FB2022_03, released June 9, 2022

Gene: Dmel\PKD

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General Information
Symbol
Dmel\PKD
Species
D. melanogaster
Name
Protein Kinase D
Annotation Symbol
CG7125
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038603
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
Protein Kinase D (PKD) encodes a Ser/Thr kinase of the PKC family of Ca[2+]/calmodulin-dependent protein kinases. It regulates actin-dynamics by controlling the activity of the phosphatase encoded by ssh. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

PKCm, dPKD

Key Links
Genomic Location
Cytogenetic map
91A2-91A2
Sequence location
Recombination map
3-63
RefSeq locus
NT_033777 REGION:18303279..18314407
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 (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables ATP binding
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
enables protein serine/threonine kinase activity
inferred from electronic annotation with InterPro:IPR015727
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein kinase D signaling
inferred from biological aspect of ancestor with PANTHER:PTN000540182
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in protein phosphorylation
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Maier et al., 2006)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Protein Kinase D (PKD) encodes a Ser/Thr kinase of the PKC family of Ca[2+]/calmodulin-dependent protein kinases. It regulates actin-dynamics by controlling the activity of the phosphatase encoded by ssh. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASES -
The Calcium/Calmodulin-dependent kinase family are serine/threonine kinases which, in general, prefer substrates containing basic residues. Many, but not all, members are regulated by calcium or calmodulin. (Adapted from FBrf0132098).
Gene Model and Products
Number of Transcripts
9
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\PKD 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 A0A0B4KHC3)

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

Gene model reviewed during 5.44

Stop-codon suppression (UGA) postulated; FBrf0216885.

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

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 5.48

A non-AUG start codon may be used for translation of one or more transcripts of this gene; based on the presence of conserved protein signatures within the 5' UTR without an in-frame AUG (FBrf0243886).

Sequence Ontology: Class of Gene
gene_with_stop_codon_read_through
(Jungreis, 2011.11.18)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
PKD-RA
FBtr0083589
NM_142453
3744
836
PKD-RB
FBtr0083590
NM_169803
3634
836
PKD-RC
FBtr0083591
NM_169804
3643
836
PKD-RD
FBtr0083592
NM_169805
3662
836
PKD-RE
FBtr0290023
NM_001144602
3611
836
PKD-RF
FBtr0330312
NM_001275775
3708
836
PKD-RG
FBtr0330313
NM_001275776
3634
906
PKD-RH
FBtr0337036
NM_001275777
1427
212
PKD-RI
FBtr0337037
NM_001275778
1537
212
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
UniProt
RefSeq ID
GenBank
PKD-PA
FBpp0083010
93.6
836
7.10
Q9VE91
NP_650710
AAF55536
PKD-PB
FBpp0083011
93.6
836
7.10
Q9VE91
NP_732325
AAN13769
PKD-PC
FBpp0083012
93.6
836
7.10
Q9VE91
NP_732326
AAF55537
PKD-PD
FBpp0083013
93.6
836
7.10
Q9VE91
NP_732327
AAN13770
PKD-PE
FBpp0288462
93.6
836
7.10
Q9VE91
NP_001138074
ACL83532
PKD-PF
FBpp0303344
93.6
836
7.10
Q9VE91
NP_001262704
AGB96084
PKD-PG
FBpp0303345
101.3
906
7.13
A0A0B4KHC3
NP_001262705
AGB96085
PKD-PH
FBpp0307965
23.4
212
6.76
A0A0B4KGF0
NP_001262706
AGB96086
PKD-PI
FBpp0307966
23.4
212
6.76
A0A0B4KGF0
NP_001262707
AGB96087
Polypeptides with Identical Sequences

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

836 aa isoforms: PKD-PA, PKD-PB, PKD-PC, PKD-PD, PKD-PE, PKD-PF
212 aa isoforms: PKD-PH, PKD-PI
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
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\PKD 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 the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. 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
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Maier et al., 2006)
Expression Deduced from Reporters
Reporter: Mi{Trojan-GAL4.0}PKDMI09308-TG4.0
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult brain | restricted
(Lee et al., 2018)
adult mushroom body
(Lee et al., 2018)
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\PKD 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
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 ( 7 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of PKD
Transgenic constructs containing regulatory region of PKD
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel6178
(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
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal oxidative stress response | adult stage
short lived | male limited
Phenotype manifest in
Allele
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
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\PRKD1
13 of 15
Yes
Yes
2  
Hsap\PRKD3
13 of 15
Yes
Yes
1  
Hsap\PRKD2
12 of 15
No
Yes
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
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\Prkd1
13 of 15
Yes
Yes
Mmus\Prkd3
13 of 15
Yes
Yes
Mmus\Prkd2
11 of 15
No
Yes
Rattus norvegicus (Norway rat) (3)
Rnor\Prkd2
11 of 13
Yes
Yes
Rnor\Prkd3
11 of 13
Yes
Yes
Rnor\Prkd1
9 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\prkd1
7 of 12
Yes
Yes
Xtro\prkd3
6 of 12
No
Yes
Danio rerio (Zebrafish) (6)
Drer\prkd3
13 of 15
Yes
Yes
Drer\prkd1
12 of 15
No
Yes
Drer\prkd4
7 of 15
No
Yes
Drer\prkd2
3 of 15
No
Yes
Drer\LOC797974
1 of 15
No
Yes
Drer\pimr213
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\dkf-2
15 of 15
Yes
Yes
Cele\dkf-1
7 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (8)
Atha\AT4G10010
1 of 9
Yes
No
Atha\CPK1
1 of 9
Yes
No
Atha\CPK2
1 of 9
Yes
No
Atha\CPK17
1 of 9
Yes
No
Atha\CPK25
1 of 9
Yes
No
Atha\CPK27
1 of 9
Yes
No
Atha\CPK31
1 of 9
Yes
No
Atha\CRK
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\CLA4
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\bzz1
1 of 12
Yes
No
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?
    PRKD1; protein kinase D1
    13 of 15
    605435
       
      PRKD3; protein kinase D3
      13 of 15
      607077
           
          PRKD2; protein kinase D2
          12 of 15
          607074
               
              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
              Interactions Browser
              Summary of Genetic Interactions
              esyN Network Diagram
              Starting gene(s)
              Interaction type
              Interacting gene(s)
              Reference
              Starting gene(s)
              Interaction type
              Interacting gene(s)
              Reference
              External Data
              Linkouts
              DroID - A comprehensive database of gene and protein interactions.
              Pathways
              Signaling Pathways (FlyBase)
              Metabolic Pathways
              External Data
              Linkouts
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              Genomic Location and Detailed Mapping Data
              Chromosome (arm)
              3R
              Recombination map
              3-63
              Cytogenetic map
              91A2-91A2
              Sequence location
              FlyBase Computed Cytological Location
              Cytogenetic map
              Evidence for location
              91A2-91A2
              Limits computationally determined from genome sequence between P{EP}Dlc90FEP3634 and P{PZ}sprd05284
              Experimentally Determined Cytological Location
              Cytogenetic map
              Notes
              References
              Experimentally Determined Recombination Data
              Location

              3-63

              (FlyBase, 2016)

              3-62.3

              (Comeron et al., 2012)
              Left of (cM)
              Right of (cM)
              Notes
              Stocks and Reagents
              Stocks (10)
              Genomic Clones (34)
              cDNA Clones (350)
               

              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
                 
                Commercially Available Antibodies
                 
                Other Information
                Relationship to Other Genes
                Source for database identify of

                Source for identity of: PKD CG7125

                (Maier, 2005.9.6)
                Source for database merge of
                Additional comments
                Other Comments
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 66 )
                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.
                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
                SignaLink - A signaling pathway resource with multi-layered regulatory networks.
                Linkouts
                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
                Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                Synonyms and Secondary IDs (8)
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (0)
                Result
                Result Type
                Title
                References (63)