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General Information
Symbol
Dmel\Pdp1
Species
D. melanogaster
Name
PAR-domain protein 1
Annotation Symbol
CG17888
Feature Type
FlyBase ID
FBgn0016694
Gene Model Status
Stock Availability
Gene Snapshot
PAR-domain protein 1 (Pdp1) encodes a member of the PAR domain bZip family of sequence-specific transcription factors. it regulates gene expression in muscles and in circadian clock neurons. [Date last reviewed: 2019-03-14]
Also Known As

Pdp1ε, pdp, Pdp-1, Pdp1&e;gr, Par domain protein 1ε

Key Links
Genomic Location
Cytogenetic map
Sequence location
3L:7,811,458..7,867,369 [-]
Recombination map

3-21

RefSeq locus
NT_037436 REGION:7811458..7867369
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (9 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000945219
(assigned by GO_Central )
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:vri; FB:FBgn0016076
inferred from direct assay
(assigned by UniProt )
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
traceable author statement
inferred from electronic annotation with InterPro:IPR040223
(assigned by InterPro )
Cellular Component (1 term)
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:PTN000945219
(assigned by GO_Central )
inferred by curator from GO:0003700
(assigned by UniProt )
Protein Family (UniProt)
-
Summaries
Gene Group (FlyBase)
BASIC LEUCINE ZIPPER TRANSCRIPTION FACTORS -
The basic leucine zipper (bZIP) transcription factors are sequence-specific DNA-binding proteins that regulate transcription. They are characterized by a 60-80 amino acid bZIP domain: a basic DNA binding domain followed by a leucine zipper dimerization domain. (Adapted from FBrf0152056).
Summary (Interactive Fly)

PAR-domain bZIP transcription factor - controls skeletal muscle genes during differentiation - regulates expression of the Tropomyosin I gene in somatic body-wall and pharyngeal muscles

Gene Model and Products
Number of Transcripts
13
Number of Unique Polypeptides
11

Please see the JBrowse view of Dmel\Pdp1 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

Low-frequency RNA-Seq exon junction(s) not annotated.

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

Stage-specific extension of 3' UTRs observed during embryogenesis (FBrf0215804); all variants may not be annotated.

Gene model reviewed during 5.45

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.46

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0076776
5065
270
FBtr0076782
4746
570
FBtr0076780
4702
647
FBtr0076775
2828
250
FBtr0076777
5107
284
FBtr0300499
3862
232
FBtr0300500
4643
633
FBtr0306535
6855
270
FBtr0332080
4197
581
FBtr0332081
5080
275
FBtr0332082
5098
281
FBtr0332083
2870
264
FBtr0346536
6398
270
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
FBpp0076491
30.4
270
7.15
FBpp0076497
63.2
570
7.62
FBpp0076495
70.0
647
7.96
FBpp0076490
28.3
250
6.80
FBpp0076492
31.9
284
8.45
FBpp0289726
26.0
232
6.52
FBpp0289727
68.4
633
7.54
FBpp0297493
30.4
270
7.15
FBpp0304390
64.4
581
8.37
FBpp0304391
30.9
275
6.80
FBpp0304392
31.6
281
8.45
FBpp0304393
29.9
264
8.09
FBpp0312154
30.4
270
7.15
Polypeptides with Identical Sequences

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

270 aa isoforms: Pdp1-PB, Pdp1-PK, Pdp1-PP
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
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\Pdp1 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
expression microarray
Stage
Tissue/Position (including subcellular localization)
Reference
adult brain

Comment: Pdp1 mRNA levels do not significantly differ between ZT4 and ZT16.

in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

organism

Comment: extended 3' UTR isoform

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
adult head

Comment: expression specific to isoforms Pdp1-RD, RJ

organism

Comment: circadian oscillating expression

Additional Descriptive Data

Expression oscillates with the circadian cycle and peaks at ZT16, with the peak becoming less pronounced as flies age. The relative amount of mRNA is less in bodies compared to heads.

Zygotic-specific isoforms of Pdp1 with long 3' UTR extensions were observed.

The Pdp1 isoforms Pdp1-RD and RJ, collectively referred in this paper as Pdp1-ε isoform, are detected in the heads of adult flies by RT-PCR. In conditions of constant darkness, the levels of both isoforms cycle, increasing gradually from CT02 until CT14, and decreasing after that until CT20.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
adult head

Comment: expression specific to isoforms Pdp1-PD, PJ

Additional Descriptive Data

The Pdp1 isoforms Pdp1-PD and PD, collectively referred in this paper as Pdp1-ε isoform, are detected in head extracts of adult flies by western blot. The isoform Pdp1-PJ is the predominant one. Both isoforms show a cycling behaviour, with levels gradually increasing from CT02 until CT18, and decrease after that until ZT22. Immunostaining reveals that at ZT20, Pdp1 protein is expressed in the dorsal and ventral lateral clock neurons (LNd and LNv) in the adult brain.

Pdp1 is predominantly nuclear at ZT18.

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\Pdp1 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
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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 ( 31 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pdp1
Transgenic constructs containing regulatory region of Pdp1
Deletions and Duplications ( 5 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (11)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
11 of 15
Yes
Yes
8 of 15
No
Yes
8 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
2  
1 of 15
No
No
1 of 15
No
No
2  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (9)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
8 of 15
No
Yes
8 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
Rattus norvegicus (Norway rat) (9)
11 of 13
Yes
Yes
8 of 13
No
Yes
8 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (10)
11 of 12
Yes
Yes
7 of 12
No
Yes
7 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
Danio rerio (Zebrafish) (18)
11 of 15
Yes
Yes
9 of 15
No
Yes
8 of 15
No
Yes
8 of 15
No
Yes
7 of 15
No
Yes
6 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (8)
6 of 15
Yes
Yes
5 of 15
No
Yes
3 of 15
No
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
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.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190E6R )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
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) ( EOG091508P5 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09GL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
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
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
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0HCL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
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) ( EOG091G0EO0 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (5)
4 of 10
2 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 ( 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.
    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
    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
    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 (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3L
    Recombination map

    3-21

    Cytogenetic map
    Sequence location
    3L:7,811,458..7,867,369 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    66A14-66A17
    Limits computationally determined from genome sequence between P{PZ}l(3)0721708223&P{EP}Rac2EP3118 and P{lacW}Nmtj1C7
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    66A12-66A17
    66A12-66A17
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (25)
    Genomic Clones (34)
    cDNA Clones (108)
     

    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)
    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 identity of: Pdp1 CG3129

    Source for database merge of

    Source for merge of: Pdp1 CG17888

    Source for merge of: Pdp1 anon-WO0140519.206

    Additional comments

    Source for merge of Pdp1 anon-WO0140519.206 was sequence comparison ( date:051113 ).

    Other Comments

    Pdp1 is sensitive to nutritional conditions, with two of its protein isoforms becoming upregulated in response to food withdrawal.

    Pdp1 is an essential clock gene. Pdp1 and vri, together with Clk, comprise a second feedback loop in the Drosophila clock.

    Identified as a gene with significant level of mRNA cycling as assessed by expression analysis using high density oligonucleotide arrays with probe generated from adult heads harvested over six time points over the course of a day. Showed cycling in Canton S and low expression in Clk mutants in microarray experiments. Identified in S2/cycloheximide assay as a direct target of Clk mediated transcriptional regulation.

    Pdp1 is likely to be involved in the transcriptional control of different developmental pathways through the use of differentially expressed Pdp1 isoforms.

    Pdp1 is involved in regulating expression of Tm2 gene in the somatic body wall and pharyngeal muscles by binding to DNA sequences within the muscle activator that are required for activator function. Results suggest Pdp1 may function as part of a large protein/DNA complex that interacts with Mef2 to regulate muscle gene transcription. Pdp1 may also be involved in terminal differentiation of the midgut endoderm, hindgut and Malpighian tubules, the epidermis and the central nervous system.

    Mutations that eliminate Pdp1 binding eliminate muscle activator function and severely reduce expression of a muscle activator.

    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 134 )
    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.
    UniProt/TrEMBL - Automatically annotated and unreviewed 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
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    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
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (31)
    Reported As
    Symbol Synonym
    PAR-domain protein 1
    anon-WO0140519.206
    Secondary FlyBase IDs
    • FBgn0035820
    • FBgn0044667
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (227)