- AAB Assoc. Aberration
- Description: none
Brief help: none
Data classes: none
Star code: *Q
Java class: flybase.abs.AssocAber (field) Inherits from: flybase.store.BasicFieldStore
- AAL Length in a.a.
- Description: The size of the polypeptide in amino acids.
Brief help: protein size in amino acids
Data classes: none
Java class: flybase.rci.Length (field) Inherits from: flybase.store.BasicFieldStore
- AALEN Peptide length
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.AminoLength (field) Inherits from: flybase.store.BasicFieldStore
- ABA Associated aberration
- Description: none
Brief help: none
Data classes: none
Star code: *P
Java class: flybase.genes.AssocAbs (field) Inherits from: flybase.store.BasicFieldStore
- ABOD Antibodies generated
- Description: Describes the type of antibody generated against the polypeptide. Possible types are polyclonal, monoclonal, or phage generated.
Brief help: Type of antibody generated
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ABSR Aberration Record
- Description: none
Brief help: none
Data classes: none
Star code: *a
Java class: flybase.abs.AberrationStore (record) Inherits from: flybase.store.DataStore
- ABSSR Parent Aberration
- Description: none
Brief help: none
Data classes: none
Java class: flybase.abs.Aberration (subrecord) Inherits from: flybase.store.SubrecFieldStore
- ABSTR Abstract
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.RecordAbstract (field) Inherits from: flybase.store.BasicFieldStore
- ABSY Symbol
- Description: none
Brief help: none
Data classes: none
Star code: *a
Java class: flybase.abs.AbsSymbol (field) Inherits from: flybase.genes.GeneSymbol, flybase.store.Abbreviation
- ACLA Class of aberration
- Description: none
Brief help: none
Data classes: none
Star code: *C
Java class: flybase.abs.AbsClass (field) Inherits from: flybase.genes.GeneClass, flybase.store.Kindname
- ACM Complements
- Description: none
Brief help: none
Data classes: none
Star code: *Q Complements:
Java class: flybase.genes.Complements (field) Inherits from: flybase.store.BasicFieldStore
- AFC Fails to complement
- Description: none
Brief help: none
Data classes: none
Star code: *Q Fails to complement:
Java class: flybase.genes.FailsComplement (field) Inherits from: flybase.store.BasicFieldStore
- AFFY Affy Oligo
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Affy (field) Inherits from: flybase.store.BasicFieldStore
- AFS Fails to rescue
- Description: none
Brief help: none
Data classes: none
Star code: *Q Fails to rescue:
Java class: flybase.genes.FailsRescue (field) Inherits from: flybase.store.BasicFieldStore
- AGT Allele or genotype used
- Description: none
Brief help: none
Data classes: none
Java class: flybase.pep.AlleleInfo (field) Inherits from: flybase.store.BasicFieldStore
- ALC Allele class
- Description: Classification of allele as to
Brief help: Class of allele, including wild-type, loss of function, etc., a controlled vocabulary
Data classes: none
Star code: *k Allele class:
Java class: flybase.genes.AleClass (field) Inherits from: flybase.store.BasicFieldStore
- ALER Allele Record
- Description: Allele record, holds all the fields pertaining to an allele report. See ALESR
Brief help: an allele record
Data classes: none
Star code: *A
Java class: flybase.alleles.AlleleStore (record) Inherits from: flybase.store.DataStore
- ALETAB Allele table
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.AlleleTableLink (field) Inherits from: flybase.store.BasicFieldStore
- ALSO Also published as
- Description: none
Brief help: none
Data classes: none
Star code: *C
Java class: flybase.refs.AlsoIn (field) Inherits from: flybase.store.BasicFieldStore
- ALTSQ Alternative sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.AltSequence (field) Inherits from: flybase.trin.Sequence
- AM Allelism info.
- Description: information concerning possible allelism between genes
Brief help: information concerning possible allelism between genes
Data classes: none
Star code: *q
Java class: flybase.genes.Alleleism (field) Inherits from: flybase.store.BasicFieldStore
- AMD Deletes/disrupts
- Description: information on allelism indicating genes deleted or disrupted by this one
Brief help: information on allelism indicating genes deleted or disrupted by this one
Data classes: none
Star code: *q Deletes or disrupts
Java class: flybase.genes.Deletes (field) Inherits from: flybase.store.BasicFieldStore
- AMDD Does not delete/disrupt
- Description: information on allelism indicating genes not deleted or disrupted by this one
Brief help: information on allelism indicating genes not deleted or disrupted by this one
Data classes: none
Star code: *q Does not delete or disrupt
Java class: flybase.genes.DoesntDelete (field) Inherits from: flybase.store.BasicFieldStore
- AMDP Duplicated for
- Description: information on allelism indicating genes duplicated
Brief help: information on allelism indicating genes duplicated
Data classes: none
Star code: *q Duplicated for
Java class: flybase.genes.Duplicated (field) Inherits from: flybase.store.BasicFieldStore
- AMIS Misc. allele information
- Description: none
Brief help: none
Data classes: none
Star code: *R
Java class: flybase.genes.MiscAllele (field) Inherits from: flybase.store.BasicFieldStore
- AMND Not duplicated for
- Description: none
Brief help: none
Data classes: none
Star code: *q Not duplicated for
Java class: flybase.genes.NotDuplicated (field) Inherits from: flybase.store.BasicFieldStore
- AMP Partially disrupts
- Description: information on allelism indicating genes partially deleted or disrupted by this one
Brief help: information on allelism indicating genes partially deleted or disrupted by this one
Data classes: none
Star code: *q Partially disrupts
Java class: flybase.genes.PartialDisrupt (field) Inherits from: flybase.store.BasicFieldStore
- AMPD Partially duplicated for
- Description: none
Brief help: none
Data classes: none
Star code: *q Partially duplicated for
Java class: flybase.genes.PartialDup (field) Inherits from: flybase.store.BasicFieldStore
- AMSO Rescue and compl. info.
- Description: none
Brief help: none
Data classes: none
Star code: *Q
Java class: flybase.genes.MiscData (field) Inherits from: flybase.store.BasicFieldStore
- ANRB Not rescued by
- Description: none
Brief help: none
Data classes: none
Star code: *Q Not rescued by:
Java class: flybase.genes.NotRescuedBy (field) Inherits from: flybase.store.BasicFieldStore
- APC Partially complements
- Description: none
Brief help: none
Data classes: none
Star code: *Q Partially complements:
Java class: flybase.genes.PartialCompl (field) Inherits from: flybase.store.BasicFieldStore
- APR Partially rescues
- Description: none
Brief help: none
Data classes: none
Star code: *Q Partially rescues:
Java class: flybase.genes.PartialRescue (field) Inherits from: flybase.store.BasicFieldStore
- APRB Partially rescued by
- Description: none
Brief help: none
Data classes: none
Star code: *Q Partially rescued by:
Java class: flybase.genes.PartRescuedBy (field) Inherits from: flybase.store.BasicFieldStore
- ARB Rescued by
- Description: none
Brief help: none
Data classes: none
Star code: *Q Rescued by:
Java class: flybase.genes.RescuedBy (field) Inherits from: flybase.store.BasicFieldStore
- ARG2 FlyBase gene annotation
- Description: none
Brief help: none
Data classes: none
Star code: *s Additional information about this mutation is available
Java class: flybase.genes.AnnoRefSeq2 (field) Inherits from: flybase.store.BasicFieldStore
- ARGS FlyBase gene annotation
- Description: Thumbnail sketch of gene structure and the DNA sequence accession that was used as the reference sequence. A click on the graphic brings up the detailed annotated reference sequence. Reference sequences are based on sequence generated by the Drosophila Genome Projects, where possible. When no genome project sequence is available, the reference sequence is based on published genomic sequence information. Experimental evidence from published literature and from the DNA databanks (DDBJ/EMBL/GenBank) is placed on the reference sequence. Features shown on the annotated reference gene sequence include exons, mRNA, coding sequence, transposon insertion sites, aberration breakpoints, rescue constructs, mutations, and regulatory elements.
Brief help: Annotated reference gene sequence, showing exons, mRNA, coding sequence, transposon insertion sites, and other sequence features of a gene
Data classes: none
Star code: *u Annotated reference sequence is available
Java class: flybase.genes.AnnoRefSeq (field) Inherits from: flybase.store.BasicFieldStore
- ARM Chromosome arm
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Chromosome (field) Inherits from: flybase.store.BasicFieldStore
- ARS Rescues
- Description: none
Brief help: none
Data classes: none
Star code: *Q Rescues:
Java class: flybase.genes.Rescues (field) Inherits from: flybase.store.BasicFieldStore
- ASAL Associated allele
- Description: For most transcripts and polypeptides, the products of the wild-type allele are described.
Brief help: none
Data classes: none
Star code: *A
Java class: flybase.abs.AssocAllele (field) Inherits from: flybase.store.BasicFieldStore
- ASBA Associated balancer
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASCO Associated construct
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASCRGN Reflects expression of
- Description: The gene whose promoter region drives the expression of a enhancer trap or reporter construct. Enhancer traps and promoter constructs generally reflect the expression of the adjacent or attached promoter sequences and the gene symbol of the associated promoter is presented here.
Brief help: gene whose promoter region drives the expression of a enhancer trap or reporter construct
Data classes: none
Java class: flybase.pep.AscribedGene (field) Inherits from: flybase.store.BasicFieldStore
- ASGN Associated gene
- Description: The polypeptide or transcript reported is the product of this gene.
Brief help: The polypeptide or transcript reported is the product of this gene.
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASM Assay mode
- Description: Indicates the method(s) used to obtain the expression pattern data being recorded for a given transcript or polypeptide. The most common modes of assay include in situ hybridization and Northern blot analysis for transcripts, and immunolocalization and Western blot analysis for polypeptides.
Brief help: assay used to obtain expression pattern data
Data classes: none
Java class: flybase.pep.AssayMode (field) Inherits from: flybase.store.BasicFieldStore
- ASPP Associated polypeptide
- Description: Proteins that are known to be encoded by the transcript under study.
Brief help: proteins known to be encoded by given transcript
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASQ Genomic sequence analysis
- Description: none
Brief help: Preliminary gene structures and adjacent genes and region (GadFly report)
Data classes: none
Star code: *u FBan
Java class: flybase.genes.AnnoSeq (field) Inherits from: flybase.store.BasicFieldStore
- ASTI Associated insertion
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASTP Associated transposon
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASTR Associated transcript
- Description: Transcripts that are known to encode a given protein.
Brief help: transcripts that encode a given protein
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ASYM Symbol
- Description: Allele symbol. See SYM
Brief help: an abbreviated, unique, name for an allele (gene variant)
Data classes: none
Java class: flybase.alleles.AlleleName (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Abbreviation
- AU Author
- Description: none
Brief help: none
Data classes: none
Star code: *a
Java class: flybase.refs.Author (field) Inherits from: flybase.store.BasicFieldStore
- BFD BFD Line
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- BGV Balancer/ Genotype variant
- Description: none
Brief help: none
Data classes: none
Star code: *I
Java class: flybase.abs.Variant (subrecord) Inherits from: flybase.alleles.Allele
- BGVR Variant Record
- Description: none
Brief help: none
Data classes: none
Star code: *I
Java class: flybase.abs.VariantStore (record) Inherits from: flybase.alleles.AlleleStore
- BGVSY Symbol
- Description: none
Brief help: none
Data classes: none
Java class: flybase.abs.VariantName (field) Inherits from: flybase.alleles.AlleleName, flybase.store.Abbreviation
- BI Biosis
- Description: none
Brief help: none
Data classes: none
Star code: *B
Java class: flybase.refs.Biosis (field) Inherits from: flybase.store.BasicFieldStore
- BIP Breakpoints inherited from progenitors
- Description: none
Brief help: none
Data classes: none
Star code: *F
Java class: flybase.abs.BreaksFromParents (field) Inherits from: flybase.store.BasicFieldStore
- BLOC Sequence map
- Description: none
Brief help: none
Data classes: none
Java class: flybase.genes.SequenceLoc (field) Inherits from: flybase.store.BasicFieldStore
- BM Aberration info.
- Description: none
Brief help: none
Data classes: none
Star code: *Z
Java class: flybase.genes.Aberrationism (field) Inherits from: flybase.store.BasicFieldStore
- BMD Disrupted in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Disrupted in
Java class: flybase.genes.AbDeletes (field) Inherits from: flybase.store.BasicFieldStore
- BMDD Not disrupted in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Not disrupted in
Java class: flybase.genes.AbDoesntDelete (field) Inherits from: flybase.store.BasicFieldStore
- BMDP Duplicated in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Duplicated in
Java class: flybase.genes.AbDuplicated (field) Inherits from: flybase.store.BasicFieldStore
- BMND Not duplicated in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Not duplicated in
Java class: flybase.genes.AbNotDuplicated (field) Inherits from: flybase.store.BasicFieldStore
- BMP Partially disrupted in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Partially disrupted in
Java class: flybase.genes.AbPartialDisrupt (field) Inherits from: flybase.store.BasicFieldStore
- BMPD Partially duplicated in
- Description: none
Brief help: none
Data classes: none
Star code: *Z Partially duplicated in
Java class: flybase.genes.AbPartialDup (field) Inherits from: flybase.store.BasicFieldStore
- BODP Expression data
- Description: A complete and readable summary of expression pattern data for transcripts and polypeptides. For a tabular presentation of expression data curated using a controlled vocabulary, see the "Expression pattern" field.
Brief help: detailed expression pattern data for transcripts and polypeptides
Data classes: none
Java class: flybase.rci.Expression (field) Inherits from: flybase.store.BasicFieldStore
- BPT Breakpoints
- Description: Locations of the aberration on the cytological (polytene chromosome) map. To the extent possible, the computed range is consistent with all data known to FlyBase. The computed location may be presented as a range of uncertainty.See CLOC - cytological location of genes and Reference manual section B.6 for details.
Brief help: Locations of the aberration on the cytological (polytene chromosome) map. To the extent possible, the computed range is consistent with all data known to FlyBase. The computed location may be presented as a range of uncertainty.
Data classes: none
Star code: *B
Java class: flybase.abs.Breakpoints (field) Inherits from: flybase.genes.CytoLoc
- BSN Balancer short name
- Description: none
Brief help: none
Data classes: none
Star code: *U
Java class: flybase.abs.BalShortname (field) Inherits from: flybase.store.BasicFieldStore
- BURL Database link base
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlBase (field) Inherits from: flybase.store.BasicFieldStore
- CC Comments
- Description: none
Brief help: none
Data classes: none
Java class: flybase.pep.Comments (field) Inherits from: flybase.store.BasicFieldStore
- CCL Construct type
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.ConstructType (field) Inherits from: flybase.store.BasicFieldStore
- CCLOC Cytological location
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.CloneCytoloc (field) Inherits from: flybase.genes.CytoLoc
- CCM Comments on cytology
- Description: none
Brief help: none
Data classes: none
Star code: *c
Java class: flybase.abs.CytoComment (field) Inherits from: flybase.store.BasicFieldStore
- CDNA cDNA
- Description: Answers the following questions on cDNAs pertaining to all or some transcripts for a given gene: Does the cDNA correspond to a specific transcript, does it contain a complete open reading frame (ORF), and has it been sequenced?
Brief help: detailed information on cDNAs
Data classes: none
Java class: flybase.egad.CDna (field) Inherits from: flybase.store.BasicFieldStore
- CDS Coding sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.genes.CDSSequenceLoc (field) Inherits from: flybase.genes.SequenceLoc
- CEL GO:Cellular component
- Description: This field, which uses a controlled vocabulary, describes the subcellular localization of the gene's product, e.g., nucleus, mitochondrion, plasma membrane.
Brief help: subcellular location of gene product, a controlled vocabulary
Data classes: none
Star code: *f
Java class: flybase.genes.CellLocation (field) Inherits from: flybase.store.BasicFieldStore
- CGSYM CG Symbol
- Description: none
Brief help: none
Data classes: none
Java class: flybase.genes.CGSymbol (field) Inherits from: flybase.store.GenericFieldStore, flybase.store.Computedfield
- CH Characteristics
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Character (field) Inherits from: flybase.store.BasicFieldStore
- CLA Class of gene
- Description: classification of the genetic element, if other than gene, including mitochondrial gene, transposon, non coding RNA gene, and others; a controlled vocabulary This field holds information about the class of the genetic element. Allowed values are:
- mitochondrial_gene: Normal components of a Drosophila mitochondrial genome. Mitochondrial encoded genes have the symbol prefix 'mt:' or 'Nnnn\mt:' if from a species other than D. melanogaster.
- transposon: Drosophila transposable elements and repetitive DNA elements whether known to be transposable or not. Includes components of such elements, e.g., P transposase. Includes satellite DNAs.
- non_coding_RNA_gene: Genes encoding RNAs that are not translated into proteins. This includes not only ribosomal, transfer RNAs etc, but also gene products that are thought to act as regulatory or structural RNAs.
- pseudogene: Nonfunctional loci with sequence identity to a functional gene.
- microsatellite: Loci composed of tandem repeats of short (1 to 10 bps) nucleotide sequences.
- virus_symbiont_pathogen: Viruses, symbionts, parasites and pathogens of Drosophila. Includes components of such entities.
- safe_element: Structural And non-coding Functional Elements (SAFE). Includes telomeres, centromeres, DNA amplification sites, scaffold sites, and boundary elements. Does not include non-coding elements of other classes, e.g., promoters, enhancers, introns, which are considered to be components of 'normal' genes.
- sire_element: Synthetic and/or Isolated Regulatory Elements (SIRE), restricted to regulatory elements widely used in an isolated context, such as mobile activating elements. Does not include regulatory elements used to drive reporter genes. An example is the synthetic GMR (glass multimer reporter) element, as used in transposon constructs designed to activate adjacent endogenous genes.
- fusion_gene: Genes synthesized as a fusion of two, or more, coding regions, at least one being a Drosophila gene. Each component of a fusion gene has a single gene entry as either a normal gene, honorary_gene or a fusion_gene.
- foreign_gene: A gene from a species other than D. melanogaster.
- honorary_gene: A foreign gene frequently used in Drosophila transposons.
- foreign_fusion: A fusion gene, as defined above, that includes a coding region from a foreign gene.
- safe_element.h: A structural and non-coding functional element from a species other than D. melanogaster (an honorary SAFE) frequently used in D. melanogaster transposons.
- sire_element.h: A SIRE (see definition above) from another species, treated as an honorary Drosophila element.
Brief help: classification of the genetic element, if other than gene, including mitochondrial gene, transposon, non coding RNA gene, and others; a controlled vocabulary
Data classes: none
Star code: *t
Java class: flybase.genes.GeneClass (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Kindname
- CLNR Clone Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.CloneStore (record) Inherits from: flybase.store.DataStore
- CLNSR Clone
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Clone (subrecord) Inherits from: flybase.store.SubrecFieldStore
- CLOC Cytogenetic map
- Description: Location of the gene on the cytological (polytene chromosome) map. These are given as extreme left and right hand limits. In the case where one of these limits is said to be a doublet, e.g., "35D1,2", then only the outermost band (in this case 35D1 if this was the left-hand end of the range) is given. The limits are separated by a hyphen.
The following information is used in computing polytene locations: - Polytene data from chromosome in situ hybridisation of clones
- Polytene localisation of aberration breakpoints (orcein data)
- Genetic (recombination) mapping data on gene order
- Complementation data between alleles and aberrations
- Genomic molecular data on gene order and proximity
The computed location may be presented as a range of uncertainty, whose ends are either polytene bands (such as 22F1) or lettered subdivisions (such as 22F). Heterochromatic bands (such as h41) are also used. To the extent possible, the computed range is consistent with all data known to FlyBase.
Syntax: left_hand_limit--right_hand_limit
e.g., 25C--25D Following the cytogenetic range there may be a statement regarding how it was established, eg by in situ hybridization. When a cytogenetic range or a statement of how it was derived appears "unattributed", i.e. not in a block headed "Data from ref. nnnn", it is computed from all available data and the tightest deducible range is shown. In cases where different reports give conflicting data, FlyBase has made a decision to mark one or more statements as suspect by prefacing them with "???". Such statements are excluded from the computations that give rise toCytoSearch data. See Reference manual section B.6 for details. If you find that an error has been made in this process, please inform us by email to flybase-updates@morgan.harvard.edu.
Brief help: Location of the gene on the cytological (polytene chromosome) map. To the extent possible, the computed range is consistent with all data known to FlyBase. The computed location may be presented as a range of uncertainty.
Data classes: none
Star code: *c
Java class: flybase.genes.CytoLoc (field) Inherits from: flybase.store.BasicFieldStore
- CLOCC Computed cytology
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.CompCytoLoc (field) Inherits from: flybase.genes.CytoLoc
- CMT Comments
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Comments (field) Inherits from: flybase.store.BasicFieldStore
- CNM Common Name
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.CommonName (field) Inherits from: flybase.store.BasicFieldStore
- CNS Carried in construct
- Description: Transposon or construct that carries allele
Brief help: Transposon or construct that carries allele
Data classes: none
Star code: *I
Java class: flybase.genes.Construct (field) Inherits from: flybase.store.BasicFieldStore
- CO Coden
- Description: none
Brief help: none
Data classes: none
Star code: *D
Java class: flybase.refs.Coden (field) Inherits from: flybase.store.BasicFieldStore
- COR Comments on origin
- Description: none
Brief help: none
Data classes: none
Star code: *R
Java class: flybase.abs.Origin (field) Inherits from: flybase.store.BasicFieldStore
- CPW Library plate-well
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Plate (field) Inherits from: flybase.store.BasicFieldStore
- CS Cloning site
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.CloneSite (field) Inherits from: flybase.store.BasicFieldStore
- CSQ Sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Sequence (field) Inherits from: flybase.store.BasicFieldStore
- CTG Physical contig
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Contig (field) Inherits from: flybase.store.BasicFieldStore
- CTSYM Transcript symbol
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.TranscriptSym (field) Inherits from: flybase.genes.GeneSymbol
- CVBODP Expression pattern
- Description: Expression pattern data for transcripts and proteins is curated from publications using a controlled vocabulary, and at the finest degree of resolution possible. Expression data includes temporal, anatomical and spatial details, and is searchable.
Brief help: subcellular region(s) of gene product localization, a controlled vocabulary
Data classes: none
Java class: flybase.rci.Expresspat (field) Inherits from: flybase.store.BasicFieldStore
- CVBODPC Expression pattern comment
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.ExpatComment (field) Inherits from: flybase.store.BasicFieldStore
- CVCEL Cell location (CV)
- Description: subcellular region(s) of gene product localization, a controlled vocabulary
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- CVEC Vector
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Vector (field) Inherits from: flybase.store.BasicFieldStore
- CYA Associated cytology
- Description: comments on cytology associated with allele
Brief help: comments on cytology associated with allele
Data classes: none
Star code: *C
Java class: flybase.genes.AssocCyto (field) Inherits from: flybase.store.BasicFieldStore
- CYC Notes on cytogenetic map
- Description: comments on cytological location
Brief help: comments on cytological location
Data classes: none
Star code: *D
Java class: flybase.genes.CytoComment (field) Inherits from: flybase.store.BasicFieldStore
- DBA DNA/RNA sequences
- Description: In these fields FlyBase stores pointers to nucleic acid sequence data, usually in the form of EMBL/Genbank/DDBJ/NCBI accession (AC) numbers. If a sequence has been published but is not yet in one of these data banks a brief journal reference is given instead (the full reference will be found inReferences). Data from the three nucleic sequence databases are received on a daily basis by FlyBase.
FlyBase is also cross-referenced to a number of other sequence databases. These are stored in the *g line (if nucleic acid) or *m line (if protein). Database codes(external-databases.txt) and database versions (versions.txt) are listed in the Allied-data/External-databases section.The EMBL/NCBI/DDBJ sequence accession numbers have no code prefix.
Syntax: *g <database_code/>accession_number
e.g., *g X12345 *g EPD/23023
If the nucleic acid sequence accession includes coding regions then each coding region has a unique PID number. These are appended to the nucleic acid sequence accession number, following a semi-colon, e.g.,
*g U42989; g1150983
Note that the number of PIDs attached to a sequence record may be more than one for two reasons. The first is that the EBI and NCBI often assign PID numbers independently to the same object; the other is that there is more than one protein product from a single gene (as the result, for example, of alternative splicing).
Brief help: nucleic acid sequence databank and other DNA accession number
Data classes: none
Star code: *g
Java class: flybase.genes.DBAccessions (field) Inherits from: flybase.store.BasicFieldStore
- DBAF Flanking sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.FlankingDBAccession (field) Inherits from: flybase.genes.DBAccessions
- DBID Database name
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlDb (field) Inherits from: flybase.store.BasicFieldStore
- DEC Descendant
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- DES Description
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Description (field) Inherits from: flybase.store.BasicFieldStore
- DHO Probable reference ortholog
- Description: "Homologous" genes in other species of drosophilid. The DHO field is a pointer between "homologous" genes in another species of drosophilid. A single species (D. melanogaster when possible) is treated as the "reference" for a given gene, and bidirectional links are made with DHO fields between the gene of the reference species and all homologous genes. No direct DHO links are made between the non-reference genes.
Links are only made where there is good genetic or phenotypic (including sequence) evidence for homology of entire genes. It is not uncommon for a gene to be present once in species a but twice (or more)in species b (e.g., Adh in D. melanogaster vs. D. mulleri). In such cases all possible pair-wise links are made via DHO fields.
Brief help: "Homologous" genes in other species of drosophilid
Data classes: none
Star code: *M
Java class: flybase.genes.DrosHomolog (field) Inherits from: flybase.store.BasicFieldStore
- DIS Discoverer
- Description: person discovering the gene or other item
Brief help: person discovering the gene or other item
Data classes: none
Star code: *w
Java class: flybase.genes.Discoverer (field) Inherits from: flybase.store.BasicFieldStore
- DOMAIN Domain
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Domain (field) Inherits from: flybase.store.BasicFieldStore
- DT Date
- Description: Dating of records and updates. All gene records have two date fields.The first, 'Date entered', is the date a gene record was entered into the Sybase tables. The second is 'Last updated', the date the record was last updated. Whenentered the two dates will be the same. The 'zero' date of all records then extant was 16 May 1994. FlyBase dates arerepresented as dd mm yy, mm being the initial 3-letter abbreviation of the month, and yy being the last two digits of theyear (e.g., 01 Jul 94).
Brief help: Date record entered or updated
Data classes: none
Star code: *H
Java class: flybase.genes.Dated (field) Inherits from: flybase.store.BasicFieldStore
- ENL Left entity
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.LeftEntity (field) Inherits from: flybase.store.BasicFieldStore
- ENR Right entity
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.RightEntity (field) Inherits from: flybase.store.BasicFieldStore
- ENZ GO:Molecular function
- Description: If a gene product is an enzyme then the enzyme name and the corresponding Enzyme Commission number (EC number) are in the *F field. Enzyme names and EC numbers are from the ENZYME database (Bairoch, 1996, Nucleic Acids Research 24: 221- 222). If an enzyme is not included in this database then the most appropriate name is used. A gene may have more than one *F field if its product carries out more than one different reaction (an obvious example is rudimentary).
Syntax: *F enzyme_name == EC_number
e.g. *F serine-protease == EC 3.4.21.4 Controlled terms may be modified by free text following the \ symbol, e.g.:
*F enzyme_name <== EC_number> \?
*F enzyme_name <== EC_number> \like
Brief help: enzyme name and enzyme commission number, a controlled vocabulary
Data classes: none
Star code: *F
Java class: flybase.genes.Enzyme (field) Inherits from: flybase.store.BasicFieldStore
- EPA Tissue/Position
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ExpresspatTissue (field) Inherits from: flybase.store.BasicFieldStore
- EPAT Expression pattern
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Expresspat1 (subrecord) Inherits from: flybase.store.SubrecFieldStore
- EPATR Expression pattern
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Expresspat1Store (record) Inherits from: flybase.store.DataStore
- EPP Pattern
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ExpresspatPattern (field) Inherits from: flybase.store.BasicFieldStore
- EPT Stage
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ExpresspatStage (field) Inherits from: flybase.store.BasicFieldStore
- ER Related publication
- Description: none
Brief help: none
Data classes: none
Star code: *E
Java class: flybase.refs.Errata (field) Inherits from: flybase.store.BasicFieldStore
- EST EST
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.EST (field) Inherits from: flybase.store.BasicFieldStore
- EVD Evidence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Evidence (subrecord) Inherits from: flybase.store.SubrecFieldStore
- EVDR Evidence Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Evidence$Store (record) Inherits from: flybase.store.DataStore
- EXNSQ Exon composition
- Description: A list of the exons that make up a particular transcript.
Brief help: list of the exons that make up a particular transcript
Data classes: none
Java class: flybase.pep.ExonSeq (field) Inherits from: flybase.store.BasicFieldStore
- ExpatTable Expression pattern
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ExpatTable (field) Inherits from: flybase.store.GenericFieldStore, flybase.store.Computedfield
- FBARGS Annotated reference sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- FBDARTS GenBank sequence report
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- FGD Formalized genetic data
- Description: none
Brief help: none
Data classes: none
Star code: *G
Java class: flybase.abs.FormalGeneData (field) Inherits from: flybase.store.BasicFieldStore
- FI File index
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.FileIndex (field) Inherits from: flybase.store.BasicFieldStore
- FLQ Flanking sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.genes.FlankingSequence (field) Inherits from: flybase.genes.DBAccessions
- FNC GO:Biological process
- Description: The terms used in this field are from a controlled vocabulary which aims to be descriptive of the function(s) of gene products. See Reference manual section B.8 for details on gene function. Controlled terms may be modified by free text following the \ symbol, e.g.:
*d controlled_term \?
*d controlled_term \like
Brief help: function(s) of gene product, a controlled vocabulary
Data classes: none
Star code: *d
Java class: flybase.genes.GeneFunction (field) Inherits from: flybase.store.BasicFieldStore
- FSQ Foreign sequence
- Description: none
Brief help: none
Data classes: none
Star code: *u Foreign sequence;
Java class: flybase.genes.ForeignSeq (field) Inherits from: flybase.store.BasicFieldStore
- GADR Annotation Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.AnnotStore (record) Inherits from: flybase.store.DataStore
- GADSR Genome Annotation
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Annot (subrecord) Inherits from: flybase.store.SubrecFieldStore
- GENR Gene Record
- Description: Gene record, contains all the fields and subrecords needed to describe the gene.
Brief help: Gene record
Data classes: none
Star code: *a
Java class: flybase.genes.GeneStore (record) Inherits from: flybase.store.DataStore
- GENSR Parent Gene
- Description: Field containing a gene record, used in Allele records and elsewhere to link parent gene.See GENR
Brief help: Gene sub-record
Data classes: none
Java class: flybase.genes.Gene (subrecord) Inherits from: flybase.store.SubrecFieldStore
- GIA Genetic interaction (effect, anatomy)
- Description: none
Brief help: none
Data classes: none
Star code: *S Gene interaction (effect, anatomy):
Java class: flybase.genes.InteractionAnatomy (field) Inherits from: flybase.store.BasicFieldStore
- GIA2 Genetic interaction (anatomy, effect)
- Description: none
Brief help: none
Data classes: none
Star code: *S Gene interaction (anatomy, effect):
Java class: flybase.genes.InteractionAnatomy2 (field) Inherits from: flybase.store.BasicFieldStore
- GIC Genetic interaction (effect, class)
- Description: none
Brief help: none
Data classes: none
Star code: *S Gene interaction (effect, class):
Java class: flybase.genes.InteractionClass (field) Inherits from: flybase.store.BasicFieldStore
- GIC2 Genetic interaction (class, effect)
- Description: none
Brief help: none
Data classes: none
Star code: *S Gene interaction (class, effect):
Java class: flybase.genes.InteractionClass2 (field) Inherits from: flybase.store.BasicFieldStore
- GII Genetic interaction info.
- Description: none
Brief help: none
Data classes: none
Star code: *S
Java class: flybase.genes.InteractionInfo (field) Inherits from: flybase.store.BasicFieldStore
- GLC Comments on genetic locn.
- Description: comments on, or alternative, genetic location
Brief help: comments on, or alternative, genetic location
Data classes: none
Star code: *B
Java class: flybase.genes.GenlocComm (field) Inherits from: flybase.store.BasicFieldStore
- GLOC Recombination map
- Description: Genetic map position. Given as Chromosome number-map position, e.g. 3-10. If a gene has not been mapped within a chromosome, then only the chromosome is indicated as, for example, 2-. This implies '2- (not located)'. Many genes have been mapped cytogenetically but not genetically. Their map positions have been estimated and are enclosed in []. (Not {} as in Lindsley and Zimm (1992).) The published map positions of some genes are clearly at variance with their cytogenetic positions. In such cases we have estimated their genetic position and indicate this by enclosing the estimate in []. *B is used to store comments on genetic map positions, including unresolved differences between some genetic map positions in Lindsley and Zimm (1992) and those in Ashburner original files.
To estimate genetic map positions from cytogenetic we use a standard table made by plotting all of the available data and then interpolating. Estimated genetic positions are normally only made to the nearest whole number. The exceptions to this rule are in regions of very low recombination relative to the cytogenetic map. The table of cytogenetic vs. genetic map positions used is available in the Maps section of FlyBase.
Syntax: *b chromosome_symbol-number
e.g., *b 1-66.0
Brief help: Location of the gene on the genetic (recombination) map.
Data classes: none
Star code: *b
Java class: flybase.genes.GeneLoc (field) Inherits from: flybase.store.BasicFieldStore
- GO Gene Ontology
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.GOTerm (field) Inherits from: flybase.store.BasicFieldStore
- GOTERM GO Term
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.GOTerm (field) Inherits from: flybase.store.BasicFieldStore
- GPD Gene product
- Description: none
Brief help: none
Data classes: none
Star code: *Y
Java class: flybase.genes.Product (field) Inherits from: flybase.store.BasicFieldStore
- GSNA Short name
- Description: none
Brief help: none
Data classes: none
Star code: *U
Java class: flybase.genes.Shortname (field) Inherits from: flybase.genes.Synonyms
- GSYM Symbol
- Description: Gene symbol. See SYM
Brief help: an abbreviated, unique, name for a gene
Data classes: none
Star code: *a
Java class: flybase.genes.GeneSymbol (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Abbreviation
- GeneInterTable Genetic Interactions
- Description: none
Brief help: none
Data classes: none
Java class: flybase.alleles.GeneInteractTable (field) Inherits from: flybase.store.GenericFieldStore, flybase.store.Computedfield
- HG Similar genes
- Description: Cross-reference to non-Drosophila homolog(s)/analogs. This field is used to indicate genes in organisms (i.e., foreign species, species other than members of the family Drosophilidae) that are said to be 'similar' to genes in Drosophila. The data for this field come from two sources; publications and other databases. The data are very heterogeneous, since different authors use different criteria for deciding upon the similarity (or 'homology') between a Drosophila gene product and one in a foreign species. By and large these criteria are structural, that is to say they are based upon sequence comparison; on occasion, however, they may be functional, being based on the ability of a gene from Drosophila to complement a mutation in a gene in a foreign species (or vice versa).
Authors often only report that a Drosophila gene is similar (or 'homologous') to a gene from a broad group, e.g., mammals or vertebrates. On other occasions, they report similarity with a gene from a relatively poorly studied organism, e.g., sheep. FlyBase attempts to make the link with genes known from human or mouse, and will only report a match to another vertebrate if either this cannot be done, or such a link is clearly more appropriate.
The purpose of these links in FlyBase is as an aid to discovering more about genes from foreign species with which Drosophila genes are said to be similar.
Links are usually established to genes of Drosophila melanogaster. If FlyBase knows about homologous genes in other drosophilids then the links to genes in foreign species are automatically propagated to these other drosophilid genes.
Syntax: HG species == <foreign_species>; gene == <gene_symbol> [(<synonym_symbol>)]; database:ID[; database:ID] [[Reference]]
Wherever possible the gene symbols used in this field have been checked with the appropriate database, and the field includes the unique identifier used by that database. Gene symbols that have not been checked with another genetic database are enclosed within single quotation marks. In the case of human gene symbols FlyBase uses only those approved by the HUGO Nomenclature Committee. The [Reference] field is only used when the source of the link is not in the FlyBase bibliography. The default is a MEDLINE ID, although a 'mini-reference' or Mouse Genome Database identifier (MGD:JNUM) may be used as a temporary expedient.
Database abbreviations are:
- human
OMIM: Online Mendelian Inheritance in Man (NCBI)
GDB: Genome Data Base (Baltimore; Hinxton)
IMAGE: The IMAGE consortium of human EST sequences database, which includes ESTs sequenced by the WashU-Merk EST project and other groups.
DRES: The Drosophila Related Expressed Sequences database (see Banfi et al., 1996,Nature Genetics 13:167--174). - mouse (Mus)
MGD: Mouse Genome Database (Bar Harbor; Hinxton) - other vertebrates
*ChickGBASE (Roslin)
*PiGBASE (Roslin)
*SheepMap (Christchurch)
*RatMAP (Gotenborg) - C. elegans
*AceDB (Moulin)
WP: WormPep (C. elegans) - yeasts
SGD: Saccharomyces Genome Database (Stanford)
*PomBase (Hinxton) - Dictyostelium discoideum
DICTDB: DicDb (Geneva) - E. coli
CGSC: E. coli Genetic Stock Center (Yale)
ECOGENE:Encyclopedia of E. coli genes and Metabolism (Stanford) - Arabidopsis
*AAtDB (Stanford)
Those marked with an asterisk appear to have no public gene identifier numbers. If a foreign species database is not available, or a gene symbol cannot be verified, then the gene symbol is enclosed within single quotation marks '<symbol>'. In this cases a cross-reference is given to what is considered to be the appropriate SWISS-PROT (SWP:) or, failing that,EMBL (EMBL:) records.
Brief help: Cross-reference to non-Drosophila homolog(s) or analogs
Data classes: none
Star code: *j
Java class: flybase.genes.Homologue (field) Inherits from: flybase.store.BasicFieldStore
- HGTAB Similar genes table
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.HomologTableLink (field) Inherits from: flybase.store.BasicFieldStore
- HITS Positive PCR assay
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.PCRhits (subrecord) Inherits from: flybase.store.SubrecFieldStore
- IBAL Usable as balancer
- Description: none
Brief help: none
Data classes: none
Star code: *u Usable as a balancer
Java class: flybase.abs.IsBalancer (field) Inherits from: flybase.store.BasicFieldStore
- ICC Comment
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- ICL Insertion class
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.InsertionClass (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Kindname
- ICO Database icon
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlIcon (field) Inherits from: flybase.store.BasicFieldStore
- ID FlyBase ID
- Description: Each gene, allele or other data record in FlyBase has a unique identifier number (see section F.1. of FlyBase Reference Manual F: Links To and From FlyBase). The primary identifier number is in the ID(*z) field, secondary identifier numbers are in ID2(*y) fields.
Syntax: ID Fbgn_integer
e.g., ID FBgn0001234
Brief help: FlyBase identifier number, a unique value for each data record
Data classes: none
Star code: *z
Java class: flybase.genes.FBid (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Id
- ID2 Secondary ID
- Description: secondary or obsolete FlyBase identifier number
Brief help: secondary or obsolete FlyBase identifier number
Data classes: none
Star code: *y
Java class: flybase.genes.FBid2nd (field) Inherits from: flybase.store.BasicFieldStore
- IFL Interactive Fly
- Description: This field is a link for a FlyBase gene record to the related the Interactive Fly document. The Interactive Fly, developed and maintained by Tom and Judy Brody, provides overviews of various developmental and cellular processes. See Reference manual section H.7 for details of Interactive Fly.
Brief help: link to the Interactive Fly document for this gene
Data classes: none
Star code: *u InterFly
Java class: flybase.genes.InterFly (field) Inherits from: flybase.store.BasicFieldStore
- INSR Insertion
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Insertion (subrecord) Inherits from: flybase.store.SubrecFieldStore
- INSY Insertion synonym
- Description: none
Brief help: none
Data classes: none
Star code: *N
Java class: flybase.genes.InsertionSyn (field) Inherits from: flybase.genes.Synonyms
- IPRO InterPro motifs
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.InterPro (field) Inherits from: flybase.store.BasicFieldStore
- ISBN Isbn
- Description: none
Brief help: none
Data classes: none
Star code: *I
Java class: flybase.refs.Isbn (field) Inherits from: flybase.store.BasicFieldStore
- ISS Issue
- Description: none
Brief help: none
Data classes: none
Star code: *Y
Java class: flybase.refs.Issue (field) Inherits from: flybase.store.BasicFieldStore
- ITP Insertion's transposon type
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.InsertionTpType (field) Inherits from: flybase.store.BasicFieldStore
- JR Journal
- Description: none
Brief help: none
Data classes: none
Star code: *w
Java class: flybase.refs.Journal (field) Inherits from: flybase.store.BasicFieldStore
- KLOC Computed kilobase location
- Description: none
Brief help: none
Data classes: none
Java class: flybase.genes.KilobaseLoc (field) Inherits from: flybase.store.BasicFieldStore
- LG Language
- Description: none
Brief help: none
Data classes: none
Star code: *L
Java class: flybase.refs.Language (field) Inherits from: flybase.store.BasicFieldStore
- LGA Addn. lang.s
- Description: none
Brief help: none
Data classes: none
Star code: *A
Java class: flybase.refs.Languages (field) Inherits from: flybase.store.BasicFieldStore
- LIB Library class
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.CloneClass (field) Inherits from: flybase.genes.GeneClass, flybase.store.Kindname
- LKAC Database link accession
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlAccession (field) Inherits from: flybase.genes.DBAccessions
- LKFL Database link field
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlField (field) Inherits from: flybase.store.BasicFieldStore
- LKHE Database link help
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlHelp (field) Inherits from: flybase.store.BasicFieldStore
- LKID Database link id
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlId (field) Inherits from: flybase.genes.GeneSymbol
- LKNA Database link name
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlName (field) Inherits from: flybase.store.BasicFieldStore
- LOCB Localization basis
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.LocalizeBasis (field) Inherits from: flybase.store.BasicFieldStore
- LOI Location inferred from insertion in
- Description: none
Brief help: none
Data classes: none
Star code: *D Location inferred from insertion in:
Java class: flybase.genes.LocInferred (field) Inherits from: flybase.store.BasicFieldStore
- LOST Availability
- Description: none
Brief help: none
Data classes: none
Star code: *X
Java class: flybase.genes.Availability (field) Inherits from: flybase.store.BasicFieldStore
- MABST Abstract
- Description: none
Brief help: none
Data classes: none
Java class: flybase.refs.MeetAbstract (field) Inherits from: flybase.store.BasicFieldStore
- MD Molecular data
- Description: Molecular data. This field keep molecular data about genes and alleles. The MD (*s) field is either free text, or has "Identified with: xxxx (BDGP-DGC)" or begins with the string "Gene order/orientation:".
The "Identified with: xxxx (BDGP-DGC)" case indicates the gene is identified with an entry in the BDGP Drosophila Gene Collection. More information on DGC is found at BDGP Gene Collection.
The Gene order/orientation case accomodates gene order/orientation data derived by molecular, rather than genetic, means. The data will be presented in the format "Gene order/orientation: osp- Adh+ Adhr+ osp-" where + indicates 5'-3' proceeds with increasing cytological location, - the opposite, and ? where the direction of transcription is not declared. Where orientation with respect to the chromosome is not known, gene sequence is preceded by the statement "Overall orientation not stated" and + and - simply reflect orientation of the transcripts with respect to each other.
Brief help: molecular information for genes and alleles
Data classes: none
Star code: *s
Java class: flybase.genes.MolecularData (field) Inherits from: flybase.store.BasicFieldStore
- MED PubMed
- Description: The PubMed (MEDLINE) accession number for this reference. Also the abstract from the US Natl. Library of Medicine PubMed server is fetched and displayed, if available. Hyperlinks to a full electronic article are included as available from PubMed. See http://www.ncbi.nlm.nih.gov/PubMed/
PubMed is a project developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It has been developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journals at Web sites of participating publishers.
Brief help: PubMed (MEDLINE) accession number and abstract, if available, from the NLM PubMed server
Data classes: none
Star code: *M
Java class: flybase.refs.Medline (field) Inherits from: flybase.store.BasicFieldStore
- MEDAB Abstract
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- MK Markers
- Description: none
Brief help: none
Data classes: none
Star code: *S
Java class: flybase.abs.Markers (field) Inherits from: flybase.store.BasicFieldStore
- MMP Molecular map
- Description: Kilobase-level resolution maps curated from publications.
Brief help: Kilobase-level resolution maps curated from publications
Data classes: none
Star code: *u Molecular map data are available
Java class: flybase.genes.MolMapData (field) Inherits from: flybase.store.BasicFieldStore
- MOD Modification of progenitor
- Description: none
Brief help: none
Data classes: none
Java class: flybase.pep.ProModification (field) Inherits from: flybase.store.BasicFieldStore
- MRK Body part marker
- Description: A polypeptide or transcript was used as a marker for a particular type of cell or structure. It allows identification of useful cell markers.
Brief help: cell type for which this gene product is a useful marker, a controlled vocabulary
Data classes: none
Java class: flybase.pep.BodyLocale (field) Inherits from: flybase.store.BasicFieldStore
- MU Mutagen
- Description: origin of, or mutagen used to produce. this allele, a controlled vocabulary
Brief help: origin of, or mutagen used to produce. this allele, a controlled vocabulary
Data classes: none
Star code: *o
Java class: flybase.genes.Mutagen (field) Inherits from: flybase.store.BasicFieldStore
- NAF DNA Features
- Description: General characteristics of DNA sequence. This field, which uses a controlled vocabulary, describes some general feature of the gene sequence, e.g., repetitive element, CAX (opa) repeat, ARS sequence.
Brief help: general characteristics of DNA sequence, a controlled vocabulary
Data classes: none
Star code: *v
Java class: flybase.genes.DNAFeatures (field) Inherits from: flybase.store.BasicFieldStore
- NAM Full name
- Description: This is the full name of the gene or allele. FlyBase takes a minimalist definition of a gene. As an example, Notch is regarded as a gene, but facet, Confluens, split etc. are not. These phenotypically distinct allelic forms that have, in the past, been named as if they were genetic loci are included as gene synonyms.
FlyBase is not entirely consistent in the way directly duplicated genes are handled: for example the five HSP70 encoding genes at Hsp70A and Hsp70B and the five larval cuticle protein encoding genes at 44D are all listed independently but the five major histone protein coding regions, tandemly repeated at the base of 2L, are each listed as a separate gene, but only once.
Syntax: *e <Nnnn>name
e.g., *e bobbed
*e DhydMinos
Some loci have only been identified by molecular methods, not having been mapped. Such loci are included in genes. Other "loci" included in this file have not been genetically mapped or characterized but are assumed to exist on the basis of, for example, a purified protein. Some loci have been impossible to name in any logical way, due to a lack of data. As a temporary expedient these are named as anon-*, where the * indicates a code. These loci will be renamed as and when more data becomes available.
Both the European and Berkeley Drosophila Genome Projects are now generating a considerable number of STS sequences. These all appear in the nucleic acid sequence data archive, and in the NCBI's dbSTS database. These short sequences are routinely matched against the universe of public sequence data and often have 'significant' matches to genes identified in species other than Drosophila. Such matches are clues that similar genes may occur in D. melanogaster. For this reason STS sequences with significant matches are identified as 'genes' in this file, and have the temporary name ESTSn (for STS sequences from the European project) or BSTSn (for those from Berkeley), where n is the code used by the Genome Proect (e.g., ESTS100F7T, BSTSDm0092.) The nature of the most 'significant' match will be indicated in the *d or *F (function or enzyme) fields. STS sequences that match known Drosophila genes will be linked to the relevant gene record by their accession numbers in the GenBank/EMBL/DDBJ and dbSTS data archives. STS sequences that have no matches whatsoever are only linked to their parental clone in the clones tables. All STSs with matches are similarly linked to their parental clones in these tables.
FlyBase includes data from all species of the family Drosophilidae.
Brief help: full name of gene, allele or other item
Data classes: none
Star code: *e
Java class: flybase.genes.GeneName (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Fullname
- NB Neighbor
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- NBR Neighbor Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- NBV Neighbor value
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- NCO New cytological order
- Description: none
Brief help: none
Data classes: none
Star code: *N
Java class: flybase.abs.NewCytoOrder (field) Inherits from: flybase.store.BasicFieldStore
- OAB Genetic data about other aber.
- Description: none
Brief help: none
Data classes: none
Star code: *T
Java class: flybase.abs.OtherAbs (field) Inherits from: flybase.store.BasicFieldStore
- OLAP Overlaps
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Overlaps (field) Inherits from: flybase.store.BasicFieldStore
- OP Offprint
- Description: Offprint field. When listed, it indicates inclusion of a copy of this article in the extensive Drosophila Offprint Collection maintained by FlyBase (Cambridge). If you require a copy of such a paper, and are completely unable to obtain one from a local library, laboratory, inter-library loan, or author then e-mail flybase-offprint@morgan.harvard.edu requesting the article. State the FlyBase ID of the reference(s) in your message, as well as your postal address to which the offprint should be delivered.
Brief help: Indicates a copy of this article is in the Drosophila Offprint Collection maintained by FlyBase (Cambridge)
Data classes: none
Star code: *J
Java class: flybase.refs.Offprint (field) Inherits from: flybase.store.BasicFieldStore
- OPVR External database
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlProviderStore (record) Inherits from: flybase.store.DataStore
- OPVSR External database
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlProvider (subrecord) Inherits from: flybase.store.SubrecFieldStore
- ORI Orientation
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Orientation (field) Inherits from: flybase.store.BasicFieldStore
- OTH Other information
- Description: miscellaneous information concerning a gene, as free text.
Brief help: miscellaneous information on genes and alleles
Data classes: none
Star code: *u
Java class: flybase.genes.OtherInfo (field) Inherits from: flybase.store.BasicFieldStore
- OURL Database link
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrl (subrecord) Inherits from: flybase.store.SubrecFieldStore
- OURLR External database links
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlSetStore (record) Inherits from: flybase.store.DataStore
- OURLR1 Database link SR
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlStore (record) Inherits from: flybase.store.DataStore
- OURLSR External database links
- Description: none
Brief help: none
Data classes: none
Java class: flybase.openurl.OpenUrlSet (subrecord) Inherits from: flybase.store.SubrecFieldStore
- PAC Protein sequences
- Description: This field stores pointers to protein sequence data, usually in the form of SWISS-PROT/TREMBL/PIR protein sequence databank accession (AC) numbers. Because of potential clashes between the accession numbers between databases the AC numbers are prefixed "SWP/", "TREMBL/" or "PIR/".
These fields are also used for cross-references between FlyBase and structural data onDrosophila proteins held on PDB (Protein Data Bank, Brookhaven), the NRL_3D databank and the G protein-coupled receptor database (GCRDb). These records have the prefixes PDB/, NRL_3D/ and GCR/ respectively. Cross-references to the 'factors' table of the TRANSFAC database (E. Wingender, J. Biotechnol. 35:273-280, 1994) have the prefix TF/.
Syntax: *m database_code/accession_number
e.g. *m SWP/P12428
Brief help: protein database accession numbers
Data classes: none
Star code: *m
Java class: flybase.genes.ProtAcc (field) Inherits from: flybase.store.BasicFieldStore
- PB Publisher
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.refs.Publisher (field) Inherits from: flybase.store.BasicFieldStore
- PCL Cell loc. summary
- Description: A complete and readable summary of the subcellular distribution of a gene product. For the shorter, controlled vocabulary version, see the "Cell location (CV)".
Brief help: subcellular region(s) of gene product localization
Data classes: none
Java class: flybase.pep.CellLocation (field) Inherits from: flybase.store.BasicFieldStore
- PDOM Protein domains
- Description: Description of the structural features of gene products. These are derived from the PROSITE database (Bairoch et al., 1996, Nucleic Acids Research 24: 189-196) if the data are available therein. If not, then a similar term is invented (but will be replaced once the gene product is included in PROSITE). Terms invented by FlyBase always end in the word 'protein' (rather than 'domain'. 'signature', 'site', 'domain', 'profile', 'repeat' or 'pattern').
Syntax for PROSITE cross references:
Prosite_number == Prosite_accession_name
e.g., PS00018 == EF-hand calcium-binding domain.
Controlled terms may be modified by free text following the \ symbol, e.g.:
controlled_term \?
controlled_term \like
Brief help: Protein domain information
Data classes: none
Star code: *J
Java class: flybase.genes.ProtDomain (field) Inherits from: flybase.store.BasicFieldStore
- PED Position-effect data
- Description: none
Brief help: none
Data classes: none
Star code: *V
Java class: flybase.abs.PositionEffect (field) Inherits from: flybase.store.BasicFieldStore
- PEPST Peptide Status
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.PepStatus (field) Inherits from: flybase.store.BasicFieldStore
- PEV Position-effect variegation
- Description: Aberrations causing position-effect variegation of gene. This is a controlled field to indicate aberrations that cause position-effect variegation of a gene.
Syntax: <aberration_symbol>
Dominance, recessive and other variants are indicated with separate field keys PEVR, PEVN, PEVD
Brief help: aberrations causing position-effect variegation of gene, a controlled vocabulary
Data classes: none
Star code: *n
Java class: flybase.genes.PositionEffect (field) Inherits from: flybase.store.BasicFieldStore
- PEVD Dominant PEV in
- Description: See PEV
Brief help: aberrations causing Dominant position-effect variegation of gene, a controlled vocabulary
Data classes: none
Star code: *n dominant PEV in:
Java class: flybase.genes.DominantPEV (field) Inherits from: flybase.store.BasicFieldStore
- PEVN No PEV in
- Description: See PEV
Brief help: No position-effect variegation of gene, a controlled vocabulary
Data classes: none
Star code: *n no PEV in:
Java class: flybase.genes.NoPEV (field) Inherits from: flybase.store.BasicFieldStore
- PEVR Recessive PEV in
- Description: See PEV
Brief help: aberrations causing Recessive position-effect variegation of gene, a controlled vocabulary
Data classes: none
Star code: *n recessive PEV in:
Java class: flybase.genes.RecessivePEV (field) Inherits from: flybase.store.BasicFieldStore
- PG Pages
- Description: none
Brief help: none
Data classes: none
Star code: *z
Java class: flybase.refs.Pages (field) Inherits from: flybase.store.BasicFieldStore
- PHC Phenotypic class
- Description: phenotypic class into which the allele falls.A genotype in curly brackets indicates the phenotypic class is dependent on the second genotype in the brackets. This field can be multicomponent, storing information about the recessive/dominant and conditional and stage specific aspects of allele in addition to the phenotypic class into which the allele falls. Vertical bars separate the components:
lethal | embryonic | maternal effect | recessive
An allele can legitimately have multiple PHC lines.
lethal | recessive
suppressor | dominant
Where a genotype appears in curly brackets at the end of the line, that phenotypic class of the allele is dependent on the {second site} genotype in the brackets.
visible | dominant {wa}
Brief help: phenotypic class into which the allele falls.A genotype in curly brackets indicates the phenotypic class is dependent on the second genotype in the brackets.
Data classes: none
Star code: *k Phenotypic class:
Java class: flybase.genes.PhenoClass (field) Inherits from: flybase.store.BasicFieldStore
- PHI Mutant phenotype
- Description: Mutant phenotype. This holds the phenotypic description of the mutant allele. See also PHC (Phenotypic class), PHM (Phenotype manifest in).
This field is free text, except for Mode of assay. This field is mandatory for all alleles that have "MU in vitro construct". The possible entries in this Mode of assay field are:
In transgenic Drosophila
Whole-organism transient assay
Drosophila cell culture
In transgenic Drosophila (allele of one species in genome of another)
Whole-organism transient assay (allele from one species assayed in another)
Cell-free system
Yeast assay
Xenopus oocyte
other
Brief help: phenotypic information on alleles
Data classes: none
Star code: *k
Java class: flybase.genes.PhenotypicInfo (field) Inherits from: flybase.store.BasicFieldStore
- PHM Phenotype manifest in
- Description: Phenotype manifest in: This field describes the body part affected by the mutant allele, using the body part terms as listed in the controlled vocabulary.
wing vein L5
Where a genotype appears in brackets at the end of the line, the phenotype in that body part is dependent on the {second site} genotype in the brackets.
metathoracic leg { brm[2]/brm[+] }
The presence of a term in this field means simply that the named structure can demonstrate a mutant phenotype as a consequence of the mutant allele. Thus for maternal effect alleles, the embryo in which the named body part is affected is not necessarily mutant for that allele in question, though its mother was. Also, the phenotype need not be 100% penetrant and expressed for the affected body part to be recorded in a "Phenotype manifest in:" field. Terms can be combined using an & symbol:
cuticle & procephalon
scutellum & macrochaetae
Brief help: the body part affected by the mutant allele, controlled vocabulary.
Data classes: none
Star code: *k Phenotype manifest in:
Java class: flybase.genes.PhenoManifest (field) Inherits from: flybase.store.BasicFieldStore
- PHP Phenotypic info.
- Description: This field holds phenotypic information about a gene (or, as explained above, about its mutant alleles in some cases). This field is free text and, by and large, has not yet been standardized with respect to its vocabulary. [Free text.]
Brief help: phenotypic information on genes
Data classes: none
Star code: *p
Java class: flybase.genes.PhenotypeP (field) Inherits from: flybase.store.BasicFieldStore
- PHS Status
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.Status (field) Inherits from: flybase.store.BasicFieldStore
- POL Polymorphic variant
- Description: Other polypeptides that may be variants of given polypeptide.
Brief help: other polypeptides that may be variants of given polypeptide
Data classes: none
Java class: flybase.pep.PeptideVariant (field) Inherits from: flybase.store.BasicFieldStore
- PPB Place pub.
- Description: none
Brief help: none
Data classes: none
Star code: *P
Java class: flybase.refs.Placepub (field) Inherits from: flybase.store.BasicFieldStore
- PPC Population comments
- Description: Comments on population and polymorphism data
Brief help: Comments on population and polymorphism data
Data classes: none
Star code: *h
Java class: flybase.genes.PopulationData (field) Inherits from: flybase.store.BasicFieldStore
- PPR Polypeptide Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.PolypeptideStore (record) Inherits from: flybase.store.DataStore
- PPS Population info
- Description: none
Brief help: none
Data classes: none
Star code: *h samp
Java class: flybase.genes.PopSample (field) Inherits from: flybase.store.BasicFieldStore
- PPSR Polypeptide
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Polypeptide (subrecord) Inherits from: flybase.store.SubrecFieldStore
- PRG Progenitor
- Description: progenitor allele or chromosome if relevant to allele
Brief help: progenitor allele or chromosome if relevant to allele
Data classes: none
Star code: *O
Java class: flybase.genes.Progenitor (field) Inherits from: flybase.store.BasicFieldStore
- PSZ Protein size (kD)
- Description: The size of the protein in kilodaltons (kD). If the size has been predicted, "predicted" is appended to the size; "observed" is appended if the size has been experimentally determined.
Brief help: protein size in kilodaltons (kD)
Data classes: none
Java class: flybase.rci.ProteinSize (field) Inherits from: flybase.store.BasicFieldStore
- PT Part
- Description: none
Brief help: none
Data classes: none
Star code: *v
Java class: flybase.refs.PartTitle (field) Inherits from: flybase.store.BasicFieldStore
- PTD Protein & Transcript
- Description: Detailed information on transcripts and polypeptides, including size and expression data, is curated from publications.
Brief help: Detailed information on transcripts and polypeptides
Data classes: none
Star code: *u Protein & Transcript data are available
Java class: flybase.genes.ProtTransData (subrecord) Inherits from: flybase.store.SubrecFieldStore, flybase.store.Flagfield
- PTR Protein & Transcript
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ProtTrans (subrecord) Inherits from: flybase.store.SubrecFieldStore
- PTRR Protein & Transcript Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ProtTransStore (record) Inherits from: flybase.store.DataStore
- PhenoTable Allele phenotypes
- Description: none
Brief help: none
Data classes: none
Java class: flybase.alleles.PhenManifestTable (field) Inherits from: flybase.store.GenericFieldStore, flybase.store.Computedfield
- ProtTransTable Proteins & Transcripts
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.ProtTransTable (field) Inherits from: flybase.store.GenericFieldStore, flybase.store.Computedfield
- RCI Related transgene constructs and insertions
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.RelatedTpTi (subrecord) Inherits from: flybase.store.SubrecFieldStore
- RCIR Related transgene constructs and insertions
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.RelatedTpTiStore (record) Inherits from: flybase.store.DataStore
- RDID Ref.
- Description: See ID
Brief help: FlyBase identifier number for Attributed data
Data classes: none
Java class: flybase.genes.RefdataName (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Id
- RDL Data from reference
- Description: none
Brief help: none
Data classes: none
Java class: flybase.refs.Datalink (field) Inherits from: flybase.store.BasicFieldStore
- RDL1 Data from reference
- Description: none
Brief help: none
Data classes: none
Java class: flybase.refs.Datalink1 (field) Inherits from: flybase.refs.Datalink
- RDLSR Data from reference
- Description: none
Brief help: Table of data reports attributed to this reference
Data classes: none
Java class: flybase.refs.SubrecTable (field) Inherits from: flybase.store.BasicFieldStore
- REF References
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.genes.References (subrecord) Inherits from: flybase.store.SubrecFieldStore
- REFDR Ref. Data Record
- Description: none
Brief help: none
Data classes: none
Star code: *E
Java class: flybase.genes.RefdataStore (record) Inherits from: flybase.store.DataStore
- REFDSR Data from ref.
- Description: none
Brief help: none
Data classes: none
Star code: *E
Java class: flybase.genes.Refdata (subrecord) Inherits from: flybase.store.SubrecFieldStore
- REFF Reference
- Description: none
Brief help: none
Data classes: none
Java class: flybase.refs.Ref (subrecord) Inherits from: flybase.store.SubrecFieldStore
- REFM Mini ref.
- Description: none
Brief help: none
Data classes: none
Java class: flybase.refs.MinirefRecord (field) Inherits from: flybase.store.BasicFieldStore
- REFR Reference Record
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.refs.RefStore (record) Inherits from: flybase.store.DataStore
- REFTAB Reference table
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.RefTableLink (field) Inherits from: flybase.store.BasicFieldStore
- RESZ Record size
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.RecordSize (field) Inherits from: flybase.store.BasicFieldStore
- RETE Table Entry
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.RecordTableEntry (field) Inherits from: flybase.store.BasicFieldStore
- REV Recent reviews
- Description: none
Brief help: none
Data classes: none
Star code: *T
Java class: flybase.genes.RecentReview (field) Inherits from: flybase.store.BasicFieldStore
- RG Ring
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- RL Ref. list
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.genes.Reflist (subrecord) Inherits from: flybase.store.SubrecFieldStore
- RLR References
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.genes.ReferencesStore (record) Inherits from: flybase.store.DataStore
- RLSR References
- Description: none
Brief help: none
Data classes: none
Star code: *x
Java class: flybase.genes.ReflistStore (record) Inherits from: flybase.store.DataStore
- RNAT RNA type
- Description: The class of transcript, such as mRNA, tRNA, rRNA, etc.; a controlled vocabulary.
Brief help: class of transcript, such as mRNA, tRNA, rRNA, etc.; a controlled vocabulary
Data classes: none
Java class: flybase.pep.RnaType (field) Inherits from: flybase.store.BasicFieldStore
- RPA Rep. protein sequence
- Description: none
Brief help: Most representative protein sequence
Data classes: none
Java class: flybase.genes.RefProtein (field) Inherits from: flybase.genes.ProtAcc
- RPTC2 Available reports
- Description: none
Brief help: Sections of report: Synopsis, just the salient points, Abridged, a reduced report, Full, for all details,
GadFly, gene structures and adjacent genes and region, Interactive Fly report associated with this gene,
Alleles, a table of alleles, Proteins & transcripts, associated products, Recent reviews, review publications for this record, References, listing all publications for a data record, Sequences & similarities, links to sequence and species homology data, Synonyms, other names and symbols for this item, Attributed data, data attributed to particular publications. Recently updated data that has not yet been integrated with the full set.
Italics indicate a section is contained in the current report.
Data classes: none
Java class: flybase.report.ReportStyle (field) Inherits from: flybase.store.BasicFieldStore
- RPTCAN Available reports
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.ReportStyle (field) Inherits from: flybase.store.BasicFieldStore
- RPTCONTENT Available reports
- Description: The section of data that is reported (not a data field). This can include
- Brief, a summarized report. This is the default content. The information on a gene or other item is summarize to a few pages up to 10-15 pages at most.
- Full, a detailed report. This includes all information relevant to the gene, aberration, or other data class. In some cases it can be a few hundred pages of text.
- Alleles, Balancers and other subset reports. These are usually presented as tables, with hyperlinks to a full report for that sub-record.
- References, a detailed list of references for this data, with hyperlinks to full reference reports.
- Attributed data, a report of data attributed to particular references. In most cases, attributed data contains much more detail than the brief report.
- Recently updated data, new data that has not yet been integrated with the full set. This information may be updated nightly.
Italics indicate a section is contained in the current report
Brief help: Section of report: Synopsis, just the salient points, Abridged, a reduced report, Full, for all details,
GadFly, gene structures and adjacent genes and region, Interactive Fly report associated with this gene,
Alleles, a table of alleles, Proteins & transcripts, associated products, Recent reviews, review publications for this record, References, listing all publications for a data record, Sequences & similarities, links to sequence and species homology data, Synonyms, other names and symbols for this item, Attributed data, data attributed to particular publications. Recently updated data that has not yet been integrated with the full set.
Italics indicate a section is contained in the current report.
Data classes: none
Java class: flybase.report.ReportStyle (field) Inherits from: flybase.store.BasicFieldStore
- RPTL Data report
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.FBReportLink (field) Inherits from: flybase.store.BasicFieldStore
- RS Restriction site
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.RestSite (field) Inherits from: flybase.store.BasicFieldStore
- RSQ Rep. DNA sequence
- Description: none
Brief help: Most representative DNA sequence
Data classes: none
Java class: flybase.genes.RefSequence (field) Inherits from: flybase.genes.DBAccessions
- SCAF Scaffold
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Scaffold (field) Inherits from: flybase.genes.DBAccessions
- SEG Segment
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- SEP Separable component
- Description: none
Brief help: none
Data classes: none
Star code: *Y
Java class: flybase.abs.SepComponent (subrecord) Inherits from: flybase.alleles.Allele
- SEPR Sep. component Record
- Description: none
Brief help: none
Data classes: none
Star code: *Y
Java class: flybase.abs.SepComponentStore (record) Inherits from: flybase.alleles.AlleleStore
- SER Series
- Description: none
Brief help: none
Data classes: none
Star code: *S
Java class: flybase.refs.Series (field) Inherits from: flybase.store.BasicFieldStore
- SGTP Segment type
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- SK Stocks
- Description: Drosophila stock flies with this gene or entity, available from stock centers
Brief help: Drosophila stock flies with this gene or entity, available from stock centers
Data classes: none
Star code: *u Stocks
Java class: flybase.genes.Stocks (field) Inherits from: flybase.store.BasicFieldStore
- SKC Stocks count
- Description: none
Brief help: none
Data classes: none
Star code: *u Stocks count
Java class: flybase.genes.StockCount (field) Inherits from: flybase.store.BasicFieldStore
- SPSY Symbol
- Description: none
Brief help: none
Data classes: none
Java class: flybase.abs.SepComponentName (field) Inherits from: flybase.alleles.AlleleName, flybase.store.Abbreviation
- SQ Sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Sequence (field) Inherits from: flybase.store.BasicFieldStore
- SQLEN mRNA length
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.SeqLength (field) Inherits from: flybase.store.BasicFieldStore
- STS STS
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.STSComponent (subrecord) Inherits from: flybase.store.SubrecFieldStore
- STSNAM Name
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.STSName (field) Inherits from: flybase.genes.GeneSymbol, flybase.store.Abbreviation
- STSR STS Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.clone.STSComponentStore (record) Inherits from: flybase.store.DataStore
- SUMX Summary
- Description: none
Brief help: a generated text summary of the data
Data classes: none
Java class: flybase.report.SummaryXml (field) Inherits from: flybase.store.BasicFieldStore
- SYM Symbol
- Description: This is the standard abbreviation (gene symbol) for the name of the gene. In the genes file, gene records are sorted alphabetically. The order of precedence is: all-greek symbols (in alphabetical order), symbols that begin with a number (in numerical order, secondarily sorted on suffix, i.e., 1, 2, 2a, 2b, 3), symbols that begin with a letter, lower case having precedence over upper, and numerals precedence over letters, i.e., b, B, b1, ba).
Syntax: SYM <Nnnn>\symbol
e.g., SYM bb
SYM Dhyd\Minos Nnnn is an abbreviation for the species. The default species is D. melanogaster, in which case there is no species abbreviation. If a gene is from another species of drosophilid then this is indicated by Nnnn, where N is normally the initial letter of the genus, and nnn are normally the first three letters of the specific epithet. A list of species abbreviations is in the Nomenclature section of FlyBase.
Genes encoded by the mitochondrial genome all have the prefix Nnnnmt:. The D. melanogaster gene encoding the cytochrome oxidase subunit II is, therefore, mt:CoII, the D. simulans gene encoding the mitochondrial proline tRNA is Dsimmt:tRNA:P. The record MT:DNA is used for data concerning the mitochondrial genome and its products that cannot be assigned to any single mitochondrial gene. The symbol mt:ori is used for the non-coding A+T rich region of the mitochondrial origin of replication.
FlyBase includes data on artificial gene constructs, for example fusions between different genes. Fusion genes are named using the gene symbols of their components separated by a double colon, e.g., Antp::Scr. The components are listed in alphabetical order. When a component of a construct is from a species other than D. melanogaster then its symbol is prefixed by Nnnn to indicate the species of origin. For example the LexA protein from E. coli has the symbol Ecol. A list of the species abbreviations used is to be found in the Nomenclature section of FlyBase.
Some 'foreign' genes very frequently used in constructs are regarded as being 'honorary genes' of Drosophila and the species prefix is omitted. Examples include lacZ for the beta-galactosidase gene of E. coli and FRT for the S. cerevisiae FLP recombinase target. To see a list of 'honorary genes', use the Genes complex query form with the "Class" switched from the default "all" to "honorary_gene". Highlight both "foreign_gene" and "honorary_gene" (ctrl+click to add choices) to see a list of all 'foreign' genes.
Brief help: an abbreviated, unique name
Data classes: none
Star code: *a
Java class: flybase.genes.GeneSymbol1 (field) Inherits from: flybase.genes.GeneSymbol, flybase.store.Abbreviation
- SYN Synonyms
- Description: Synonyms. As mentioned above FlyBase takes a very liberal view of synonyms, and the table gene-synonyms.txt in the Genes section is provided as a tool to allow the identification of the name, and symbol, that FlyBase uses for each gene or allele. In Genes these data are kept in the SYN field, for both gene and allele synonyms. See Reference manual section B.2 for more on synonyms.
Syntax: SYN synonym_symbol: synonym name <text, e.g. a reference>
e.g., SYN ho: heldout
Brief help: alternate and discontinued symbols and names for this item.
Data classes: none
Star code: *i
Java class: flybase.genes.Synonyms (field) Inherits from: flybase.store.BasicFieldStore
- TCC Comments
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Comments (field) Inherits from: flybase.store.BasicFieldStore
- TCH Characteristics
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Characteristics (field) Inherits from: flybase.store.BasicFieldStore
- TCL Description
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Description (field) Inherits from: flybase.store.BasicFieldStore
- TCSR Transcript
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Transcript (subrecord) Inherits from: flybase.store.SubrecFieldStore
- TCTP Transposon construct type
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.TransposonConType (field) Inherits from: flybase.store.BasicFieldStore
- TE Transposable el. data
- Description: transposable element data
Brief help: transposable element data
Data classes: none
Star code: *l
Java class: flybase.genes.TransposableEl (field) Inherits from: flybase.store.BasicFieldStore
- TFT Feature
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Feature (field) Inherits from: flybase.store.BasicFieldStore
- TGT Genotype
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Genotype (field) Inherits from: flybase.store.BasicFieldStore
- TI Title
- Description: none
Brief help: none
Data classes: none
Star code: *u
Java class: flybase.refs.Title (field) Inherits from: flybase.store.BasicFieldStore
- TIR Insertion Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.InsertionStore (record) Inherits from: flybase.store.DataStore
- TMPLCONT Report content
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- TP Type
- Description: Reference type, a controlled vocabulary. The default type is a journal article. Most references are papers in journals, but there are also papers in edited publications, theses, manuscripts, other electronic databases and, others. See Reference manual section B.13 for details.
Brief help: Reference type: abstract, book, review, etc.
Data classes: none
Star code: *T
Java class: flybase.refs.Type (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.Kindname
- TPFBMMP Molecular map
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- TPFBSQ Transposon sequence
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- TPR Transposon Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.TransposonStore (record) Inherits from: flybase.store.DataStore
- TPSY Transposon synonym
- Description: none
Brief help: none
Data classes: none
Star code: *L
Java class: flybase.genes.TransposonSyn (field) Inherits from: flybase.genes.Synonyms
- TPU Uses
- Description: none
Brief help: none
Data classes: none
Java class: flybase.trin.Uses (field) Inherits from: flybase.store.BasicFieldStore
- TRL Length (Kb)
- Description: The length of transcript in kilobases. For transcripts, the mode of size determination is indicated in parentheses. Modes of transcript size determination are Northern blot, length based on longest cDNA, compiled cDNA, sequence analysis, and cDNA (unknown whether from one or more cDNAs).
Brief help: The size in kilobases of transcript or transposon
Data classes: none
Java class: flybase.trin.Length (field) Inherits from: flybase.store.BasicFieldStore
- TRN Responsible transposon
- Description: transposon or insertion chromosome associated with allele
Brief help: transposon or insertion chromosome associated with allele
Data classes: none
Star code: *G
Java class: flybase.genes.GeneTransposon (field) Inherits from: flybase.store.BasicFieldStore
- TRNA Transposon insertions
- Description: none
Brief help: none
Data classes: none
Star code: *P
Java class: flybase.abs.AbsTransposon (field) Inherits from: flybase.genes.GeneTransposon
- TRR Transcript Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.TranscriptStore (record) Inherits from: flybase.store.DataStore
- TRREC AnnoTranscript Record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Transcript$Store (record) Inherits from: flybase.store.DataStore
- TRRECSR Transcript
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Transcript (subrecord) Inherits from: flybase.store.SubrecFieldStore
- TRSR Transposon
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.Transposon (subrecord) Inherits from: flybase.store.SubrecFieldStore
- UAB Useful aneuploid aberrations
- Description: none
Brief help: none
Data classes: none
Star code: *K
Java class: flybase.genes.Aneuploids (field) Inherits from: flybase.store.BasicFieldStore
- VCL Is valid record
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI
- VERS Release vers.
- Description: none
Brief help: none
Data classes: none
Java class: flybase.egad.Version (field) Inherits from: flybase.store.BasicFieldStore
- VL Volume
- Description: none
Brief help: none
Data classes: none
Star code: *y
Java class: flybase.refs.Volume (field) Inherits from: flybase.store.BasicFieldStore
- VPR 5' experiment info
- Description: Indicates whether the 5-prime end of the transcript has been experimentally determined. The allowed values are "yes", "no", and "uncertain".
Brief help: Has the 5' end of transcript been experimentally determined?
Data classes: none
Java class: flybase.pep.FivePrime (field) Inherits from: flybase.store.BasicFieldStore
- WT Wild-type function
- Description: This field is used for information about the wild-type function of a gene. The objective is for each gene record to have a WT field in which information about the gene function is summarized. The present situation, however, is that for the majority of genes this information is still to be found in the PHP field of the gene record. FlyBase is systematically rewriting these *p fields (historically derived from the 'Phenotype' field of Lindsley and Zimm (1992) so that the summary of wild-type function is moved to the WT field.
Brief help: information on wild-type function
Data classes: none
Star code: *r
Java class: flybase.genes.Wildtype (field) Inherits from: flybase.store.BasicFieldStore
- WTI Interacts genetically with
- Description: Holds information on gene interactions. These are expressed as follows:
WTI [gene_symbol]
Brief help: information on gene interactions
Data classes: none
Star code: *p Interacts genetically with:
Java class: flybase.genes.InteractsWith (field) Inherits from: flybase.store.BasicFieldStore
- XDA Expression data available
- Description: none
Brief help: none
Data classes: none
Java class: flybase.rci.HasExpressionData (field) Inherits from: flybase.store.BasicFieldStore
- YR Year
- Description: none
Brief help: none
Data classes: none
Star code: *t
Java class: flybase.refs.Year (field) Inherits from: flybase.store.BasicFieldStore
- ZR Zool. Rec.
- Description: none
Brief help: none
Data classes: none
Star code: *Q
Java class: flybase.refs.ZoolRec (field) Inherits from: flybase.store.BasicFieldStore
- env none
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.EnvironField (field) Inherits from: flybase.store.BasicFieldStore
- fbsym FlyBase symbol
- Description: none
Brief help: none
Data classes: none
Java class: flybase.report.FBSymbolLink (field) Inherits from: flybase.store.BasicFieldStore
- self none
- Description: none
Brief help: none
Data classes: none
Java class: flybase.store.GenericFieldStore (field) Inherits from: flybase.store.BasicFieldStore, flybase.store.GenericFieldReaderI