Human Gene PRKD3 (uc002rqd.3) Description and Page Index
  Description: Homo sapiens protein kinase D3 (PRKD3), mRNA.
RefSeq Summary (NM_005813): This gene belongs to the multigene protein kinase D family of serine/threonine kinases, which bind diacylglycerol and phorbol esters. Members of this family are characterized by an N-terminal regulatory domain comprised of a tandem repeat of cysteine-rich zinc-finger motifs and a pleckstrin domain. The C-terminal region contains the catalytic domain and is distantly related to calcium-regulated kinases. Catalytic activity of this enzyme promotes its nuclear localization. This protein has been implicated in a variety of functions including negative regulation of human airway epithelial barrier formation, growth regulation of breast and prostate cancer cells, and vesicle trafficking. [provided by RefSeq, Jan 2015]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AB015982.2, SRR1660807.200070.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000234179.7/ ENSP00000234179.2 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:37,477,646-37,544,222 Size: 66,577 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr2:37,480,320-37,543,667 Size: 63,348 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:37,477,646-37,544,222)mRNA (may differ from genome)Protein (890 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: KPCD3_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein kinase D3; EC=2.7.11.13; AltName: Full=Protein kinase C nu type; AltName: Full=Protein kinase EPK2; AltName: Full=nPKC-nu;
FUNCTION: Converts transient diacylglycerol (DAG) signals into prolonged physiological effects, downstream of PKC. Involved in resistance to oxidative stress (By similarity).
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
COFACTOR: Magnesium (By similarity).
ENZYME REGULATION: Activated by DAG and phorbol esters. Phorbol- ester/DAG-type domains 1 and 2 bind both DAG and phorbol ester with high affinity and mediate translocation to the cell membrane. Autophosphorylation of Ser-735 and phosphorylation of Ser-731 by PKC relieves auto-inhibition by the PH domain.
INTERACTION: P63027:VAMP2; NbExp=7; IntAct=EBI-1255366, EBI-520113;
SUBCELLULAR LOCATION: Cytoplasm. Membrane. Note=Translocation to the cell membrane is required for kinase activation.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. PKD subfamily.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 2 phorbol-ester/DAG-type zinc fingers.
SIMILARITY: Contains 1 protein kinase domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PRKD3
CDC HuGE Published Literature: PRKD3
Positive Disease Associations: Bipolar Disorder
Related Studies:
  1. Bipolar Disorder
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.46 RPKM in Testis
Total median expression: 235.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -114.72555-0.207 Picture PostScript Text
3' UTR -686.612674-0.257 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR020454 - DAG/PE-bd
IPR011009 - Kinase-like_dom
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR002219 - Prot_Kinase_C-like_PE/DAG-bd
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR015727 - Protein_Kinase_C_mu-related
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain
PF00130 - Phorbol esters/diacylglycerol binding domain (C1 domain)
PF00169 - PH domain
PF06293 - Lipopolysaccharide kinase (Kdo/WaaP) family
PF07714 - Protein tyrosine kinase
PF14531 - Kinase-like

SCOP Domains:
50729 - PH domain-like
56112 - Protein kinase-like (PK-like)
57889 - Cysteine-rich domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2D9Z
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on O94806
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004697 protein kinase C activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006468 protein phosphorylation
GO:0007205 protein kinase C-activating G-protein coupled receptor signaling pathway
GO:0016310 phosphorylation
GO:0030148 sphingolipid biosynthetic process
GO:0035556 intracellular signal transduction
GO:0089700 protein kinase D signaling

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  KJ904699 - Synthetic construct Homo sapiens clone ccsbBroadEn_14093 PRKD3-like gene, encodes complete protein.
KJ905441 - Synthetic construct Homo sapiens clone ccsbBroadEn_15023 PRKD3 gene, encodes complete protein.
KX533497 - Homo sapiens serine/threonine-protein kinase D3 (PRKD3) mRNA, complete cds.
AB015982 - Homo sapiens EPK2 mRNA for serine/threonine kinase, complete cds.
LF210931 - JP 2014500723-A/18434: Polycomb-Associated Non-Coding RNAs.
AK027585 - Homo sapiens cDNA FLJ14679 fis, clone NT2RP2004232, highly similar to Serine/threonine-protein kinase D3 (EC 2.7.11.13).
AK122883 - Homo sapiens cDNA FLJ16531 fis, clone OCBBF2026144, highly similar to Protein kinase C, nu type (EC 2.7.1.-).
Z25429 - H.sapiens protein-serine/threonine kinase gene, complete CDS.
MA446508 - JP 2018138019-A/18434: Polycomb-Associated Non-Coding RNAs.
JD393713 - Sequence 374737 from Patent EP1572962.
JD566430 - Sequence 547454 from Patent EP1572962.
JD294844 - Sequence 275868 from Patent EP1572962.
LF342184 - JP 2014500723-A/149687: Polycomb-Associated Non-Coding RNAs.
LF342185 - JP 2014500723-A/149688: Polycomb-Associated Non-Coding RNAs.
JD237529 - Sequence 218553 from Patent EP1572962.
JD348441 - Sequence 329465 from Patent EP1572962.
LF342186 - JP 2014500723-A/149689: Polycomb-Associated Non-Coding RNAs.
JD242969 - Sequence 223993 from Patent EP1572962.
JD136574 - Sequence 117598 from Patent EP1572962.
LF342187 - JP 2014500723-A/149690: Polycomb-Associated Non-Coding RNAs.
JD113683 - Sequence 94707 from Patent EP1572962.
JD374104 - Sequence 355128 from Patent EP1572962.
JD280056 - Sequence 261080 from Patent EP1572962.
JD184955 - Sequence 165979 from Patent EP1572962.
JD219511 - Sequence 200535 from Patent EP1572962.
JD296401 - Sequence 277425 from Patent EP1572962.
JD370928 - Sequence 351952 from Patent EP1572962.
JD274313 - Sequence 255337 from Patent EP1572962.
JD241231 - Sequence 222255 from Patent EP1572962.
JD511061 - Sequence 492085 from Patent EP1572962.
JD348938 - Sequence 329962 from Patent EP1572962.
JD146723 - Sequence 127747 from Patent EP1572962.
JD231187 - Sequence 212211 from Patent EP1572962.
JD369479 - Sequence 350503 from Patent EP1572962.
LF342188 - JP 2014500723-A/149691: Polycomb-Associated Non-Coding RNAs.
LF342189 - JP 2014500723-A/149692: Polycomb-Associated Non-Coding RNAs.
MA577761 - JP 2018138019-A/149687: Polycomb-Associated Non-Coding RNAs.
MA577762 - JP 2018138019-A/149688: Polycomb-Associated Non-Coding RNAs.
MA577763 - JP 2018138019-A/149689: Polycomb-Associated Non-Coding RNAs.
MA577764 - JP 2018138019-A/149690: Polycomb-Associated Non-Coding RNAs.
MA577765 - JP 2018138019-A/149691: Polycomb-Associated Non-Coding RNAs.
MA577766 - JP 2018138019-A/149692: Polycomb-Associated Non-Coding RNAs.
BC030706 - Homo sapiens protein kinase D3, mRNA (cDNA clone MGC:33062 IMAGE:5266769), complete cds.
JF432526 - Synthetic construct Homo sapiens clone IMAGE:100073748 protein kinase D3 (PRKD3) gene, encodes complete protein.
LF342190 - JP 2014500723-A/149693: Polycomb-Associated Non-Coding RNAs.
LF342193 - JP 2014500723-A/149696: Polycomb-Associated Non-Coding RNAs.
BC012820 - Homo sapiens protein kinase D3, mRNA (cDNA clone IMAGE:3028450).
LF342195 - JP 2014500723-A/149698: Polycomb-Associated Non-Coding RNAs.
LF342201 - JP 2014500723-A/149704: Polycomb-Associated Non-Coding RNAs.
LF342202 - JP 2014500723-A/149705: Polycomb-Associated Non-Coding RNAs.
LF342204 - JP 2014500723-A/149707: Polycomb-Associated Non-Coding RNAs.
LF342208 - JP 2014500723-A/149711: Polycomb-Associated Non-Coding RNAs.
LF342209 - JP 2014500723-A/149712: Polycomb-Associated Non-Coding RNAs.
LF342210 - JP 2014500723-A/149713: Polycomb-Associated Non-Coding RNAs.
LF342211 - JP 2014500723-A/149714: Polycomb-Associated Non-Coding RNAs.
JD350679 - Sequence 331703 from Patent EP1572962.
JD547366 - Sequence 528390 from Patent EP1572962.
JD358781 - Sequence 339805 from Patent EP1572962.
LF342212 - JP 2014500723-A/149715: Polycomb-Associated Non-Coding RNAs.
MA577767 - JP 2018138019-A/149693: Polycomb-Associated Non-Coding RNAs.
MA577770 - JP 2018138019-A/149696: Polycomb-Associated Non-Coding RNAs.
MA577772 - JP 2018138019-A/149698: Polycomb-Associated Non-Coding RNAs.
MA577778 - JP 2018138019-A/149704: Polycomb-Associated Non-Coding RNAs.
MA577779 - JP 2018138019-A/149705: Polycomb-Associated Non-Coding RNAs.
MA577781 - JP 2018138019-A/149707: Polycomb-Associated Non-Coding RNAs.
MA577785 - JP 2018138019-A/149711: Polycomb-Associated Non-Coding RNAs.
MA577786 - JP 2018138019-A/149712: Polycomb-Associated Non-Coding RNAs.
MA577787 - JP 2018138019-A/149713: Polycomb-Associated Non-Coding RNAs.
MA577788 - JP 2018138019-A/149714: Polycomb-Associated Non-Coding RNAs.
MA577789 - JP 2018138019-A/149715: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O94806 (Reactome details) participates in the following event(s):

R-HSA-429698 PRKD1,2,3 phosphorylates COL4A3BP-2
R-HSA-1660661 Sphingolipid de novo biosynthesis
R-HSA-428157 Sphingolipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: D6W587, EPK2, KPCD3_HUMAN, NM_005813, NP_005804, O94806, PRKCN, Q53TR7, Q8NEL8
UCSC ID: uc002rqd.3
RefSeq Accession: NM_005813
Protein: O94806 (aka KPCD3_HUMAN)
CCDS: CCDS1789.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005813.3
exon count: 18CDS single in 3' UTR: no RNA size: 5907
ORF size: 2673CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 5153.00frame shift in genome: no % Coverage: 99.92
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.