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PRKD1 protein kinase D1 [ Homo sapiens (human) ]

Gene ID: 5587, updated on 5-Jan-2025

Summary

Official Symbol
PRKD1provided by HGNC
Official Full Name
protein kinase D1provided by HGNC
Primary source
HGNC:HGNC:9407
See related
Ensembl:ENSG00000184304 MIM:605435; AllianceGenome:HGNC:9407
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PKD; PKCM; CHDED; PRKCM; PKC-MU
Summary
The protein encoded by this gene is a serine/threonine protein kinase involved in many cellular processes, including Golgi body membrane integrity and transport, cell migration and differentiation, MAPK8/JNK1 and Ras pathway signaling, MAPK1/3 (ERK1/2) pathway signaling, cell survival, and regulation of cell shape and adhesion. [provided by RefSeq, Jan 2017]
Expression
Broad expression in testis (RPKM 3.2), prostate (RPKM 2.7) and 22 other tissues See more
Orthologs
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Genomic context

See PRKD1 in Genome Data Viewer
Location:
14q12
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (29576479..29927847, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (23774515..24125722, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (30045685..30397053, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724934 Neighboring gene VISTA enhancer hs566 Neighboring gene VISTA enhancer hs1539 Neighboring gene VISTA enhancer hs1168 Neighboring gene VISTA enhancers hs342 and hs1523 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:29923477-29924033 Neighboring gene VISTA enhancer hs598 Neighboring gene RNA, U11 small nuclear 5, pseudogene Neighboring gene uncharacterized LOC124903297 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:30132632-30133196 Neighboring gene RNA, U6 small nuclear 1234, pseudogene Neighboring gene uncharacterized LOC105370429 Neighboring gene ribosomal protein S6 pseudogene 24

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Congenital heart defects and ectodermal dysplasia
MedGen: C4479250 OMIM: 617364 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
EBI GWAS Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies protein kinase D1, a member of the protein kinase C family (cytosolic serine/threonine kinase), is important for HIV-1 replication PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat Sulfated polymannuroguluronate (SPMG) potently arrests HIV-1 Tat-triggered protein kinase C (PKC)-dependent PKC-mu activation PubMed
tat Phospholipase C/protein kinase C signaling pathway-dependent phosphorylation of p44/42 and JNK MAP kinases participates partially in IL-1beta induction by TAT PubMed
tat Protein kinase C is required for HIV-1 Tat-mediated transactivation of the viral LTR promoter, indicating protein kinase C regulates the process of HIV-1 transactivation and may play a role in the transition of HIV from latency to productive growth PubMed
tat Protein kinase C phosphorylates HIV-1 Tat on serine residue 46 PubMed
tat HIV-1 Tat activates protein kinase C, resulting in the induction of TNF-alpha, IL-6 and IL-10 expression and the secretion of MCP-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding  
enables calcium,diacylglycerol-dependent serine/threonine kinase activity  
enables diacylglycerol-dependent serine/threonine kinase activity PubMed 
enables diacylglycerol-dependent serine/threonine kinase activity  
enables diacylglycerol-dependent, calcium-independent serine/threonine kinase activity  
enables heat shock protein binding  
enables identical protein binding PubMed 
enables kinase activity PubMed 
enables metal ion binding  
enables phosphatidylinositol 3-kinase activator activity PubMed 
enables protein binding PubMed 
enables protein kinase C binding  
enables protein serine kinase activity PubMed 
enables protein serine/threonine kinase activity  
enables protein serine/threonine kinase activity PubMed 
enables protein serine/threonine kinase activity PubMed 
enables protein serine/threonine kinase activity PubMed 
Items 1 - 25 of 59
Process Evidence Code Pubs
involved_in Golgi organization PubMed 
involved_in Golgi vesicle transport  
involved_in angiogenesis  
involved_in apoptotic process  
involved_in cell differentiation  
involved_in cellular response to amino acid starvation PubMed 
involved_in cellular response to angiotensin  
involved_in cellular response to endothelin  
involved_in cellular response to hydroperoxide PubMed 
involved_in cellular response to norepinephrine stimulus  
involved_in cellular response to oxidative stress PubMed 
involved_in cellular response to phorbol 13-acetate 12-myristate  
involved_in cellular response to vascular endothelial growth factor stimulus PubMed 
involved_in cellular response to vascular endothelial growth factor stimulus PubMed 
involved_in defense response to Gram-negative bacterium  
involved_in inflammatory response  
involved_in innate immune response  
involved_in integrin-mediated signaling pathway PubMed 
involved_in intracellular signal transduction  
involved_in intracellular signal transduction PubMed 
involved_in negative regulation of endocytosis PubMed 
involved_in nervous system development  
involved_in peptidyl-serine phosphorylation PubMed 
involved_in peptidyl-threonine phosphorylation PubMed 
acts_upstream_of peptidyl-threonine phosphorylation  
involved_in phospholipase C-activating G protein-coupled receptor signaling pathway  
involved_in positive regulation of NF-kappaB transcription factor activity PubMed 
involved_in positive regulation of NLRP3 inflammasome complex assembly  
involved_in positive regulation of angiogenesis PubMed 
involved_in positive regulation of angiogenesis PubMed 
involved_in positive regulation of autophagy PubMed 
involved_in positive regulation of blood vessel endothelial cell migration PubMed 
involved_in positive regulation of blood vessel endothelial cell migration PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction PubMed 
involved_in positive regulation of cell size  
involved_in positive regulation of endothelial cell chemotaxis PubMed 
involved_in positive regulation of endothelial cell chemotaxis PubMed 
involved_in positive regulation of endothelial cell migration PubMed 
involved_in positive regulation of endothelial cell proliferation PubMed 
involved_in positive regulation of gene expression  
involved_in positive regulation of neuron projection development PubMed 
involved_in positive regulation of osteoblast differentiation  
involved_in positive regulation of peptide hormone secretion  
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction PubMed 
involved_in positive regulation of protein export from nucleus  
involved_in positive regulation of protein import into nucleus  
involved_in positive regulation of sarcomere organization  
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in positive regulation of transcription by RNA polymerase II PubMed 
involved_in protein autophosphorylation PubMed 
involved_in protein autophosphorylation PubMed 
involved_in regulation of integrin-mediated signaling pathway PubMed 
involved_in regulation of keratinocyte proliferation  
involved_in regulation of release of sequestered calcium ion into cytosol  
involved_in regulation of skeletal muscle contraction by modulation of calcium ion sensitivity of myofibril  
involved_in signal transduction PubMed 
involved_in sphingolipid biosynthetic process  
involved_in vascular endothelial growth factor receptor signaling pathway PubMed 
involved_in vascular endothelial growth factor receptor signaling pathway PubMed 
Items 1 - 25 of 59
Component Evidence Code Pubs
located_in Golgi apparatus PubMed 
located_in Z disc  
located_in autophagosome membrane PubMed 
located_in cell cortex  
located_in cell-cell junction  
is_active_in cytosol  
located_in cytosol  
located_in cytosol  
located_in cytosol  
located_in nucleus  
located_in perinuclear region of cytoplasm  
located_in plasma membrane  
located_in trans-Golgi network PubMed 

General protein information

Preferred Names
serine/threonine-protein kinase D1
Names
nPKC-D1
nPKC-mu
protein kinase C mu type
protein kinase C, mu
protein kinase D
NP_001316998.1
NP_001335319.1
NP_002733.2
XP_011535267.1
XP_047287545.1
XP_047287546.1
XP_054232371.1
XP_054232372.1
XP_054232373.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052879.1 RefSeqGene

    Range
    4847..356215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001330069.2NP_001316998.1  serine/threonine-protein kinase D1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL135858, AL355053, AL356756
    Consensus CDS
    CCDS81796.1
    UniProtKB/TrEMBL
    F8WBA3, Q1KKQ2
    Related
    ENSP00000390535.2, ENST00000415220.6
    Conserved Domains (5) summary
    smart00220
    Location:595847
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd00029
    Location:279328
    C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
    cd01239
    Location:424551
    PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
    cd14082
    Location:587846
    STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
    pfam00130
    Location:147196
    C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
  2. NM_001348390.1NP_001335319.1  serine/threonine-protein kinase D1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL135858, AL355053, AL356756
    UniProtKB/TrEMBL
    Q1KKQ2
    Conserved Domains (4) summary
    cd00029
    Location:183232
    C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
    cd01239
    Location:328455
    PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
    cd14082
    Location:491750
    STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
    pfam00130
    Location:51100
    C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
  3. NM_002742.3NP_002733.2  serine/threonine-protein kinase D1 isoform 2

    See identical proteins and their annotated locations for NP_002733.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 2
    Source sequence(s)
    AL355053, BX645735, CN412379, X75756
    Consensus CDS
    CCDS9637.1
    UniProtKB/Swiss-Prot
    A6NL64, B2RAF6, Q15139
    UniProtKB/TrEMBL
    Q1KKQ2
    Related
    ENSP00000333568.6, ENST00000331968.11
    Conserved Domains (5) summary
    smart00220
    Location:587839
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd00029
    Location:271320
    C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
    cd01239
    Location:416543
    PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
    cd14082
    Location:579838
    STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
    pfam00130
    Location:147196
    C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    29576479..29927847 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431589.1XP_047287545.1  serine/threonine-protein kinase D1 isoform X1

    UniProtKB/TrEMBL
    Q1KKQ2
    Related
    ENST00000616995.5
  2. XM_011536965.3XP_011535267.1  serine/threonine-protein kinase D1 isoform X2

    UniProtKB/TrEMBL
    Q1KKQ2
    Conserved Domains (4) summary
    cd00029
    Location:183232
    C1; Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second ...
    cd01239
    Location:328455
    PH_PKD; Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain
    cd14082
    Location:491750
    STKc_PKD; Catalytic domain of the Serine/Threonine kinase, Protein Kinase D
    pfam00130
    Location:51100
    C1_1; Phorbol esters/diacylglycerol binding domain (C1 domain)
  3. XM_047431590.1XP_047287546.1  serine/threonine-protein kinase D1 isoform X3

    UniProtKB/TrEMBL
    Q1KKQ2

RNA

  1. XR_943493.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    23774515..24125722 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376396.1XP_054232371.1  serine/threonine-protein kinase D1 isoform X1

    UniProtKB/TrEMBL
    Q1KKQ2
  2. XM_054376397.1XP_054232372.1  serine/threonine-protein kinase D1 isoform X2

    UniProtKB/TrEMBL
    Q1KKQ2
  3. XM_054376398.1XP_054232373.1  serine/threonine-protein kinase D1 isoform X3

    UniProtKB/TrEMBL
    Q1KKQ2

RNA

  1. XR_008488884.1 RNA Sequence

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