Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PDCD2 Gene

Aliases for PDCD2 Gene

  • Programmed Cell Death 2 2 3 5
  • Zinc Finger MYND Domain-Containing Protein 7 3 4
  • Zinc Finger Protein Rp-8 3 4
  • ZMYND7 3 4
  • RP8 3 4
  • Programmed Cell Death Protein 2 3

External Ids for PDCD2 Gene

Previous GeneCards Identifiers for PDCD2 Gene

  • GC06M170079
  • GC06M170500
  • GC06M170742
  • GC06M170804
  • GC06M168391
  • GC06M170884
  • GC06M170579
  • GC06M170582
  • GC06M170584
  • GC06M170585

Summaries for PDCD2 Gene

Entrez Gene Summary for PDCD2 Gene

  • This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]

GeneCards Summary for PDCD2 Gene

PDCD2 (Programmed Cell Death 2) is a Protein Coding gene. Diseases associated with PDCD2 include Chronic Fatigue Syndrome. GO annotations related to this gene include enzyme binding. An important paralog of this gene is PDCD2L.

UniProtKB/Swiss-Prot for PDCD2 Gene

  • May be a DNA-binding protein with a regulatory function. May play an important role in cell death and/or in regulation of cell proliferation.

Gene Wiki entry for PDCD2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDCD2 Gene

Genomics for PDCD2 Gene

Regulatory Elements for PDCD2 Gene

Enhancers for PDCD2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F170243 1.4 Ensembl ENCODE 32.8 +340.6 340574 1.9 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 PDCD2 PSMB1 TBP LOC105378147 ENSG00000272848 FAM120B LOC285804 LOC154449 RPL12P23
GH06F170551 1.2 ENCODE 36.4 +31.1 31124 5.0 HDGF PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 PDCD2 PSMB1 ENSG00000266896 TBP FAM120B
GH06F169750 1.2 ENCODE 30.7 +832.9 832940 3.3 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 PSMB1 PDCD2 TBP ENSG00000266896 FAM120B WDR27 ENSG00000236173 ERMARD LOC105378147
GH06F170277 1.5 FANTOM5 Ensembl ENCODE 13.8 +305.1 305112 3.7 SIN3A FEZF1 GLI4 GLIS2 KLF7 FOS ZNF263 SP3 YY2 TSHZ1 ENSG00000266896 TBP PDCD2 PSMB1 LOC285804 FAM120B LINC01624 DLL1 TCTE3 WDR27
GH06F170582 1.1 ENCODE 18.2 -0.1 -82 4.0 HDGF PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 ZNF143 KLF13 PSMB1 PDCD2 TBP PIR58046
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDCD2 on UCSC Golden Path with GeneCards custom track

Promoters for PDCD2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001502915 174 2001 HDGF PKNOX1 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 ZNF143 KLF13

Genomic Location for PDCD2 Gene

Chromosome:
6
Start:
170,575,295 bp from pter
End:
170,584,774 bp from pter
Size:
9,480 bases
Orientation:
Minus strand

Genomic View for PDCD2 Gene

Genes around PDCD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDCD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDCD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD2 Gene

Proteins for PDCD2 Gene

  • Protein details for PDCD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16342-PDCD2_HUMAN
    Recommended name:
    Programmed cell death protein 2
    Protein Accession:
    Q16342
    Secondary Accessions:
    • E9PCU7
    • F5GYS7
    • Q58HM9
    • Q58HN0
    • Q9UH12

    Protein attributes for PDCD2 Gene

    Size:
    344 amino acids
    Molecular mass:
    38592 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PDCD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDCD2 Gene

Post-translational modifications for PDCD2 Gene

No data available for DME Specific Peptides for PDCD2 Gene

Domains & Families for PDCD2 Gene

Gene Families for PDCD2 Gene

Protein Domains for PDCD2 Gene

Graphical View of Domain Structure for InterPro Entry

Q16342

UniProtKB/Swiss-Prot:

PDCD2_HUMAN :
  • Contains 1 MYND-type zinc finger.
Similarity:
  • Contains 1 MYND-type zinc finger.
genes like me logo Genes that share domains with PDCD2: view

Function for PDCD2 Gene

Molecular function for PDCD2 Gene

GENATLAS Biochemistry:
programmed cell death (apoptosis) 2,rat RP8 homolog
UniProtKB/Swiss-Prot Function:
May be a DNA-binding protein with a regulatory function. May play an important role in cell death and/or in regulation of cell proliferation.

Gene Ontology (GO) - Molecular Function for PDCD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 19146857
GO:0019899 enzyme binding IPI 23382074
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDCD2: view
genes like me logo Genes that share phenotypes with PDCD2: view

Animal Models for PDCD2 Gene

MGI Knock Outs for PDCD2:

Animal Model Products

miRNA for PDCD2 Gene

miRTarBase miRNAs that target PDCD2

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDCD2 Gene

Localization for PDCD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD2 Gene

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 PDCD2 gene
Compartment Confidence
extracellular 5
nucleus 4
plasma membrane 2
cytosol 2

Gene Ontology (GO) - Cellular Components for PDCD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PDCD2: view

Pathways & Interactions for PDCD2 Gene

SuperPathways for PDCD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDCD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process IEA,TAS --
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process IDA 20605493
GO:0012501 programmed cell death IEA --
GO:0043065 positive regulation of apoptotic process IDA 20605493
GO:1901532 regulation of hematopoietic progenitor cell differentiation IMP 22922207
genes like me logo Genes that share ontologies with PDCD2: view

No data available for Pathways by source and SIGNOR curated interactions for PDCD2 Gene

Drugs & Compounds for PDCD2 Gene

(1) Drugs for PDCD2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PDCD2: view

Transcripts for PDCD2 Gene

Unigene Clusters for PDCD2 Gene

Programmed cell death 2:
Representative Sequences:

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - - - -
SP4: - - - -
SP5: - - - -
SP6: - - - - - - - -
SP7: - -
SP8: - -
SP9: - - - - - - -
SP10: -

Relevant External Links for PDCD2 Gene

GeneLoc Exon Structure for
PDCD2
ECgene alternative splicing isoforms for
PDCD2

Expression for PDCD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDCD2 Gene

Protein differential expression in normal tissues from HIPED for PDCD2 Gene

This gene is overexpressed in Pancreas (38.6), Fetal Brain (8.3), and Fetal ovary (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDCD2 Gene



Protein tissue co-expression partners for PDCD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDCD2 Gene:

PDCD2

SOURCE GeneReport for Unigene cluster for PDCD2 Gene:

Hs.367900

mRNA Expression by UniProt/SwissProt for PDCD2 Gene:

Q16342-PDCD2_HUMAN
Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with PDCD2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PDCD2 Gene

Orthologs for PDCD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDCD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDCD2 34 35
  • 98.03 (n)
dog
(Canis familiaris)
Mammalia PDCD2 34 35
  • 86.59 (n)
cow
(Bos Taurus)
Mammalia PDCD2 34 35
  • 86.3 (n)
mouse
(Mus musculus)
Mammalia Pdcd2 34 16 35
  • 83.67 (n)
rat
(Rattus norvegicus)
Mammalia Pdcd2 34
  • 82.22 (n)
oppossum
(Monodelphis domestica)
Mammalia PDCD2 35
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD2 35
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDCD2 34 35
  • 65.76 (n)
lizard
(Anolis carolinensis)
Reptilia PDCD2 35
  • 47 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdcd2 34
  • 61.79 (n)
African clawed frog
(Xenopus laevis)
Amphibia pdcd2-prov 34
zebrafish
(Danio rerio)
Actinopterygii pdcd2 34 35
  • 57.11 (n)
zgc63685 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1807 34
fruit fly
(Drosophila melanogaster)
Insecta Zfrp8 34 35
  • 53.18 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005582 34
  • 52.68 (n)
worm
(Caenorhabditis elegans)
Secernentea pdcd-2 34 35
  • 49.7 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G02220 34
  • 46.4 (n)
rice
(Oryza sativa)
Liliopsida Os03g0300200 34
  • 49.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6606 35
  • 43 (a)
OneToOne
Species where no ortholog for PDCD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDCD2 Gene

ENSEMBL:
Gene Tree for PDCD2 (if available)
TreeFam:
Gene Tree for PDCD2 (if available)

Paralogs for PDCD2 Gene

Paralogs for PDCD2 Gene

Pseudogenes.org Pseudogenes for PDCD2 Gene

genes like me logo Genes that share paralogs with PDCD2: view

Variants for PDCD2 Gene

Sequence variations from dbSNP and Humsavar for PDCD2 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs10946282 -- 170,576,704(+) CCCTT(A/G)TTTTG nc-transcript-variant, utr-variant-3-prime
rs111707289 -- 170,583,830(+) GAAAA(-/ACTC)TAACA intron-variant
rs111779044 -- 170,584,218(+) GCCGC(A/C)GTCCC intron-variant
rs111784233 -- 170,575,922(+) GCAGT(C/T)ATAAC nc-transcript-variant, utr-variant-3-prime
rs111886226 -- 170,580,527(+) CTGGC(C/T)AACAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDCD2 Gene

Variant ID Type Subtype PubMed ID
nsv830874 CNV loss 17160897
nsv605580 CNV gain 21841781
nsv428158 CNV gain 18775914
nsv1033491 CNV loss 25217958
nsv1015584 CNV gain 25217958
esv3611742 CNV gain 21293372
esv3571551 CNV loss 25503493
esv2759497 CNV gain+loss 17122850
dgv6209n100 CNV gain 25217958
dgv6208n100 CNV gain 25217958

Variation tolerance for PDCD2 Gene

Residual Variation Intolerance Score: 70% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDCD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDCD2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD2 Gene

Disorders for PDCD2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PDCD2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
chronic fatigue syndrome
  • cfs
- elite association - COSMIC cancer census association via MalaCards
Search PDCD2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PDCD2

Genetic Association Database (GAD)
PDCD2
Human Genome Epidemiology (HuGE) Navigator
PDCD2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDCD2
genes like me logo Genes that share disorders with PDCD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDCD2 Gene

Publications for PDCD2 Gene

  1. Isolation and mapping of a human gene (PDCD2) that is highly homologous to Rp8, a rat gene associated with programmed cell death. (PMID: 7606924) Kawakami T. … Nakamura Y. (Cytogenet. Cell Genet. 1995) 2 3 4 22 64
  2. Programmed cell death-2 isoform1 is ubiquitinated by parkin and increased in the substantia nigra of patients with autosomal recessive Parkinson's disease. (PMID: 19146857) Fukae J. … Hattori N. (FEBS Lett. 2009) 3 4 64
  3. Evaluation of IDDM8 susceptibility locus in a Russian simplex family data set. (PMID: 15848047) Chistiakov D.A. … Nosikov V.V. (J. Autoimmun. 2005) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for PDCD2 Gene

Sources for PDCD2 Gene

Content
Loading form....