A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

Gene Dmel\att-ORFB

General Information
SymbolDmel\att-ORFBSpeciesD. melanogaster
Namealternative testis transcripts open reading frame BAnnotation symbolCG33488
Feature typeprotein_coding_geneFlyBase IDFBgn0067782
Gene Model StatusCurrent Stock availability 1 publicly available
Genomic Location
Chromosome (arm)3RRecombination map
Cytogenetic map92F1-92F1Sequence location3R:16,378,357..16,380,131 [-]

Genomic Maps

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Automatically generated summary

See sections below for more information
The gene alternative testis transcripts open reading frame B is referred to in FlyBase by the symbol Dmel\att-ORFB (CG33488, FBgn0067782). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. The biological processes in which it is involved are not known. One allele is reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of low expression. Peak expression observed in adult male stages. This gene is annotated by FlyBase as a dicistronic gene, meaning that some or all of its transcripts encode two or more polypeptide-coding open reading frames (ORFs) , with each ORF assigned to a different gene. The distribution of RNA-Seq coverage data amongst the different encoded genes cannot be determined. Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult central nervous system, adult crop, adult midgut, adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, adult salivary gland, adult female reproductive system, adult male reproductive system, adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1633573_a_at aligns to a genomic region shared by exons of 2 FlyBase-annotated genes; hence it is impossible to interpret the expression pattern and levels of att-ORFB expression signal. See the GBrowse view of att-ORFB to determine the overlapping gene(s). Gene sequence location is 3R:16378357..16380131.

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Description
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FB2013_03
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FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
92F1-92F1  
Limits computationally determined from genome sequence between P{PZ}l(3)1058510585 and P{EP}SyndEP409  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
92E3-92E4  
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
hide Gene Model & Products
Please see the GBrowse view of Dmel\att-ORFB for information on other features GBrowse View Help
To submit a correction to a gene model please use the Contact FlyBase form
detailed view FBtr0089485 FBtr0334586 FBtr0100457 FBtr0334582 FBtr0089484 FBtr0334584 FBtr0334585 FBtr0089486 FBtr0334581 FBtr0089487 FBtr0334583 FBtr0090034 FBtr0089481 FBtr0089480 FBtr0089482 FBpp0088486 FBpp0089077 FBpp0088485 FBpp0088980 FBti0057491 FBti0025592 FBti0113385 FBti0105783 FBti0105829 FBti0011537 FBti0110855 FBti0106513 FBti0028965 FBti0029374 FBti0030015 FBti0102248 FBti0105045 FBti0106201 FBti0110655 FBti0126179 FBti0066519 FBti0066031 FBti0041675 FBti0047253
Comments on Gene Model
Complete overlap: the att locus encodes two proteins, att-ORFA and att-ORFB, that overlap in the DNA sequences that encode them but not in amino acid sequence, due to use of different reading frames (FBrf0089733).
Multiphase exon postulated: this gene shares a region of coding sequence with an overlapping gene, but different reading frames are utilized in the overlapping coding region.
Gene model reviewed during 5.47
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
FBtr0090034
  1336
  197
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
FBpp0089077  
20.9  
197  
11.36  
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
 
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL
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Mapped Features have been reorganized, please see this article for details.
Additional mapped features and mutations can be found on GBrowse or related reports.
Type
Symbol & Location
Additional Notes
References
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Crossreferences
hide Expression Data
hideTranscript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
hide Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term
References
hide Expression Deduced from Reporters
hide High-Throughput Expression Data
Associated Tools
Reference
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
hide FlyAtlas Anatomy Microarray

FlyAtlas Anatomical Expression Data

(FlyAtlas-RNA.adult)

(FlyAtlas-RNA.larva)


   Styles
   Scales

Summary of FlyAtlas Anatomical Expression Data: Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, adult central nervous system, adult crop, adult midgut, adult hindgut, larval/adult Malpighian tubules, adult heart, larval/adult fat body, adult salivary gland, adult female reproductive system, adult male reproductive system, adult carcass.
[download data (TSV)]

Guide to FlyAtlas expression level colors
 
No expression (0 - 9.999)
 
Low expression (10 - 99.999)
 
Moderate expression (100 - 499.999)
 
High level expression (500 - 999.999)
 
Very high expression (>999.999)

Linear, scaled to maximum expression level
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
Linear, scaled to Moderate expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
Linear, scaled to High level expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
 Very high 
Linear, scaled to Very high expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 Very high 
log, scaled to maximum expression level
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
log, scaled to Moderate expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
log, scaled to High level expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
 Very high 
log, scaled to Very high expression
Tissue   Expression Level
Larval Central Nervous System
 
 35.125
Larval Midgut
 
 60.7
Larval Hindgut
 
 55.1
Larval Malpighian Tubules
 
 181.9
Larval Fat Body
 
 221.5
Larval Salivary Gland
 
 39.7
Larval Trachea
 
 41.925
Larval Carcass
 
 67.8
Adult Head
 
 152.8
Adult Eye
 
 110.6
Adult Brain
 
 175.4
Adult Thoracic-Abdominal Ganglion
 
 166.2
Adult Crop
 
 108.7
Adult Midgut
 
 123.4
Adult Hindgut
 
 146.7
Adult Malpighian Tubules
 
 231.3
Adult Fat Body
 
 150.3
Adult Salivary Gland
 
 202.7
Adult Heart
 
 159.275
Adult VirginFemale Spermatheca
 
 126
Adult InseminatedFemale Spermatheca
 
 93.3
Adult Ovary
 
 104.4
Adult Testis
 
 378
Adult Male Accessory Gland
 
 106.9
Adult Carcass
 
 228.1
Expression Level Scale
 None 
 Low 
 Moderate 
 High 
 Very high 
Heatmap
Tissue   Expression Level
Larval Central Nervous System
 
 
Larval Midgut
 
 
Larval Hindgut
 
 
Larval Malpighian Tubules
 
 
Larval Fat Body
 
 
Larval Salivary Gland
 
 
Larval Trachea
 
 
Larval Carcass
 
 
Adult Head
 
 
Adult Eye
 
 
Adult Brain
 
 
Adult Thoracic-Abdominal Ganglion
 
 
Adult Crop
 
 
Adult Midgut
 
 
Adult Hindgut
 
 
Adult Malpighian Tubules
 
 
Adult Fat Body
 
 
Adult Salivary Gland
 
 
Adult Heart
 
 
Adult VirginFemale Spermatheca
 
 
Adult InseminatedFemale Spermatheca
 
 
Adult Ovary
 
 
Adult Testis
 
 
Adult Male Accessory Gland
 
 
Adult Carcass
 
 

FlyAtlas Organ/Tissue Expression, larval vs. adult
Larval Expression Level Tissue Adult Expression Level
 
NA 
Head
 
 152.8
 
NA 
Eye
 
 110.6
 
NA 
Brain
 
 175.4
 
35.125 
Central Nervous System
 
 NA
 
NA 
Thoracic-Abdominal Ganglion
 
 166.2
 
NA 
Crop
 
 108.7
 
60.7 
Midgut
 
 123.4
 
55.1 
Hindgut
 
 146.7
 
181.9 
Malpighian Tubules
 
 231.3
 
221.5 
Fat Body
 
 150.3
 
39.7 
Salivary Gland
 
 202.7
 
NA 
Heart
 
 159.275
 
41.925 
Trachea
 
 NA
 
NA 
VirginFemale Spermatheca
 
 126
 
NA 
InseminatedFemale Spermatheca
 
 93.3
 
NA 
Ovary
 
 104.4
 
NA 
Testis
 
 378
 
NA 
Male Accessory Gland
 
 106.9
 
67.8 
Carcass
 
 228.1

FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
hide modENCODE Anatomy RNA-Seq
hide modENCODE Development RNA-Seq
modENCODE Temporal Expression Data (Graveley et al., 2011)
hide modENCODE Cell Lines RNA-Seq
hide modENCODE Treatments RNA-Seq
hide Expression Clusters
A cluster of genes with similar mRNA expression dynamics across development.
hide External Data & Images
Linkouts
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
hide Alleles & Phenotypes
hide Summary of Allele Phenotypes
Phenotype manifest in
Allele
hide Classical Alleles ( 1 )
For All Classical Alleles Show

Allele of att-ORFBClassMutagenStocksKnown lesion
att-ORFBe031441 Yes
hide Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show

Allele of att-ORFBClassMutagenStocksKnown lesion
hide Aneuploid Aberrations
hide Transgenic Constructs & Insertions
Transgenic Constructs
Type of construct
Name
Expression data
UAS construct
Insertions
Type of insertions
Name
Expression data
miscellaneous insertions
hide Gene Ontology: Function, Process & Cellular Component ( 0 unique terms )

There is no information supporting a biological process, cellular component or molecular function term for this gene.

(Based on a review of available data on: 2011-07-06)

hide Terms Based on Experimental Evidence ( 0 terms )
hide Terms Based on Predictions or Assertions ( 0 terms )
hide Sequence Ontology: Class of Gene
hide Interactions & Pathways
hide Summary of Physical Interactions
hide Summary of Genetic Interactions
Interacts with
Please look at the allele data for full details of the genetic interactions
att-ORFB allele
Gene
References
hide External Data
Linkouts
DroID - A comprehensive database of gene and protein interactions.
hide Orthologs
hide OrthoDB Orthologs (0) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
Drosophila inclusive ortholog search
No orthologs identified
Dipteran inclusive ortholog search
No orthologs identified
Insect inclusive ortholog search
No orthologs identified
Arthropod inclusive ortholog search
No orthologs identified
Metazoa inclusive ortholog search
No orthologs identified
Orthologs in Drosophila Species (None identified)
No orthologies identified
Orthologs in non-Drosophila Dipterans (None identified)
No non-Drosophilid orthologies identified
Orthologs in non-Dipteran Insects (None identified)
No non-Dipteran orthologies identified
Orthologs in non-Insect Arthropods (None identified)
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (None identified)
No non-Arthropod Metazoa orthologies identified
hide Human Orthologs (0)
Gene
OMIM
HGNC
hideAAA Orthologs (0) based on analysis using Dmel annotation version 4.3
No orthologs identified
hide Stocks & Reagents
hide Stocks Listed in FlyBase ( 1 )
Bloomington
hide Genomic Clones ( 2 )
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
hide cDNA Clones ( 20 )
Please Note
This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
hide RNAi & Array Information
Linkouts
DRSC - Results from RNAi screens.
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
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hide Etymology
hide Identification
hide Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
The relationship between the "att" locus (encoding att-ORFA and att-ORFB), l(3)92Ea and l(3)92Eb is unclear.
hide Other Comments
Annotation CG33488 represents the att-ORFB open reading frame.
The "att" locus is alternatively expressed at both the RNA and protein levels. The locus encodes RNAs expressed in the soma and a testis specific RNA. The somatic RNAs encode a protein (att-ORFA) with homology to the mammalian Graves' disease carrier proteins. The testis RNA encodes two different proteins from two reading frames. One of these initiates at a CUG codon and represents an N-terminally truncated version of the protein encoded by the somatic RNAs (att-ORFA). The other protein (att-ORFB) initiates at an AUG codon in testis-specific exon 3 (in a different frame from att-ORFA) and is completely novel. Overall orientation not stated: anon-92Ee+ att-ORFB+ anon-92Ef?
hide External Crossreferences & Linkouts
Sequence Crossreferences
RefSeq (Transcripts)
RefSeq (Proteins)
Entrez Gene - A searchable database of RefSeq genes.
Other Crossreferences
Linkouts
DroID - A comprehensive database of gene and protein interactions.
DRSC - Results from RNAi screens.
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans
GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents
modMine - Data generated by the modENCODE project.
hide Synonyms & Secondary IDs ( 6 )
Reported As
Symbol Synonym
CG33488
 
Name Synonym
alternative testis transcripts
alternative testis transcripts open reading frame B
 
Secondary FlyBase IDs
  • FBgn0019839
hide References ( 8 )
Research paper
Lee and Reinhardt, 2012, Genome Biol. Evol. 4(4): 533--549
Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster. [FBrf0218109]
Madigan et al., 1996, Mol. Cell. Biol. 16(8): 4222--4230
att, a target for regulation by tra2 in the testes of Drosophila melanogaster, encodes alternative RNAs and alternative proteins. [FBrf0089733]
Supplementary material
The modENCODE Consortium, 2010, Science 330(6012):
DataS14: Gene co-expression clusters. [FBrf0213979]
Personal communication to FlyBase
Bloomington Drosophila Stock Center, 2004.11.6, Exelixis insertion alleles that are not in FlyBase.
Exelixis insertion alleles that are not in FlyBase. [FBrf0179797]
FlyBase analysis
FlyBase Curators, 2010-, Gene Ontology (GO) annotation review.
Gene Ontology (GO) annotation review. [FBrf0216433]
FlyBase Genome Annotators, 2004, Changes affecting gene model number or type in release 3.2 of the annotated D.melanogaster genome.
Changes affecting gene model number or type in release 3.2 of the annotated D.melanogaster genome. [FBrf0166453]
FlyBase Curators, 2002-, Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase.
Use of the ND evidence code for Gene Ontology (GO) terms in FlyBase. [FBrf0159398]
FlyBase, 1996-, FlyBase inference based on genome sequence analysis.
FlyBase inference based on genome sequence analysis. [FBrf0104946]