FlyBase:Gene Report
Last Updated: 26 April 2012
The Gene Report provides information on individual genes. The report also contains summaries and links to individual reports relating to objects associated with the gene, such as mutant alleles of the gene (including both classical alleles and alleles carried within transgenic constructs), transcripts and proteins encoded by the gene and their expression pattern data, and transgenic constructs and insertions. A link to search for stocks carrying these objects is also provided.
A locus may have been mapped to the genome and have an annotation, or it may only have been identified genetically via its mutant phenotype. Both types of locus are given gene reports in FlyBase.
As well as including gene reports for genes derived from species within the family Drosophilidae, FlyBase also includes gene reports for non-drosophilid genes ("foreign genes") that have been introduced into Drosophila via transgenic constructs and for engineered objects such as a fusion gene between two D.melanogaster genes.
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data. The exception in the Gene Report is the GENERAL INFORMATION section which contains a summary of the identity of the gene, the GENOMIC LOCATION section which contains a summary of location data, and summary tables in the GENE PRODUCTS & EXPRESSION and ALLELES & PHENOTYPES sections, which provide links to objects associated with the gene.
This is a field-by-field guide to the information provided in the Gene Report.
General Information
| Symbol | The valid symbol that is used in FlyBase for the gene.
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 | The valid full name that is used in FlyBase for the gene. |
| Feature type | A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the key type of the gene.
The single term in this field is computed by FlyBase from the full list of SO terms listed in the SEQUENCE ONTOLOGY: Class of gene section of the Gene Report. See Computed Feature type of genes for a detailed description of how the term is selected. |
| Created/Updated | The date that the gene was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the gene report was last updated. The dates are in the format: year-mm-dd. |
| Species | The organism that the gene originates from, with the initial letter of the genus and the full species name listed. |
| Annotation symbol | The current symbol for the annotation that represents the gene (if applicable). |
| FlyBase ID | The Primary FlyBase identifier number of the gene, used to uniquely identify the gene in the database.
A gene may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Gene Report. |
Genomic Location
| Chromosome (arm) | The chromosome arm that the gene is located on. This field is only filled in for genes with annotations. |
| Cytogenetic Map | A computed cytological location, based on the position on the genome to which the gene maps. This field is only filled in for genes with annotations.
See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated. |
| Recombination map | A computed genetic map position for the gene, derived from the full list of terms listed in the EXPERIMENTALLY DETERMINED RECOMBINATION DATA subsection of the DETAILED MAPPING DATA section of the Gene Report.
The genetic map position is given as chromosome number-map position, or simply chromosome number-, if the gene has not been mapped within the chromosome. |
| Sequence location | The extent of the transcription unit on the genome, prefixed with the chromosome arm that the gene is located on. The strand to which the gene maps is indicated in square brackets after the sequence coordinates.
This field is only filled in for genes with annotations. |
| Map (GBrowse) | A GBrowse thumbnail showing the location of the gene (highlighted in pink) in the genome.
To the right of the GBrowse thumbnail, there is a box containing pull down menus to download sequences associated with the gene. The top menu allows you to download the genomic region containing the gene, in one of three formats:
GenBank GFF
The following sequences can be downloaded:
Extended Gene region Translations Transcripts 3' UTR 5' UTR |
Tag or Foreign Gene Data
This section is only displayed in an individual Gene Report if the gene is a "tag" or a "foreign gene". (A "tag" is a DNA fragment that is used to confer a novel property to a gene product, and may be artificial or derived from a Drosophilid or non-drosophilid gene. A "foreign gene" is any non-drosophilid gene that has been introduced into Drosophila, for example via a transgenic construct.) For tags, this section shows the species from which the gene is derived, the nature of the tag, and either a sequence accession number (if available) or a brief description of the tag. For foreign genes, this section shows the species from which the gene is derived, the gene symbol, and where possible an accession number for the gene (either an identifier number from a model organism database, or a sequence accession number).
Families, Domains and Molecular Function
| Gene Group Membership (FlyBase) | Lists any Flybase Gene Groups the gene is a member of, with a hyperlink to the Gene Group Report. |
| Protein Family (UniProt, Sequence Similarities) | Lists any UniProt Protein Families shown in their 'Sequence similarities' section, with the evidence code and a hyperlink to corresponding UniProt page. |
| Protein Domains/Motifs | Lists Protein Domains or motifs found in the protein encoded by the gene.
UniProt- Any Protein Domain or Motifs listed in the UniProt 'Sequence similarities' section, with the evidence code and a hyperlink to corresponding UniProt page. Interpro- Any Protein Domains listed in InterPro with hyperlinks to the corresponding Interpro page. |
| Molecular Function (see GO section for details) | A summary of the Gene Ontology Molecular Function terms associated with the gene, divided into terms with Experimental Evidence and Predictions/Assertions. Each term is hyperlinked to the appropriate Term Report.
For the full Gene Ontology (GO) data, including evidence and attribuions, see the Gene Ontology (GO) section. |
Summaries
The Automatically generated summary is generated automatically from information in the gene report and related allele reports. For more information about each statement in the summary see the relevant section in the gene gene/allele report.
Gene Group Membership
Each FlyBase Gene Group that the gene is a member of is listed with a description of that group. The Gene Group name is hyperlinked to the corresponding Gene Group Report.
UniProt Contributed Data
Shows the summary shown in the UniProt 'Function' section, with the evidence code and a hyperlink to corresponding UniProt page.
User Contributed Data
A link to the FlyGene Wiki page for the gene. The FlyGene Wiki allows you to write your own summary for the gene which is visible to the public and editable by others.
External Summaries
Links to any external summaries for the gene.
Detailed Mapping Data
FlyBase Computed Cytological Location
An inferred cytological location, based on the position on the genome to which the gene maps, or on polytene localization, recombination, complementation or molecular information for the gene. The evidence that was used to derive the inferred location is also given.
See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated.
Experimentally Determined Cytological Location
A table of cytological locations that have been reported for the gene in the literature. The table also contains additional notes on the reported location, such as a comment that the cytological location is inferred from the location of a transposable element insertion causing an allele of a gene.
Experimentally Determined Recombination Data
A table of genetic map data that have been reported for the gene in the literature. The table contains reported genetic map positions, given as chromosome number-map position, or simply chromosome number-, if the gene has not been mapped within the chromosome.
The table also lists other genes to which the gene has been mapped to the left of or right of, and additional notes on the reported location.
If a gene has been mapped cytogenetically but not genetically, an estimated genetic position may be given in square brackets, inferred from a standard Map Conversion Table.
Gene Model & Features
A GBrowse graphic showing the gene model. The extent of the transcription unit on the genome (highlighted in pink), its transcripts, CDS and any transgene insertion sites in the region are shown. For a more detailed view showing more features, a link to open GBrowse in a separate window is provided above the graphic.
Comments on the Gene Model
Comments regarding the annotation of the gene, including whether the gene model contains any unconventional features.
Sequences Supporting the Gene Model
A table of sequence accession numbers that support the gene model. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived. Sequences associated with genes that do not yet have an annotation are also listed in this section.
The table contains accession numbers from the following databases:
DDBJ/EMBL/GenBank - nucleic acid accession number and associated protein ID number (if applicable).
UniProtKB/Swiss-Prot - protein accession number.
UniProtKB/TrEMBL - protein accession number.
These accessions are both FlyBase curated links and associations made by automated assessment of aligned cDNA and EST nucleotide sequences.
Mapped Features & Mutations
A table listing features associated with the gene, additional to the basic transcript and polypeptide structure, that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains the feature's name as well as its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.
External Data
A list of links to external databases that are relevant to the gene model as a whole, but not specifically to individual gene products.
The links are either Linkouts, which are indicated by a LinkOut label in parentheses after the field label, or are accession numbers which are FlyBase curated links. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
The external databases currently displayed in this section are:
FlyBase-curated links
EPD - Eukaryotic Promoter Database (Bucher)
Linkouts
DEDB - Drosophila Exon Database
These links are also displayed together with all other external data links for the gene in the EXTERNAL CROSSREFERENCES & LINKOUTS section of the Gene Report.
Gene Products & Expression
Transcript Data
Annotated Transcripts
A table listing the annotated transcripts of the gene, their FlyBase identifier number, length in nucleotides and length in amino acid residues of the associated coding sequence (CDS). Clicking on a transcript symbol will take you to the relevant Transcript Report.
Additional Transcript Data & Comments
| Reported transcript sizes (kB) | A list of transcript sizes that have been reported in the literature along with the associated reference. |
| Comments | Miscellaneous free text comments related to reported transcripts along with the associated reference. |
External Data
A list of accession numbers from external databases that are relevant to the transcripts of the gene. The accession numbers are FlyBase curated links.
Accession numbers from the following databases are currently displayed in this section:
MIR - miRBase, microRNA data
Rfam - RNA families database of alignments and CMs
These links are also displayed together with all other external data links for the gene in the EXTERNAL CROSSREFERENCES & LINKOUTS section of the Gene Report.
Polypeptide Data
Annotated Polypeptides
A table listing the annotated polypeptides of the gene, their FlyBase identifier number, predicted molecular weight (kD), length in amino acid residues, theoretical pI, and GenBank protein accession numbers. Clicking on a polypeptide symbol will take you to the relevant Polypeptide Report.
Additional Polypeptide Data & Comments
| Reported protein sizes (kB) | A list of protein sizes that have been reported in the literature along with the associated reference. |
| Comments | Miscellaneous free text comments related to reported proteins along with the associated reference. |
External Data
A list of links to external databases that are relevant to the polypeptides encoded by the gene. The links are either Linkouts, which are indicated by a "LinkOut" label in parentheses after the field label, or are accession numbers which are FlyBase curated links. Clicking on the accession number or linkout identifier will take you to the appropriate entry in the external database from which they are derived.
The external databases currently displayed in this section are:
FlyBase-curated links
GCR - The G protein-coupled receptor database
InterPro - a database of protein families, domains and functional sites
MEROPS - Protease database
MITODROME - The MitoDrome database
NRL_3D - NRL_3D database
PDB - Protein Data Bank (Brookhaven)
TransFac - The TRANSFAC database of transcription factors and their binding sites
Linkouts
PANTHER - Protein Classification System
These links are also displayed together with all other external data links for the gene in the EXTERNAL CROSSREFERENCES & LINKOUTS section of the Gene Report.
Expression Data
A link to the FlyBase Gene Expression Report, which groups expression pattern information for all transcripts and polypeptides derived from a given gene.
A list of links to external databases that are relevant to expression data is also displayed. The links are Linkouts, which are indicated by a "LinkOut" label in parentheses after the field label. Clicking on the linkout identifier will take you to the appropriate entry in the external database from which they are derived.
The external databases currently displayed in this section are:
FLIGHT - Integrating Genomic and High-Throughput data
FlyAtlas - the Drosophila adult expression atlas
GEO - NCBI's Gene Expression Omnibus
BDGP in situ Gene Expression Database - Patterns of gene expression in Drosophila embryogenesis
FlyExpress - A Drosophila melanogaster expression pattern search engine
These links are also displayed together with all other external data links for the gene in the EXTERNAL CROSSREFERENCES & LINKOUTS section of the Gene Report.
High-Throughput Expression Data subsection → 'search for similarly expressed genes' button:
Expression data comparisons were not generated by the modENCODE consortium but by FlyBase software. The 'search for similarly expressed genes' button on a gene report initiates a 'fixed' variant of a comparative search (using some fixed predefined search settings specific to expression).
Searching is performed by comparison of gene expression level changes through the set of [similarly ordered] 'experiments' which represent known expression values under different experimental conditions (for staging data, experiments are the different developmental stages, for FlyAtlas data they are expression levels in different bodyparts/ tissues and so on). The purpose of the declared search is to compare sets of expression values from different genes, to determine the tendency of two datasets to vary together, in a somewhat correlated manner. The correlation coefficient is the best statistical test serving such a purpose.
Predefined search settings (currently) include all developmental stages from modENCODE staging data. Sets of expression values from all genes are compared to the 'test' gene, resulting in an output of top matches. This is in the form of a custom HitList which includes graphical representation of the expression profiles. Visual inspection of these profiles might allow the user an idea about the interpretation of the obtained correlation (note, the 'test' gene profile in almost all cases is located at the top of the HitList as naturally, being compared to itself, it gives perfect 100% correlation match).
FlyBase provides a simple comparison tool for the modENCODE expression data. We hope this will aid the user in interpreting the expression patterns but we also appreciate that there are more complicated ways of comparing and interpreting the data.
Alleles & Phenotypes
Summary of Allele Phenotypes
A table containing a summary of the phenotypes of alleles of the gene. The table lists controlled vocabulary terms describing the phenotype, together with the allele(s) of the gene which have been reported to show this phenotype.
To see the detail of the phenotype (including publications where the phenotype has been reported and additional free text comments), click on the allele symbol to go to the relevant Allele Report and look at the PHENOTYPIC DATA section.
Clicking on the controlled vocabulary term will take you to the relevant CV Term Report, which includes a definition of the term (where available).
The table is divided into 4 sections.
Lethality - a list of reported lethal/viable phenotypes.
Sterility - a list of reported sterile/fertile phenotypes.
Other Phenotypes - a list of other reported phenotypic classes.
Phenotype manifest in - a list of the parts of the animal reported to be affected in the mutant alleles.
Classical Alleles
The number in parentheses shows the total number of classical alleles that exist in FlyBase for this gene.
A table listing all the classical alleles of the gene together with summary information, including the allele class, mutagen used to generate the allele, stock availability and whether or not the lesion that causes the allele is known.
To see the full allele information, click on the allele symbol to go to the relevant Allele Report.
Alleles Carried on Transgenic Constructs
The number in parentheses shows the total number of alleles carried on transgenic constructs that exist in FlyBase for this gene.
A table listing all the alleles carried on transgenic constructs of the gene together with summary information, including the allele class, mutagen used to generate the allele, stock availability and whether or not the lesion that causes the allele is known.
To see the full allele information, click on the allele symbol to go to the relevant Allele Report.
Deletions and Duplications
| Disrupted in | A list of aberrations that have been reported to completely delete/disrupt the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
| Partially disrupted in | A list of aberrations that have been reported to partially disrupt the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
| Not Disrupted in | A list of aberrations that have been reported not to disrupt the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
| Duplicated in | A list of aberrations that have been reported to completely duplicate the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
| Partially duplicated in | A list of aberrations that have been reported to partially duplicate the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
| Not duplicated in | A list of aberrations that have been reported not to duplicate the gene, determined by either complementation or molecular analysis.
Clicking on an aberration symbol will take you to the relevant Aberration Report. This field is only displayed in an individual Gene Report if it contains data. |
Transgenic Constructs & Insertions
Transgenic Constructs
Insertions
Gene Ontology: Function, Process & Cellular Component
Gene Ontology (GO) controlled vocabulary (CV) terms assigned to genes based on evidence in external publications and internal analysis. Note that terms are assigned to genes but apply to the product of that gene. The number in parentheses shows the total number of different terms assigned to a gene.
More information about how GO terms are assigned can be found under the Classification of Gene Products using Gene Ontology (GO) terms.
The current release of GO data for all FlyBase genes can be found in the gene_association.fb file. The latest version of this data is available for download here from the Gene Ontology consortium site. Details about the file format and comments on version differences can be found in the documentation on the Classification of Gene Products using Gene Ontology (GO) terms.
Molecular Function
A list of GO molecular function terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided.
CV term
Clicking on the term in the CV term column will take you to the relevant GO CV Term Report, which includes a definition of the GO term (where available).
GO CV terms may be preceeded by qualifiers. The qualifier NOT is used to make an explicit note that the gene product is not associated with the GO term. The qualifier contributes_to is used when an individual gene product that is part of a complex can be annotated to terms that describe the function of the complex. contributes_to can only be used to qualify GO molecular function terms.
Evidence
The type of evidence used to support the GO term is indicated in the evidence column. The evidence code documentation contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology Guide to GO Evidence Codes.
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the GO.xrf_abbs file. The evidence code documentation explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
Biological Process
A list of GO biological process terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided.
CV term
Clicking on the term in the CV term column will take you to the relevant GO CV Term Report, which includes a definition of the term (where available).
GO CV terms may be preceeded by qualifiers. The qualifier NOT is used to make an explicit note that the gene product is not associated with the GO term.
Evidence
The type of evidence used to support the GO term is indicated in the evidence column. The evidence code documentation contains details of the evidence codes used by FlyBase. More information is available in the Gene Ontology Guide to GO Evidence Codes.
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the GO.xrf_abbs file. The evidence code documentation explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
Cellular Component
A list of GO cellular component terms associated with the product(s) of the gene. For each term, the type of evidence used to assign the term and the reference containing the evidence are provided.
CV term
Clicking on the term in the CV term column will take you to the relevant GO CV Term Report, which includes a definition of the term (where available).
GO CV terms may be preceeded by the qualifiers. The qualifier NOT is used to make an explicit note that the gene product is not associated with the GO term. The qualifier colocalizes_with is used when a gene product is transiently or peripherally associated with an organelle or complex. It is also used in cases where the resolution of an assay is not accurate enough to say that the gene product is a bona fide component member. colocalizes_with can only be used to qualify GO cellular component CV terms.
Evidence
The type of evidence used to support the GO term is indicated in the evidence column. The evidence code documentation contains details of the evidence codes used by FlyBase.
Some types of evidence can be supported by other database objects. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the GO.xrf_abbs file. The evidence code documentation explains which codes can be used with other database objects and the special meaning attached to using multiple objects in evidence.
Sequence Ontology: Class of Gene
A list of controlled vocabulary terms from the Sequence Ontology (SO), which describe the class of the gene. Aspects of the gene class which are described by the SO terms include (but are not limited to):
- the type of molecule (e.g. protein, tRNA, rRNA) encoded by the gene.
- where the gene is encoded (e.g. nucleus, mitochondrion).
Interactions & Pathways
Summary of Genetic Interactions
A table containing a summary of genetic interactions between this and other genes. The table lists alleles of this gene that have been shown to interact genetically with alleles of other genes, and the gene they have been reported to interact with.
Clicking on an allele symbol will take you to the relevant Allele Report.
Clicking on a gene symbol will take you to the relevant Gene Report for the interacting gene.
To see the full details of the genetic interactions (including the nature of the interactions and additional free text comments), click on the allele symbol to go to the relevant Allele Report and look at the GENETIC INTERACTIONS section.
External Data
A list of links to external databases that are relevant to expression data is also displayed. The links are Linkouts, which are indicated by a "LinkOut" label in parentheses after the field label. Clicking on the linkout identifier will take you to the appropriate entry in the external database from which they are derived.
The external databases currently displayed in this section are:
BioGRID - General Repository for Interaction Datasets
Drosophila PIMRider - The Drosophila Protein Interaction map
These links are also displayed together with all other external data links for the gene in the EXTERNAL CROSSREFERENCES & LINKOUTS section of the Gene Report.
Orthologs
The orthology calls in FlyBase are D. melanogaster-centric. We only report orthologies between D. melanogaster and other species.
OrthoDB Orthologs
This section presents a uniform set of orthology calls from OrthoDB. At the top of this section is the “OrthoDB Ortholog Groups” subsection. This subsection contains links to OrthoDB for each of the groups mentioned above. Clicking on the link will take you to OrthoDB where you can see additional details of the genes contained in the group. Below this is the list of genes organized by each of the groups. The groups and species within them are listed in order of increasing phylogenetic distance relative to D. melanogaster. The columns include Organism, Common Name, OrthoDB Group, and Gene. The OrthoDB Group column may contain one or more OrthoDB group IDs. In the “Gene” column you will find the target gene that is indicated as being an ortholog of the current gene. This column provides the symbol and a link to an appropriate database when possible.
For non D. melanogaster FlyBase gene reports, the Orthologs sections includes links to the OrthoDB Ortholog groups (if any are identified) as well as a link to the orthologous D. melanogaster gene (where one has been identified).
Human Orthologs
Information about potentially orthologous human genes is presented in a table. The first column displays the symbol for a human gene ortholog predicted by OrthoDB, which links to the corresponding Ensembl gene page. The second column lists the Online Mendelian Inheritance in Man MIM number for this human gene, which links to the corresponding OMIM report. The third column contains the HUGO Gene Nomenclature Committee approved name or names for this human gene, which links to the corresponding HGNC gene symbol report.
AAA Orthologs
This table displays the orthologs called using a GLEANR analysis performed by the Drosophila 12 Genomes Consortium (FBrf0200326), from D. melanogaster to eleven other Drosophila species.
Stocks & Reagents
Stocks Listed in FlyBase
Clicking on the "Search for Stocks" button allows you to search for stocks that contain mutant alleles of the gene, or transgenic constructs or insertions related to the gene.
Genomic Clones
A list of genomic clones that are associated with this gene.
cDNA Clones
This section lists cDNA clones that have been associated with this gene. It is subdivided to distinguish fully sequenced clones from those which have only been partially characterized. Clones that are part of the BDGP DGC collection are listed separately from the other clones.
These associations are primarily automated and at this time include clones containing inserts that support the gene model as well as clones containing inserts that overlap the gene model but do not support any of the currently annotated transcripts. Efforts have been made to eliminate from this list clones that overlap the gene model but support another gene model in the same genomic region (i.e. a gene nested within an intron of another gene). In addition, clones containing sequences that overlap transposable elements have been excluded from this list.
We plan to subdivide clones into those that completely support a gene model and those that overlap but do not support an annotation in a future iteration of the report but at this time care should be taken to assess the sequences linked to the clone before using a clone as a reagent.
RNAi & Array Information
Antibody Information
A list of publications in which the generation of antibodies against the subject polypeptide has been reported. Each entry is categorized as "polyclonal" or "monoclonal" to indicate the nature of the antibodies. In cases where a monoclonal antibody is available from the Developmental Studies Hybridoma Bank in Iowa, a link the DSHB website is provided.
Other Information
Discoverer
A list of the individuals who identified the gene.
Etymology
The explanation behind the gene name as reported by the authors.
Relationship to Other Genes
| Source for database identity of | A statement indicating that the valid symbol used in FlyBase for the gene has been changed, because it previously had an arbitrary symbol, for example a gene that was identified by genomic sequencing projects e.g. CG8896, or was a lethal locus named solely by its cytogenetic location, e.g. l(3)64Aj. The publication that was the source of the change is listed.
The statement consists of the new symbol and previously used symbol of the gene at the time of the rename, prefixed with "Source for identity of: " See Gene symbols and names in the nomenclature document for cases when renaming may occur. |
| Source for database merge of | A statement indicating that two (or more) gene records have been merged into a single gene record in the database, together with the publication that was the source of the merge.
The statement consists of the valid symbols of the gene at the time of the merge, prefixed with "Source for merge of: " |
| Member gene of | If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
This field is displayed in the Gene Report for the individual member of the cluster and lists the gene symbol of the generic record, representing the whole cluster, that the gene is a member of. Clicking on the gene symbol will take you to the Gene Report for the generic record representing the whole cluster. This field is only displayed in an individual Gene Report if it contains data. |
| Component gene(s) | If a gene is present as a cluster in the genome, where each member of the cluster is so similar that they are traditionally referred to by a single name, then FlyBase creates a gene report for each individual member of the cluster, and also a "generic" report representing the cluster as a whole. For example, a generic gene record exists for "5SrRNA" and also for individual members of the cluster, such as "5SrRNA:CR33353".
This field is displayed in the Gene Report for the generic record, representing the whole cluster, and lists the gene symbols of the individual members of the cluster. Clicking on a gene symbol will take you to the Gene Report for individual member of the cluster. This field is only displayed in an individual Gene Report if it contains data. |
| Encoded by | This field is typically displayed in a Gene Report for genes encoded by natural transposons, and lists the symbol of the natural transposon that encodes the gene.
Clicking on the symbol will take you to the Report for the natural transposon. This field is only displayed in an individual Gene Report if it contains data. |
| Tags | This field is displayed in a Gene Report that represents an engineered tag that has been used in a transgenic construct to mark genes or their products. This includes epitope tags such as "Avic\GFP" and function tags such as nuclear localization signals.
The field lists the alleles that contain the tag. Clicking on the symbol will take you to the relevant Allele Report. This field is only displayed in an individual Gene Report if it contains data. |
| Additional comments | Free text comments about the relationship of the gene to other genes or groups of alleles. |
Other Comments
Miscellaneous free text comments about the gene.
External Crossreferences & Linkouts
A complete list of links to external databases for the gene. These links may also be present in other sections of the Gene Report, where appropriate. The SEQUENCE CROSSREFERENCES and OTHER CROSSREFERENCES sections contain accession numbers which are FlyBase curated links. The LINKOUTS section contains 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.
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/Swiss-Prot - UniProt Knowledgebase, Swiss-Prot section
UniProtKB/TrEMBL - UniProt Knowledgebase, TrEMBL section
The OTHER CROSSREFERENCES section contains accession numbers from the following databases:
EPD - Eukaryotic Promoter Database (Bucher)
GCR - The G protein-coupled receptor database
InterPro - a database of protein families, domains and functional sites
MEROPS - Protease database
MIR - miRBase, microRNA data
MITODROME - The MitoDrome database
NRL_3D - NRL_3D database
PDB - Protein Data Bank (Brookhaven)
Rfam - RNA families database of alignments and CMs
TransFac - The TRANSFAC database of transcription factors and their binding sites
The LINKOUTS section contains linkout identifiers from the following databases:
BDGP in situ Gene Expression Database - Patterns of gene expression in Drosophila embryogenesis
BioGRID - General Repository for Interaction Datasets
DEDB - Drosophila Exon Database
Drosophila PIMRider - The Drosophila Protein Interaction map
DRSC - Drosophila RNAi Screening Center
FLIGHT - Integrating Genomic and High-Throughput data
Flyatlas - the Drosophila adult expression atlas
FlyMine - An integrated database for Drosophila and Anopheles genomics
FlyView - A Drosophila Image Database
Genome RNAi, Heidelberg - a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells
Inparanoid - Eukaryotic Ortholog Groups
Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
GEO - NCBI's Gene Expression Omnibus
Reactome - Curated Database of Biological Pathways
PANTHER - Protein Classification System
Yale Developmental Gene Expression
Synonyms & Secondary IDs
Reported As
| Symbol Synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the gene. |
| Name Synonym | A list of names that have been used in the literature, or by FlyBase, to describe the gene. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the gene.
If a gene 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. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.
References
A list of publications that discuss the gene, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Gene Report.