || This field is used to report the second component of a binary reporter assay, for example, the UAS reporter used with a | + | |'''Reporter construct used in assay''' || This field is used to report the second component of a binary reporter assay, for example, the UAS reporter used with a GAL4 driver/enhancer trap. |
|- | |- | ||
|'''External Images''' || Linkout to external database(s) that house reporter expression data. Currently: FlyView, A Drosophila Image Database | |'''External Images''' || Linkout to external database(s) that house reporter expression data. Currently: FlyView, A Drosophila Image Database | ||
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Fields in this section are attributed data fields, meaning they include citations for the sources of the data. | Fields in this section are attributed data fields, meaning they include citations for the sources of the data. | ||
| − | If the insertion that is subject of report is derived from a previously existing insertion, the FlyBase symbol for the originating insertion is indicated here (hyperlinked to the relevant Insertion Report). | + | If the insertion that is subject of report is derived from a previously existing insertion, the FlyBase symbol for the originating insertion is indicated here (hyperlinked to the relevant Insertion Report). Progenitors are classified into 4 types: (1) "Transposed descendant of" defined as progenitor at distinct location, transposition event; (2) "Recombinant descendant of (donor)" defined as progenitor at distinct location, recombination event; (3) "Replacement descendant of (target): defined as progenitor replaced at original location, recombination event (target); (4) "Modified descendant of" defined as progenitor modified at original location. Categories 2 and 3 may both be reported, when the original transposon in an insertion is replaced with a new transposon using recombination with another insertion within the genome. |
==Related Aberration or Balancer== | ==Related Aberration or Balancer== | ||
Latest revision as of 17:46, 20 December 2022
Last Updated: 15 Dec. 2017
The insertion report is used to present data on insertions of transgenic constructs, insertions of natural transposons in the sequenced strain, and insertions of natural transposons in strains other than the sequenced strain.
This is a field-by-field guide to the information in the Insertion Report.
General Information
| Symbol | The valid symbol that is used in FlyBase for the insertion. If the insertion results in a described allele, the allele symbol is included within the insertion symbol.
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 gene symbol is used throughout FlyBase. For D.melanogaster genes, the species prefix is only displayed in the General Information section at the top of a report. |
| Name | This field is not used for insertions of transgenic constructs and transposons. |
| Feature type | A single controlled vocabulary term from the Sequence Ontology (SO), which describes this sequence entity. The feature type transposable_element_insertion_site is used for two classes: insertions of transgenic constructs and insertions of natural transposons into a strain other than the sequenced strain. If mapping data are available, these insertion classes may be mapped to a single site on the sequenced genome. The feature type transposable_element is used for the third class, natural transposons in the sequenced strain. This class is mapped to an extent (or region) on the sequenced genome, corresponding to a specific individual transposon within the sequenced strain (at the time it was sequenced). |
| Species | The organism in which this specific insertion exists, with the initial letter of the genus and the full species name listed. |
| FlyBase ID | The Primary FlyBase identifier number of the insertion, used to uniquely identify the insertion in the database.
An insertion may also have any number of Secondary FlyBase identifier numbers, which are listed in the Secondary FlyBase IDs section of the Insertion Report. |
Description
| Inserted element | This field contains the transposable-element based transgenic construct inserted or the natural transposon class inserted. Clicking on the symbol will take you to the relevant Recombinant Construct Report or Natural Transposon Report as appropriate. Detailed information is to be found in the Inserted Element section, below. |
| Affected gene(s) | Gene(s) reported to be affected by the insertion (hyperlinked to the relevant Gene Report); the insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression. This field includes both genes within the genomic region surrounding the insertion and also genes carried in the inserted element. Detailed information is to be found in the Affected Gene(s) section, below. |
| Associated allele(s) | Allele(s) created by the presence of the insertion (hyperlinked to the relevant Allele Report). This field includes both alleles of genes within the genomic region surrounding the insertion and also alleles carried in the inserted element. Detailed information is to be found in the Alleles and Phenotypes section, below. |
| LINE ID | The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated. Additional information is to be found in the Data on Genetic Line section, below. |
| Expression data | If Ecol\lacZ enhancer trap expression data or Scer\GAL4 reporter/driver data have been curated for this specific insertion, it is indicated by "lacZ reporter" or "GAL4 reporter/driver". Detailed information is to be found in the Expression Data section, below. |
| Viability/fertility | This field is populated if the homozygous stock has been reported as "viable" and/or "fertile". Lethal or sterile phenotypes are not reported; this information is reported in the Alleles and Phenotypes section, below. |
| Stock availability | If stocks of this insertion are available, it is indicated by "publicly available" (if available from one of the public stock centers) or "not publicly available" (if stock may be available from an individual lab). Specific information may be found in the Stocks section, below. |
Genomic Location
| Chromosomal location | The chromosome arm on which the insertion is located, followed by cytological location in parentheses. See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated. See the Detailed Mapping Data section, below, for sources of these data. |
| Sequence location | Site of insertion on the genomic sequence, if mapped to the sequenced strain. If the precise point of insertion is not known, this value may be a range. Includes orientation of the inserted element relative to the conventional representation of the chromosome arm (if also reported), indicated in brackets. See the Detailed Mapping Data section, below, for source of this data. |
| Target / Docking site | For insertion progenitors of the type "Replacement descendant of (target)", defined as "progenitor replaced at original location, recombination event (target)", the insertion progenitor is also indicated in this field. See the section below "Progenitor(s) within the Genome". |
| Genomic Maps (JBrowse) | A JBrowse thumbnail graphic showing the location of the insertion in the genome. The insertion of interest is highlighted in yellow. This map is present only for insertions for which the site of insertion has been mapped to the sequenced genome. Insertions are indicated by blue triangles (which indicate orientation of the insertion) or diamonds (if orientation is not known). See also the JBrowse evidence tiers help document.
The "JBrowse" links go to a fully interactive JBrowse views of the same region. |
Member of Large Scale Dataset(s)
| Dataset | If the insertion is a member of large scale dataset, the name of the dataset is listed here (hyperlinked to the relevant dataset report). |
| Description | A description of the attributes of the dataset with a citation for the source of the data. |
Detailed Mapping Data
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
| Chromosome (arm) | Genomic location as reported, if to level of arm or chromosome. |
| Sequence Location | Genomic location as reported, if mapped at sequence level to the sequenced genome; expressed in whole-arm coordinates of the current genomic sequence release. Includes orientation of the inserted element (if also reported), indicated in brackets. |
| Orientation | Orientation of the inserted element (using conventional representation of the element's 5' and 3' ends) relative to the conventional representation of the chromosome. Orientation information appears here in some cases where it has been reported without sequence location. |
| Cytological location (computed by FlyBase) | Inferred cytological location based on reported sequence location (marked as "inferred by FlyBase from sequence location"); or on report of affected gene for which sequence or cytological location is known (marked as "near gene of known cytology"). For more information see Computed cytological data. |
| Cytological location (reported) | Cytological location as reported; marked as "reported as inferred from sequence location" or "in situ hybridization reported". |
Sequence Data
| Flanking sequence | DDBJ/EMBL/GenBank accession(s) reporting the sequence of the region flanking the inserted element. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived. These accession numbers are FlyBase curated links. |
Inserted Element
The data in this section are promoted from fields in the relevant Recombinant Construct Report or Natural Transposon Report
| Construct | This field contains the transposable-element based transgenic construct inserted or the natural transposon class inserted. Clicking on the symbol will take you to the relevant Recombinant Construct Report or Natural Transposon Report as appropriate. |
| Location-dependent role | Description of function(s) contained within the inserted element that impact the genomic region of an insertion, or genes within that region. Examples include enhancer trap, gene trap, mobile activating element, deletion generation component. |
| Size (Kb) | Size of the inserted element, in kilobases, if known. Refer to the relevant Recombinant Construct Report or Natural Transposon Report for details and attribution(s). |
| Component Allele(s) | Alleles curated by FlyBase describing components of the inserted element (hyperlinked to the relevant Allele Report). |
| Molecular map | If available, map generated by FlyBase of the inserted element, based on compiled sequence data curated by FlyBase. Refer to the relevant Recombinant Construct Report for compiled sequence data and attribution(s). |
Affected Gene(s)
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
| Insertion may affect gene | Gene(s) reported as affected by the insertion (hyperlinked to the relevant Gene Report). The insertion may be located within the transcribed extent of the gene, and/or may cause misexpression or a reduction in expression, or may be related by other specified criteria. |
Alleles and Phenotypes
This section lists alleles associated with the insertion with links to any phenotypic data annotated to those alleles. It includes alleles of genes within the genomic region surrounding the insertion as well as alleles carried in the inserted element.
| Allele | Allele associated with the insertion (hyperlinked to the relevant Allele Report). |
| Reference(s) | A list of the references associated with the given allele (each hyperlinked to the relevant Reference Report). |
| Phenotypic Data | Buttons that link to the 'Phenotypic Class', 'Phenotype Manifest in' or 'Detailed Description' section of the given allele. |
Expression Data
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
| Reporter Expression | A structured description of the expression pattern, broken down into stage and anatomical distribution. |
| Additional Information | Free text description of reporter expression pattern. |
| Marker for | If the reporter is used as an anatomical marker, the region or body part is specified, using controlled vocabulary anatomical terms. |
| Reflects expression of | If the reporter is described as reflecting the normal expression of an endogeneous gene, the gene is listed, using the FlyBase gene symbol (hyperlinked to the relevant Gene Report). If the expression pattern is described as reflecting a part of the normal expression pattern of that gene, the gene symbol is followed by the term "subset". |
| Reporter construct used in assay | This field is used to report the second component of a binary reporter assay, for example, the UAS reporter used with a GAL4 driver/enhancer trap. |
| External Images | Linkout to external database(s) that house reporter expression data. Currently: FlyView, A Drosophila Image Database |
Data on Genetic Line
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
| Line ID | The line identification number used by one of the large-scale gene disruption projects (eg., the BDGP, the GDP, or DrosDel), if relevant. A line identification number refers to an isolated genetic line, and thus may apply to more than one insertion, if multiple insertions are co-isolated. |
| Origin as a multiple insertion line | If reported that insertion was originally isolated in a genetic line with multiple insertions, "yes" or "probable" is indicated in this field. |
Progenitors within the Genome
Fields in this section are attributed data fields, meaning they include citations for the sources of the data.
If the insertion that is subject of report is derived from a previously existing insertion, the FlyBase symbol for the originating insertion is indicated here (hyperlinked to the relevant Insertion Report). Progenitors are classified into 4 types: (1) "Transposed descendant of" defined as progenitor at distinct location, transposition event; (2) "Recombinant descendant of (donor)" defined as progenitor at distinct location, recombination event; (3) "Replacement descendant of (target): defined as progenitor replaced at original location, recombination event (target); (4) "Modified descendant of" defined as progenitor modified at original location. Categories 2 and 3 may both be reported, when the original transposon in an insertion is replaced with a new transposon using recombination with another insertion within the genome.
Related Aberration or Balancer
| Aberration | If the insertion is on an aberration chromosome, or created an aberration, the FlyBase symbol for the aberration is indicated here (hyperlinked to the relevant Aberration Report). |
| Balancer | If the insertion is on a balancer chromosome, the FlyBase symbol for the balancer is indicated here (hyperlinked to the relevant Balancer Report). |
Stocks
A list of the stocks from the public stocks centers that contain this insertion; genotypes may be provided. If there are a large number of such stocks, the list may be truncated. For participating stock centers, clicking on the stock number will take you to the appropriate stock report.
Linkouts
Contains hyperlinks to relevant Linkouts. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived. These links may also be present in other sections of the Insertion Report, where appropriate.
Linkouts FlyView
Comments
Miscellaneous free text comments about the insertion.
Synonyms & Secondary IDs
Reported As
| Symbol Synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the insertion. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the insertion. If an insertion has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database.
References
The number in parentheses indicates the number of references listed.
A list of publications that discuss the insertion, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Insertion Report.