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General Information
Symbol
Dmel\Hr39
Species
D. melanogaster
Name
Hormone receptor-like in 39
Annotation Symbol
CG8676
Feature Type
FlyBase ID
FBgn0261239
Gene Model Status
Stock Availability
Gene Snapshot
Hormone receptor-like in 39 (Hr39) encodes a nuclear hormone receptor protein in subfamily 5. It is a master regulator of female reproductive gland development from the bipotential genital disc, and in adults is required for reproductive gland secretion, ovulation and additional functions. [Date last reviewed: 2019-03-07]
Also Known As
DHR39, ftz-F1β, fs(2)neo8, fs(2)04443, NR5B1
Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:21,237,250..21,259,675 [+]
Recombination map
2-54
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the nuclear hormone receptor family. NR5 subfamily. (Q05192)
Summaries
Gene Group (FlyBase)
NUCLEAR RECEPTOR (LIGAND-DEPENDENT) TRANSCRIPTION FACTORS -
Nuclear receptors (NR) are C4 zinc finger ligand-dependent DNA-binding transcription factors. Members of the NR superfamily are defined by the presence of a highly conserved DNA-binding domain and a less conserved C-terminal ligand-binding domain. (Adapted from FBrf0184203).
Protein Function (UniProtKB)
Acts as a cofactor to fushi tarazu (ftz). Facilitates the binding of ftz to DNA. Binds the sequence element 5'-YCYYGGYCR-3' in the zebra element of ftz. Probably also functions as a receptor for a yet unknown ligand.
(UniProt, Q05192)
Summary (Interactive Fly)
nuclear receptor superfamily - master regulator of a program for the production of female reproductive glands and other secretory tissues
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Hr39 or the JBrowse view of Dmel\Hr39 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model
Annotated transcripts do not represent all supported alternative splices within 5' UTR.
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.45
Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0081480
3291
808
FBtr0081479
4844
808
FBtr0081478
2722
701
FBtr0081481
4828
808
Additional Transcript Data and Comments
Reported size (kB)
5.0, 3.5 (northern blot); 2.734 (longest cDNA)
5.1, 3.5 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0081009
87.3
808
7.50
FBpp0081008
87.3
808
7.50
FBpp0081007
74.8
701
7.49
FBpp0081010
87.3
808
7.50
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

808 aa isoforms: Hr39-PA, Hr39-PB, Hr39-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
808, 701 (aa)
Comments
Hr39 protein binds to a AGGTCA binding site in vitro but does not require the presence of any of 5 Drosophila nuclear receptor superfamily members tested.
The 701aa Hr39 protein has the same N-terminal sequences as the 808aa Hr39 protein but is missing the carboxy terminal sequences which contain the ligand-binding domain. In cotransfection experiments, this protein had no effect on Adh distal transcription presumably due to the lack of the carboxy terminal end of the protein.
The Hr39 protein was shown to bind the Adh adult enhancer (AAE) and repress distal Adh expression in a dosage dependent manner (in co-transfection experiments). Hr39 protein binds the same DNA sequences as ftz-f1 protein.
Bacterially expressed Hr39 protein was shown to specifically bind to a site that is also bound by ftz-f1 protein in the zebra stripe promoter element of ftz.
One of a couple of protein products generated by alternative splicing.
External Data
Subunit Structure (UniProtKB)
Monomer; forms a complex with ftz.
(UniProt, Q05192)
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Hr39 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (15 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from physical interaction with UniProtKB:Q86BY9
(assigned by UniProt )
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001723
(assigned by InterPro )
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001628, InterPro:IPR013088
(assigned by InterPro )
Biological Process (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000639680
(assigned by GO_Central )
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Hr39 expression was studied in staged third instar larvae and prepupae collected at two hour intervals. Transcripts can first be detected in early third instar larvae and continue to be present at low levels until 106-108hr. After that, they accumulate to high levels, peaking in early prepupae. Hr39 transcripts drop in abundance in mid prepupae, rise again in 10hr prepupae, and continue to be present through the beginning of pupal development. In staged prepupal salivary glands, Hr39 transcripts are abundant at 0hr, decline in 2hr glands, and then are reintroduced, peaking 6-8hr after puparium formation. Hr39 transcripts are rapidly induced by ecdysone.
5kb Hr39 transcripts are present at all developmental stages. In embryos, transcripts are most abundant at 6-9 hr. Hr39 transcripts are detected in the stomodeum of stage 13 embryos. In stage 16 embryos, transcripts are most prominent in the central nervous system and in the brain lobes.
Hr39 3.5kb transcripts are most abundant in 0-3 hour embryos and are probably maternally inherited.
5.1kb Hr39 transcripts are not present in early embryos but are detected at all other stages of development. An elevated transcript level is observed during puparium formation. Transcripts are uniformly distributed in early embryos. At later stages, high levels of expression are observed in the ventral cord, brain, and hindgut.
3.5kb Hr39 transcripts are maternally expressed. They are uniformly distributed in early embryos.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Hr39 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 40 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Hr39
Transgenic constructs containing regulatory region of Hr39
Deletions and Duplications ( 2 )
Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
3 of 15
Yes
No
2 of 15
No
No
 
2 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
2 of 15
Yes
No
 
2 of 15
Yes
No
2 of 15
Yes
No
Rattus norvegicus (Norway rat) (2)
2 of 13
Yes
No
2 of 13
Yes
No
Xenopus tropicalis (Western clawed frog) (3)
1 of 12
Yes
No
1 of 12
Yes
No
1 of 12
Yes
No
Danio rerio (Zebrafish) (7)
3 of 15
Yes
No
3 of 15
Yes
No
3 of 15
Yes
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (6)
2 of 15
Yes
No
2 of 15
Yes
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919030R )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915037B )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04U6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X043W )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (10)
2 of 10
2 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
     
    Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    RNA-RNA
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Monomer; forms a complex with ftz.
    (UniProt, Q05192 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-54
    Cytogenetic map
    Sequence location
    2L:21,237,250..21,259,675 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    39C-60
    Limits computationally determined from genome sequence between P{lacW}l(2)k07215k07215&P{lacW}snRNA:U4:39Bk09410 and P{lacW}l(2)k14505k14505&P{lacW}l(2)k05106k05106; Left limit from (method unavailable) (FBrf0106405) Right limit from (method unavailable) (FBrf0106405)
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    39C-39C
    39B-39C
    (determined by in situ hybridisation)
    39C-39C
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (42)
    Genomic Clones (16)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (340)
     

    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 sequences
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for database merge of
    Source for merge of: Hr39 fs(2)neo8 fs(2)04443
    Additional comments
    Other Comments
    Hr39 is involved in αbgr; axon guidance and fasciculation but is necessarily downregulated in γ axons for pruning to occur.
    Hr39 does not play an essential role during development.
    Temporal profile of gene expression is not altered in Eip74EF mutant background.
    Hr39 and Hr46 contribute to the regulatory hierarchy activated by the steroid hormone 20E at the onset of metamorphosis.
    ftz-f1 and Hr39 bind as monomers to oligonucleotides corresponding to the ftz-f1 recognition element (F1RE) located within the zebra element of ftz promoter. Antagonism between the two receptors contributes to the net F1RE-dependent transcription of a reporter gene in cotransfection assays. Results suggest common target genes may be coregulated at the transcriptional level by a mechanism of competition between ftz-f1 and Hr39 monomers for binding to a common element.
    Hr39 cloned by screening an expression library with oligonucleotide probe corresponding to the positive element of the Adh adult enhancer: DNA sequence analysis showed Hr39 belongs to the steroid hormone receptor superfamily. Whereas ftz-f1, which binds to the same sequence, acts as an activator of distal Adh transcription, Hr39 acts to repress distal Adh transcription.
    Hr39 is a member of the nuclear receptor family which exhibit structural and functional properties similar to those of ftz-f1. A single copy gene.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 67 )
    Sequence Crossreferences
    NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
    GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
    RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
    UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DPiM - Drosophila Protein interaction map
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (23)
    Reported As
    Symbol Synonym
    DHR39/Ftz-F1β
    fs(2)04443
    fs(2)neo8
    Name Synonyms
    Hormone receptor-like in 39
    NR5A-class nuclear hormone receptor
    fs(2)04443
    fs(2)neo8
    hormone receptor like in 39
    hormone receptor-like in 39
    Secondary FlyBase IDs
    • FBgn0010229
    • FBgn0014175
    • FBgn0013458
    • FBgn0026243
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (138)