Aliases for PKDCC Gene

Aliases for PKDCC Gene

  • Protein Kinase Domain Containing, Cytoplasmic 2 3 5
  • Vertebrate Lonesome Kinase 2 3 4
  • Protein Kinase Domain-Containing Protein, Cytoplasmic 3 4
  • Extracellular Tyrosine-Protein Kinase PKDCC 3 4
  • Protein Kinase-Like Protein SgK493 3 4
  • Sugen Kinase 493 3 4
  • SGK493 3 4
  • Vlk 2 3
  • Protein Kinase Domain Containing, Cytoplasmic Homolog (Mouse) 2
  • Protein Kinase Domain Containing, Cytoplasmic Homolog 3
  • EC 2.7.10.2 4
  • SgK493 2
  • RLSDF 3
  • PKDCC 5
  • VLK 4

External Ids for PKDCC Gene

Previous GeneCards Identifiers for PKDCC Gene

  • GC02P042130
  • GC02P042275
  • GC02P041976

Summaries for PKDCC Gene

GeneCards Summary for PKDCC Gene

PKDCC (Protein Kinase Domain Containing, Cytoplasmic) is a Protein Coding gene. Diseases associated with PKDCC include Rhizomelic Limb Shortening With Dysmorphic Features. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and non-membrane spanning protein tyrosine kinase activity. An important paralog of this gene is MAP3K7.

UniProtKB/Swiss-Prot Summary for PKDCC Gene

  • Secreted tyrosine-protein kinase that mediates phosphorylation of extracellular proteins and endogenous proteins in the secretory pathway, which is essential for patterning at organogenesis stages. Mediates phosphorylation of MMP1, MMP13, MMP14, MMP19 and ERP29 (PubMed:25171405). Probably plays a role in platelets: rapidly and quantitatively secreted from platelets in response to stimulation of platelet degranulation (PubMed:25171405). May also have serine/threonine protein kinase activity. Required for longitudinal bone growth through regulation of chondrocyte differentiation. May be indirectly involved in protein transport from the Golgi apparatus to the plasma membrane (By similarity).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PKDCC Gene

Genomics for PKDCC Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PKDCC Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J042045 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 606.4 +7.1 7140 20.6 HNRNPL GATAD2A CTCF ATF7 TEAD4 PRDM10 ZNF629 TFE3 SOX13 IKZF1 PKDCC HSALNG0014455 EML4 C2orf91 HSALNG0014452 lnc-PKDCC-1
GH02J041930 Enhancer 1.6 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 21.7 -115.5 -115520 5.4 RELA ZIC2 REST PKNOX1 EP300 SCRT2 EED CEBPB SP1 DPF2 lnc-PKDCC-5 C2orf91 PKDCC LINC01914
GH02J041878 Promoter/Enhancer 1.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 19.3 -169.0 -168991 3.9 REST ZIC2 SP1 ZNF341 FOXA2 CEBPB ZNF423 NFYB POLR2A RAD21 LINC01913 lnc-C2orf91-2 lnc-C2orf91-6 PKDCC C2orf91 RF01045-063 LINC01914
GH02J042100 Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 15.7 +57.2 57192 9.2 SP1 HNRNPL GATAD2A ATF7 TEAD4 TFE3 SOX13 KDM1A RCOR2 BACH1 EML4 PKDCC EML4-AS1 COX7A2L lnc-C2orf91-4 lnc-PKDCC-9
GH02J041925 Enhancer 1 Ensembl ENCODE dbSUPER 21.2 -120.4 -120421 3.6 SP1 NR3C1 CEBPB FOS JUN RCOR1 JUND FOSL1 MAX NR2F2 PKDCC LINC01914 C2orf91 lnc-PKDCC-5 RF01045-063
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PKDCC on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PKDCC

Genomic Locations for PKDCC Gene

Genomic Locations for PKDCC Gene
chr2:42,048,021-42,058,517
(GRCh38/hg38)
Size:
10,497 bases
Orientation:
Plus strand
chr2:42,275,160-42,285,668
(GRCh37/hg19)
Size:
10,509 bases
Orientation:
Plus strand

Genomic View for PKDCC Gene

Genes around PKDCC on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PKDCC Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PKDCC Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PKDCC Gene

Proteins for PKDCC Gene

  • Protein details for PKDCC Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q504Y2-PKDCC_HUMAN
    Recommended name:
    Extracellular tyrosine-protein kinase PKDCC
    Protein Accession:
    Q504Y2
    Secondary Accessions:
    • D6W5A0
    • Q96I09

    Protein attributes for PKDCC Gene

    Size:
    493 amino acids
    Molecular mass:
    54132 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH94697.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAI10514.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAI10515.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for PKDCC Gene

Post-translational modifications for PKDCC Gene

  • N-glycosylated.
  • Phosphorylated on tyrosines; probably via autophosphorylation.
  • Glycosylation at Asn137, Asn320, Asn369, Asn400, Asn460, and Asn484
  • Modification sites at PhosphoSitePlus

Other Protein References for PKDCC Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Boster Bio Antibodies for PKDCC
  • Santa Cruz Biotechnology (SCBT) Antibodies for PKDCC

No data available for DME Specific Peptides for PKDCC Gene

Domains & Families for PKDCC Gene

Gene Families for PKDCC Gene

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted secreted proteins

Protein Domains for PKDCC Gene

Suggested Antigen Peptide Sequences for PKDCC Gene

GenScript: Design optimal peptide antigens:
  • Vertebrate lonesome kinase (PKDCC_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q504Y2

UniProtKB/Swiss-Prot:

PKDCC_HUMAN :
  • Belongs to the protein kinase superfamily.
Family:
  • Belongs to the protein kinase superfamily.
genes like me logo Genes that share domains with PKDCC: view

Function for PKDCC Gene

Molecular function for PKDCC Gene

UniProtKB/Swiss-Prot Function:
Secreted tyrosine-protein kinase that mediates phosphorylation of extracellular proteins and endogenous proteins in the secretory pathway, which is essential for patterning at organogenesis stages. Mediates phosphorylation of MMP1, MMP13, MMP14, MMP19 and ERP29 (PubMed:25171405). Probably plays a role in platelets: rapidly and quantitatively secreted from platelets in response to stimulation of platelet degranulation (PubMed:25171405). May also have serine/threonine protein kinase activity. Required for longitudinal bone growth through regulation of chondrocyte differentiation. May be indirectly involved in protein transport from the Golgi apparatus to the plasma membrane (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]; Xref=Rhea:RHEA:10596, Rhea:RHEA-COMP:10136, Rhea:RHEA-COMP:10137, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:46858, ChEBI:CHEBI:82620, ChEBI:CHEBI:456216; EC=2.7.10.2; Evidence={ECO:0000269|PubMed:25171405};.

Enzyme Numbers (IUBMB) for PKDCC Gene

Phenotypes From GWAS Catalog for PKDCC Gene

Gene Ontology (GO) - Molecular Function for PKDCC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0004672 protein kinase activity ISS --
GO:0004713 protein tyrosine kinase activity IEA --
GO:0004715 non-membrane spanning protein tyrosine kinase activity IEA,IDA 25171405
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with PKDCC: view
genes like me logo Genes that share phenotypes with PKDCC: view

Animal Models for PKDCC Gene

MGI Knock Outs for PKDCC:

Animal Model Products

CRISPR Products

miRNA for PKDCC Gene

miRTarBase miRNAs that target PKDCC

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PKDCC

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PKDCC Gene

Localization for PKDCC Gene

Subcellular locations from UniProtKB/Swiss-Prot for PKDCC Gene

Secreted. Golgi apparatus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PKDCC gene
Compartment Confidence
extracellular 5
golgi apparatus 4
cytoskeleton 2
mitochondrion 2
cytosol 2
plasma membrane 1
nucleus 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PKDCC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA,IDA 25171405
GO:0005794 Golgi apparatus ISS --
genes like me logo Genes that share ontologies with PKDCC: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PKDCC Gene

Pathways & Interactions for PKDCC Gene

PathCards logo

SuperPathways for PKDCC Gene

No Data Available

Gene Ontology (GO) - Biological Process for PKDCC Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA --
GO:0001503 ossification IEA --
GO:0006468 protein phosphorylation IEA --
GO:0007275 multicellular organism development IEA --
GO:0015031 protein transport IEA --
genes like me logo Genes that share ontologies with PKDCC: view

No data available for Pathways by source and SIGNOR curated interactions for PKDCC Gene

Drugs & Compounds for PKDCC Gene

No Compound Related Data Available

Transcripts for PKDCC Gene

mRNA/cDNA for PKDCC Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PKDCC

Alternative Splicing Database (ASD) splice patterns (SP) for PKDCC Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - - - -
SP2: -
SP3: -
SP4:

Relevant External Links for PKDCC Gene

GeneLoc Exon Structure for
PKDCC

Expression for PKDCC Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PKDCC Gene

mRNA differential expression in normal tissues according to GTEx for PKDCC Gene

This gene is overexpressed in Muscle - Skeletal (x4.1).

Protein differential expression in normal tissues from HIPED for PKDCC Gene

This gene is overexpressed in Pancreatic juice (32.0), Heart (17.6), and NK cells (16.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PKDCC Gene



Protein tissue co-expression partners for PKDCC Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PKDCC

SOURCE GeneReport for Unigene cluster for PKDCC Gene:

Hs.408542

mRNA Expression by UniProt/SwissProt for PKDCC Gene:

Q504Y2-PKDCC_HUMAN
Tissue specificity: Highly expressed in platelets.

Evidence on tissue expression from TISSUES for PKDCC Gene

  • Muscle(4.5)
  • Nervous system(2.3)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with PKDCC: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PKDCC Gene

Orthologs for PKDCC Gene

This gene was present in the common ancestor of chordates.

Orthologs for PKDCC Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PKDCC 30 31
  • 99.59 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PKDCC 30 31
  • 92.06 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PKDCC 30 31
  • 91.86 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pkdcc 30 17 31
  • 90.53 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PKDCC 31
  • 90 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pkdcc 30
  • 89.65 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia PKDCC 31
  • 74 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LOC421390 30
  • 70.52 (n)
PKDCC 31
  • 57 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PKDCC 31
  • 76 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pkdcc.2 30
  • 69.06 (n)
Zebrafish
(Danio rerio)
Actinopterygii si:ch211-239i4.3 30
  • 61.48 (n)
PKDCC 31
  • 55 (a)
OneToOne
Species where no ortholog for PKDCC was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PKDCC Gene

ENSEMBL:
Gene Tree for PKDCC (if available)
TreeFam:
Gene Tree for PKDCC (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PKDCC: view image

Paralogs for PKDCC Gene

Paralogs for PKDCC Gene

genes like me logo Genes that share paralogs with PKDCC: view

Variants for PKDCC Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PKDCC Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs761532715 Likely Pathogenic: RHIZOMELIC LIMB SHORTENING WITH DYSMORPHIC FEATURES; Inborn genetic diseases 42,053,250(+) C/A NONSENSE
rs763243200 Likely Pathogenic: RHIZOMELIC LIMB SHORTENING WITH DYSMORPHIC FEATURES; Inborn genetic diseases 42,048,839(+) G/T SPLICE_DONOR_VARIANT

Additional dbSNP identifiers (rs#s) for PKDCC Gene

Structural Variations from Database of Genomic Variants (DGV) for PKDCC Gene

Variant ID Type Subtype PubMed ID
dgv6818n54 CNV loss 21841781
dgv6819n54 CNV gain 21841781
dgv6820n54 CNV gain+loss 21841781
esv26899 CNV loss 19812545
nsv1005527 CNV gain 25217958
nsv1118865 CNV deletion 24896259
nsv581614 CNV gain 21841781
nsv581616 CNV loss 21841781
nsv581626 CNV gain 21841781
nsv833903 CNV gain 17160897
nsv953772 CNV deletion 24416366

Variation tolerance for PKDCC Gene

Residual Variation Intolerance Score: 47.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.92; 79.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PKDCC Gene

Human Gene Mutation Database (HGMD)
PKDCC
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PKDCC

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PKDCC Gene

Disorders for PKDCC Gene

MalaCards: The human disease database

(1) MalaCards diseases for PKDCC Gene - From: OMIM and GeneCards

Disorder Aliases PubMed IDs
rhizomelic limb shortening with dysmorphic features
  • rlsdf
- elite association - COSMIC cancer census association via MalaCards
Search PKDCC in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PKDCC

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PKDCC: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PKDCC Gene

Publications for PKDCC Gene

  1. Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula. (PMID: 27016259) Ding Y … De Robertis EM (Developmental biology 2017) 2 3
  2. A secreted tyrosine kinase acts in the extracellular environment. (PMID: 25171405) Bordoli MR … Whitman M (Cell 2014) 3 4
  3. A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). (PMID: 19961619) Castro-Giner F … de Cid R (BMC medical genetics 2009) 3 41
  4. The novel protein kinase Vlk is essential for stromal function of mesenchymal cells. (PMID: 19465597) Kinoshita M … Nishikawa S (Development (Cambridge, England) 2009) 2 3
  5. Short limbs, cleft palate, and delayed formation of flat proliferative chondrocytes in mice with targeted disruption of a putative protein kinase gene, Pkdcc (AW548124). (PMID: 19097194) Imuta Y … Sasaki H (Developmental dynamics : an official publication of the American Association of Anatomists 2009) 2 3

Products for PKDCC Gene

Sources for PKDCC Gene