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PKDCC protein kinase domain containing, cytoplasmic [ Homo sapiens (human) ]

Gene ID: 91461, updated on 23-Nov-2023

Summary

Official Symbol
PKDCCprovided by HGNC
Official Full Name
protein kinase domain containing, cytoplasmicprovided by HGNC
Primary source
HGNC:HGNC:25123
See related
Ensembl:ENSG00000162878 MIM:614150; AllianceGenome:HGNC:25123
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Vlk; RLSDF; SGK493
Summary
Enables non-membrane spanning protein tyrosine kinase activity. Involved in peptidyl-tyrosine phosphorylation and skeletal system development. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in ovary (RPKM 28.2), endometrium (RPKM 26.6) and 22 other tissues See more
Orthologs
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Genomic context

See PKDCC in Genome Data Viewer
Location:
2p21
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (42048021..42058517)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (42053518..42064014)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (42275161..42285657)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905996 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:42164451-42165045 Neighboring gene Sharpr-MPRA regulatory region 382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42166828-42167422 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42175498-42176148 Neighboring gene long intergenic non-protein coding RNA 2898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11392 Neighboring gene VISTA enhancer hs2553 Neighboring gene uncharacterized LOC105374517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58491 Neighboring gene Sharpr-MPRA regulatory region 7749 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:42220647-42221044 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:42222752-42223418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11393 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:42259331-42259881 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42273538-42274041 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42274042-42274546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42276763-42277264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42279935-42280650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42280651-42281365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42285233-42285733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15636 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:42296167-42296331 Neighboring gene uncharacterized LOC105374531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42328443-42329270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15642 Neighboring gene MPRA-validated peak3676 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15643 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42359847-42360820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42360821-42361792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42367980-42368777 Neighboring gene EML4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42396227-42396879 Neighboring gene EMAP like 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Rhizomelic limb shortening with dysmorphic features
MedGen: C5394173 OMIM: 618821 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS).
EBI GWAS Catalog
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ18197, MGC125960

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables non-membrane spanning protein tyrosine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables non-membrane spanning protein tyrosine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in bone mineralization IEA
Inferred from Electronic Annotation
more info
 
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic digestive tract development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in lung alveolus development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of Golgi to plasma membrane protein transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in peptidyl-tyrosine phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of bone mineralization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
 
involved_in roof of mouth development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in extracellular region IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular region IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
extracellular tyrosine-protein kinase PKDCC
Names
protein kinase domain containing, cytoplasmic homolog
protein kinase domain-containing protein, cytoplasmic
protein kinase-like protein SgK493
sugen kinase 493
vertebrate lonesome kinase
NP_612379.2

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.

mRNA and Protein(s)

  1. NM_138370.3NP_612379.2  extracellular tyrosine-protein kinase PKDCC precursor

    See identical proteins and their annotated locations for NP_612379.2

    Status: VALIDATED

    Source sequence(s)
    AC013480, BC062988, BC110513, BM738316, CF131963, DB231841, DB457034
    Consensus CDS
    CCDS33186.2
    UniProtKB/Swiss-Prot
    D6W5A0, Q504Y2, Q96I09
    Related
    ENSP00000294964.5, ENST00000294964.6
    Conserved Domains (1) summary
    cl21453
    Location:200370
    PKc_like; Protein Kinases, catalytic domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    42048021..42058517
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    42053518..42064014
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)