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Aliases for PDCD6 Gene

Aliases for PDCD6 Gene

  • Programmed Cell Death 6 2 3 5
  • Probable Calcium-Binding Protein ALG-2 3 4
  • Apoptosis-Linked Gene 2 Protein 3 4
  • ALG2 3 4
  • Apoptosis-Linked Gene-2 2
  • ALG-2 3
  • PEF1B 3

External Ids for PDCD6 Gene

Previous GeneCards Identifiers for PDCD6 Gene

  • GC05P000423
  • GC05M000303
  • GC05P000304
  • GC05P000324
  • GC05P000258

Summaries for PDCD6 Gene

Entrez Gene Summary for PDCD6 Gene

  • This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]

GeneCards Summary for PDCD6 Gene

PDCD6 (Programmed Cell Death 6) is a Protein Coding gene. Diseases associated with PDCD6 include ocular melanoma. Among its related pathways are Metabolism and Transport to the Golgi and subsequent modification. GO annotations related to this gene include calcium ion binding and identical protein binding. An important paralog of this gene is CAPNS2.

UniProtKB/Swiss-Prot for PDCD6 Gene

  • Calcium-binding protein required for T-cell receptor-, Fas-, and glucocorticoid-induced cell death. May mediate Ca(2+)-regulated signals along the death pathway (By similarity). Calcium-dependent adapter necessary for the association between PDCD6IP and TSG101. Interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity. May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphoprylation of the Akt signaling pathway. Seems to play a role in the regulation of the distribution and function of MCOLN1 in the endosomal pathway. Isoform 2 has a lower Ca(2+) affinity than isoform 1. Isoform 1 and, to a lesser extend, isoform 2, can stabilize SHISA5.

Gene Wiki entry for PDCD6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDCD6 Gene

Genomics for PDCD6 Gene

Regulatory Elements for PDCD6 Gene

Promoters for PDCD6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PDCD6 on UCSC Golden Path with GeneCards custom track

Genomic Location for PDCD6 Gene

Chromosome:
5
Start:
271,621 bp from pter
End:
353,856 bp from pter
Size:
82,236 bases
Orientation:
Plus strand

Genomic View for PDCD6 Gene

Genes around PDCD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDCD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDCD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD6 Gene

Proteins for PDCD6 Gene

  • Protein details for PDCD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75340-PDCD6_HUMAN
    Recommended name:
    Programmed cell death protein 6
    Protein Accession:
    O75340
    Secondary Accessions:
    • B2RD16
    • E7ESR3
    • Q2YDC2
    • Q5TZS0

    Protein attributes for PDCD6 Gene

    Size:
    191 amino acids
    Molecular mass:
    21868 Da
    Quaternary structure:
    • Isoform 1 and isoform 2 self-associate; probably forming homodimers. Interacts with CPNE4 (via VWFA domain) (By similarity). Interacts with PDCD6IP; the interaction is calcium-dependent (PubMed:16957052, PubMed:18256029, PubMed:18940611, PubMed:20691033). Interacts with SHISA5 (PubMed:17889823). Interacts with PEF1 (PubMed:11278427, PubMed:11883899). Interacts with RBM22 (PubMed:17045351). Interacts with PLSCR4 (PubMed:18256029). Interacts with ANXA7 and TSG101 (PubMed:18256029, PubMed:20691033). Interacts with DAPK1 (PubMed:16132846). Interacts with SEC31A; the interaction is calcium-dependent (PubMed:16957052, PubMed:18256029). Interacts with ANXA11 (via N-terminus); the interaction is calcium-dependent (PubMed:11883939, PubMed:18256029, PubMed:18940611). Interacts with PLSCR3 (via N-terminus); the interaction is calcium-dependent (PubMed:18256029). Interacts with MCOLN1; the interaction is calcium-dependent (PubMed:19864416). Seems to play a role in the regulation of the distribution and function of MCOLN1 in the endosomal pathway (PubMed:19864416). Interacts with KDR (PubMed:21893193). Isoform 2 does not interact with SHISA5 (PubMed:17889823). Isoform 2 does not interact with PDCD6IP, TSG101, ANXA7 and ANXA11.

    Three dimensional structures from OCA and Proteopedia for PDCD6 Gene

    Alternative splice isoforms for PDCD6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDCD6 Gene

Proteomics data for PDCD6 Gene at MOPED

Post-translational modifications for PDCD6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for PDCD6 Gene

Domains & Families for PDCD6 Gene

Gene Families for PDCD6 Gene

Protein Domains for PDCD6 Gene

Suggested Antigen Peptide Sequences for PDCD6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O75340

UniProtKB/Swiss-Prot:

PDCD6_HUMAN :
  • Contains 5 EF-hand domains.
Domain:
  • Contains 5 EF-hand domains.
genes like me logo Genes that share domains with PDCD6: view

Function for PDCD6 Gene

Molecular function for PDCD6 Gene

GENATLAS Biochemistry:
programmed cell death 6,Ca(2+)-binding protein required for T cell receptor-,Fas-, and glucocorticoid-induced cell death
UniProtKB/Swiss-Prot Function:
Calcium-binding protein required for T-cell receptor-, Fas-, and glucocorticoid-induced cell death. May mediate Ca(2+)-regulated signals along the death pathway (By similarity). Calcium-dependent adapter necessary for the association between PDCD6IP and TSG101. Interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity. May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphoprylation of the Akt signaling pathway. Seems to play a role in the regulation of the distribution and function of MCOLN1 in the endosomal pathway. Isoform 2 has a lower Ca(2+) affinity than isoform 1. Isoform 1 and, to a lesser extend, isoform 2, can stabilize SHISA5.

Gene Ontology (GO) - Molecular Function for PDCD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046983 protein dimerization activity IPI 11883899
genes like me logo Genes that share ontologies with PDCD6: view
genes like me logo Genes that share phenotypes with PDCD6: view

Animal Models for PDCD6 Gene

MGI Knock Outs for PDCD6:

Animal Model Products

miRNA for PDCD6 Gene

miRTarBase miRNAs that target PDCD6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDCD6 Gene

Localization for PDCD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD6 Gene

Nucleus membrane; Peripheral membrane protein. Endoplasmic reticulum membrane; Peripheral membrane protein. Nucleus. Endosome. Note=Interaction with RBM22 induces relocalization from the cytoplasm to the nucleus. Translocated from the cytoplasm to the nucleus after heat shock cell treatment. Accumulates in cytoplasmic vesicle-like organelles after heat shock treatment, which may represent stress granules. {ECO:0000269 PubMed:21122810}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDCD6 Gene COMPARTMENTS Subcellular localization image for PDCD6 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
nucleus 5
endosome 4
cytosol 2

Gene Ontology (GO) - Cellular Components for PDCD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 21122810
GO:0005783 endoplasmic reticulum IDA 17196169
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PDCD6: view

Pathways & Interactions for PDCD6 Gene

genes like me logo Genes that share pathways with PDCD6: view

Gene Ontology (GO) - Biological Process for PDCD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001938 positive regulation of endothelial cell proliferation IDA 21893193
GO:0006886 intracellular protein transport IDA 21122810
GO:0010595 positive regulation of endothelial cell migration IDA 21893193
GO:0045766 positive regulation of angiogenesis IDA 21893193
GO:0051592 response to calcium ion ISS --
genes like me logo Genes that share ontologies with PDCD6: view

No data available for SIGNOR curated interactions for PDCD6 Gene

Drugs & Compounds for PDCD6 Gene

(1) Drugs for PDCD6 Gene - From: Novoseek and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PDCD6: view

Transcripts for PDCD6 Gene

Unigene Clusters for PDCD6 Gene

Programmed cell death 6:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD6 Gene

No ASD Table

Relevant External Links for PDCD6 Gene

GeneLoc Exon Structure for
PDCD6
ECgene alternative splicing isoforms for
PDCD6

Expression for PDCD6 Gene

mRNA expression in normal human tissues for PDCD6 Gene

Protein differential expression in normal tissues from HIPED for PDCD6 Gene

This gene is overexpressed in Bone (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PDCD6 Gene



SOURCE GeneReport for Unigene cluster for PDCD6 Gene Hs.50823

genes like me logo Genes that share expression patterns with PDCD6: view

Protein tissue co-expression partners for PDCD6 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PDCD6 Gene

Orthologs for PDCD6 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PDCD6 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDCD6 35
  • 89.24 (n)
  • 98.94 (a)
PDCD6 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDCD6 35
  • 89.77 (n)
  • 98.94 (a)
PDCD6 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdcd6 35
  • 86.74 (n)
  • 98.95 (a)
Pdcd6 16
Pdcd6 36
  • 99 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDCD6 35
  • 99.3 (n)
  • 99.48 (a)
PDCD6 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdcd6 35
  • 86.74 (n)
  • 98.95 (a)
oppossum
(Monodelphis domestica)
Mammalia PDCD6 36
  • 94 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD6 36
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDCD6 35
  • 79.56 (n)
  • 91.67 (a)
PDCD6 36
  • 86 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDCD6 36
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdcd6 35
  • 76.19 (n)
  • 88.69 (a)
Str.6903 35
African clawed frog
(Xenopus laevis)
Amphibia pdcd6-prov 35
zebrafish
(Danio rerio)
Actinopterygii pdcd6 35
  • 76.59 (n)
  • 88.69 (a)
zgc63952 35
pdcd6 36
  • 83 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.606 35
fruit fly
(Drosophila melanogaster)
Insecta CG17661 37
  • 70 (a)
CG17765 37
  • 41 (a)
Alg-2 35
  • 61.48 (n)
  • 68.86 (a)
Alg-2 36
  • 48 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea M04F3.4 37
  • 59 (a)
CELE_M04F3.4 35
  • 57.03 (n)
  • 59.64 (a)
M04F3.4 36
  • 59 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR570W 35
  • 40.61 (n)
  • 28.87 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PEF1 36
  • 13 (a)
OneToMany
PEF1 38
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3171 35
bread mold
(Neurospora crassa)
Ascomycetes NCU02738 35
  • 53.42 (n)
  • 44.1 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9645 36
  • 59 (a)
OneToOne
Species with no ortholog for PDCD6:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for PDCD6 Gene

ENSEMBL:
Gene Tree for PDCD6 (if available)
TreeFam:
Gene Tree for PDCD6 (if available)

Paralogs for PDCD6 Gene

Paralogs for PDCD6 Gene

(6) SIMAP similar genes for PDCD6 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PDCD6: view

Variants for PDCD6 Gene

Sequence variations from dbSNP and Humsavar for PDCD6 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_035459 A breast cancer sample
rs348120 -- 279,747(+) tgatT(C/T)TAATA intron-variant
rs438911 -- 280,012(-) TATCG(C/G)TCCCT intron-variant
rs438949 -- 279,939(-) GGAAG(C/G)TAGAT intron-variant
rs450983 -- 279,956(-) CCCGT(C/T)TCCTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDCD6 Gene

Variant ID Type Subtype PubMed ID
essv22552 CNV CNV 17122850
dgv1733e1 CNV Complex 17122850
esv2752083 CNV Gain 17911159
dgv1734e1 CNV Complex 17122850
nsv428458 CNV Loss 18775914
nsv880815 CNV Loss 21882294
nsv518607 CNV Gain 19592680
esv2295089 CNV Deletion 18987734
nsv880786 CNV Loss 21882294
esv2659039 CNV Deletion 23128226
esv28295 CNV Gain 19812545
nsv461887 CNV Gain 19166990
nsv881337 CNV Loss 21882294
nsv881437 CNV Loss 21882294
esv2664555 CNV Deletion 23128226
esv2106320 CNV Deletion 18987734
nsv880946 CNV Loss 21882294
esv2369327 CNV Deletion 18987734
nsv329327 CNV Loss 16902084
esv995455 CNV Deletion 20482838
esv1500777 CNV Deletion 17803354
esv2502817 CNV Insertion 19546169
esv1175822 CNV Insertion 17803354
nsv509041 CNV Insertion 20534489

Variation tolerance for PDCD6 Gene

Residual Variation Intolerance Score: 47.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.00; 74.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDCD6 Gene

HapMap Linkage Disequilibrium report
PDCD6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD6 Gene

Disorders for PDCD6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PDCD6 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
ocular melanoma
  • eye melanoma
- elite association - COSMIC cancer census association via MalaCards
Search PDCD6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PDCD6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDCD6
genes like me logo Genes that share disorders with PDCD6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDCD6 Gene

Publications for PDCD6 Gene

  1. Peflin and ALG-2, members of the penta-EF-hand protein family, form a heterodimer that dissociates in a Ca2+-dependent manner. (PMID: 11278427) Kitaura Y. … Maki M. (J. Biol. Chem. 2001) 3 4 23 67
  2. Interfering with apoptosis: Ca(2+)-binding protein ALG-2 and Alzheimer's disease gene ALG-3. (PMID: 8560270) Vito P. … D'Adamio L. (Science 1996) 2 3 23
  3. Penta-EF-hand protein ALG-2 functions as a Ca2+-dependent adaptor that bridges Alix and TSG101. (PMID: 19520058) Okumura M. … Maki M. (Biochem. Biophys. Res. Commun. 2009) 3 23
  4. Identification of the penta-EF-hand protein ALG-2 as a Ca2+-dependent interactor of mucolipin-1. (PMID: 19864416) Vergarajauregui S. … Puertollano R. (J. Biol. Chem. 2009) 3 23
  5. Identification of Alix-type and non-Alix-type ALG-2-binding sites in human phospholipid scramblase 3: differential binding to an alternatively spliced isoform and amino acid-substituted mutants. (PMID: 18256029) Shibata H. … Maki M. (J. Biol. Chem. 2008) 3 23

Products for PDCD6 Gene

Sources for PDCD6 Gene

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