FB2022_02, released March 29, 2022

Gene: Dmel\prd1

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General Information
Symbol
Dmel\prd1
Species
D. melanogaster
Name
pruning defect 1
Annotation Symbol
CG17360
Feature Type
protein_coding_gene
FlyBase ID
FBgn0037949
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
86E18-86F7
Sequence location
Recombination map
3-51
RefSeq locus
NT_033777 REGION:11781131..11787014
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables small GTPase binding
inferred from physical interaction with FLYBASE:Rab39; FB:FBgn0029959
(Gillingham et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables kinesin binding
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
involved_in Golgi organization
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in lysosome localization
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in positive regulation of membrane tubulation
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in regulation of protein localization
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in Golgi apparatus
inferred from direct assay
(Gillingham et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in endosome membrane
inferred from biological aspect of ancestor with PANTHER:PTN002926757
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\prd1 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
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VGI1)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
prd1-RA
FBtr0082531
NM_141858
5206
1354
prd1-RB
FBtr0333819
NM_001275557
4894
1330
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
prd1-PA
FBpp0082005
149.7
1354
5.80
NP_650115
AAF54698
prd1-PB
FBpp0305953
147.1
1330
5.98
NP_001262486
AGB95868
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\prd1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in Golgi apparatus
inferred from direct assay
(Gillingham et al., 2014)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\prd1 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 9 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of prd1
Transgenic constructs containing regulatory region of prd1
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel7310
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal - all die during pharate adult stage (with Df(3R)Exel7310)
partially lethal, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Other Phenotypes
Allele
abnormal neuroanatomy | prepupal stage P1 | somatic clone
abnormal neuroanatomy | pupal stage P5, with Scer\GAL4ppk.PU
abnormal neuroanatomy | pupal stage P5 (with Df(3R)Exel7310)
abnormal neuroanatomy | pupal stage P5 (with Df(3R)PS2)
abnormal neuroanatomy | pupal stage P5 | somatic clone
abnormal size | prepupal stage P1 | somatic clone
abnormal size | pupal stage P5, with Scer\GAL4ppk.PU
abnormal size | pupal stage P5 (with Df(3R)Exel7310)
abnormal size | pupal stage P5 (with Df(3R)PS2)
abnormal size | pupal stage P5 | somatic clone
some die during pupal stage, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
Phenotype manifest in
Allele
dendritic tree | prepupal stage P1 | somatic clone
dendritic tree | pupal stage P5, with Scer\GAL4ppk.PU
dendritic tree | pupal stage P5 (with Df(3R)Exel7310)
dendritic tree | pupal stage P5 (with Df(3R)PS2)
dendritic tree | pupal stage P5 | somatic clone
larval dorsal multidendritic neuron ddaC | prepupal stage P1 | somatic clone
larval dorsal multidendritic neuron ddaC | pupal stage P5, with Scer\GAL4ppk.PU
larval dorsal multidendritic neuron ddaC | pupal stage P5 (with Df(3R)Exel7310)
larval dorsal multidendritic neuron ddaC | pupal stage P5 (with Df(3R)PS2)
larval dorsal multidendritic neuron ddaC | pupal stage P5 | somatic clone
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\PLEKHM2
4 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Plekhm2
4 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Plekhm2
3 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\plekhm2
2 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\plekhm2
2 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
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.
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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 ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 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?
    PLEKHM2; pleckstrin homology and RUN domain containing M2
    4 of 15
    609613
        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
        View in Interactions Browser
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        prd1 - AP-1-2β
        anti tag coimmunoprecipitation, anti tag western blot
        (Zong et al., 2018)
        prd1 - AP-2α
        anti tag coimmunoprecipitation, anti tag western blot
        (Zong et al., 2018)
        prd1 - Rab39
        pull down, peptide massfingerprinting, western blot
        (Gillingham et al., 2014, Gillingham et al., 2014)
        prd1 - unc-104
        anti tag coimmunoprecipitation, anti tag western blot
        (Zong et al., 2018)
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        Please look at the allele data for full details of the genetic interactions
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        prd1
        enhanceable
        AP-2α
        (Zong et al., 2018)
        prd1
        enhanceable
        Cul1
        (Zong et al., 2018)
        prd1
        enhanceable
        Mical
        (Zong et al., 2018)
        prd1
        suppressible
        Nrg
        (Zong et al., 2018)
        prd1
        enhanceable
        unc-104
        (Zong et al., 2018)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        AP-2α
        enhanceable
        prd1
        (Zong et al., 2018)
        External Data
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-51
        Cytogenetic map
        86E18-86F7
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        86E18-86F7
        Limits computationally determined from genome sequence between P{EP}Lk6EP886 and P{PZ}svp07842
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-51

        (FlyBase, 2016)

        3-48.8

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (12)
         

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

        cDNA Clones (36)
         

        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
        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)
        BDGP DGC clones
        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
         

        polyclonal

        (Zong et al., 2018)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: prd1 CG17360

        (Zong et al., 2018)
        Source for database merge of

        Source for merge of: CG17360 BcDNA:RH29885

        (FlyBase, 1996-)
        Additional comments

        Source for merge of CG17360 BcDNA:RH29885 was a shared cDNA ( date:030728 ).

        (FlyBase, 1996-)
        Other Comments
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 49 )
        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 Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        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/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (4)
        Reported As
        Symbol Synonym
        BcDNA:RH29885
        CG17360
        (Zong et al., 2018, Li et al., 2015, Gillingham et al., 2014, Luck et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Weiler, 2012.3.1, Keleman et al., 2009.8.5)
        prd1
        (Zong et al., 2018)
        Name Synonyms
        pruning defect 1
        (Zong et al., 2018)
        Secondary FlyBase IDs
        • FBgn0064826
        Datasets (8)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (8)
        Result
        Result Type
        Title
        scRNAseq_2020_Cattenoz_NI_seq_clustering
        Clustering analysis of hemocytes from non-infested third instar larvae
        scRNAseq_2020_Cattenoz_WI_seq_clustering
        Clustering analysis of hemocytes from wasp-infested third instar larvae
        scRNAseq_2020_Cho_NI72LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
        scRNAseq_2020_Cho_NI96LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI120LG_seq_clustering
        Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
        scRNAseq_2020_Cho_WI96LG_seq_clustering
        Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI96HL_seq_clustering
        Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
        scRNAseq_2020_Cho_NI120HL_seq_clustering
        Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
        References (26)