DPPA4 Gene (Protein Coding)

Developmental Pluripotency Associated 4

GC03M109326
GIFtS:
40
This gene encodes a nuclear factor that is involved in the maintenance of pluripotency in stem cells and essential for embryogenesis. The encoded protein has a scaffold-attachment factor A/B, acinus and PIAS (SAP) domain that binds DNA and is thought to modify chromatin. Mice with a homozygous knockout of the orthologous gene die during late embryonic development or within hour... See more...

Aliases for DPPA4 Gene

Aliases for DPPA4 Gene

  • Developmental Pluripotency Associated 4 2 3 5
  • Developmental Pluripotency-Associated Protein 4 3 4
  • 2410091M23Rik 3
  • FLJ10713 2
  • DPPA4 5

External Ids for DPPA4 Gene

Previous GeneCards Identifiers for DPPA4 Gene

  • GC00U909445
  • GC03M110365
  • GC03M110527
  • GC03M109045
  • GC03M106419

Summaries for DPPA4 Gene

Entrez Gene Summary for DPPA4 Gene

  • This gene encodes a nuclear factor that is involved in the maintenance of pluripotency in stem cells and essential for embryogenesis. The encoded protein has a scaffold-attachment factor A/B, acinus and PIAS (SAP) domain that binds DNA and is thought to modify chromatin. Mice with a homozygous knockout of the orthologous gene die during late embryonic development or within hours after birth. Knockout embryos are normal in size at embryonic day 18.5 but exhibit skeletal and lung tissue abnormalities. This gene, when mutated, is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers and is thought to play an important role in tumor progression. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

GeneCards Summary for DPPA4 Gene

DPPA4 (Developmental Pluripotency Associated 4) is a Protein Coding gene. Diseases associated with DPPA4 include Germ Cell And Embryonal Cancer and Astigmatism. Among its related pathways are Transcriptional regulation of pluripotent stem cells and Developmental Biology. An important paralog of this gene is DPPA2.

UniProtKB/Swiss-Prot Summary for DPPA4 Gene

  • May be involved in the maintenance of active epigenetic status of target genes. May inhibit differentiation of embryonic cells into a primitive ectoderm lineage.

Additional gene information for DPPA4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DPPA4 Gene

Genomics for DPPA4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for DPPA4 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
GH03J109332 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 259.1 +3.3 3255 8 POLR2A YY1 ETS1 SIN3A JUND HNF4A TAF1 RAD21 CHD1 REST DPPA4 HSALNG0027940 RF00017-3675 lnc-DPPA4-1-002 lnc-C3orf85-4 DPPA2 piR-46831 lnc-DPPA4-1-001
GH03J109353 Enhancer 0.9 Ensembl ENCODE dbSUPER 5.1 -15.7 -15717 5.5 POLR2A YY1 SIN3A RXRA HNF4A MAX SP1 POU5F1 NANOG CHD2 MORC1-AS1 DPPA4 GUCA1C lnc-DPPA4-1-001 lnc-C3orf85-4 HSALNG0027940
GH03J109325 Enhancer 0.3 ENCODE 7.4 +14.0 14026 0.9 POLR2A SIN3A DPPA4 DPPA2 piR-46831 lnc-DPPA4-1-001
GH03J109372 Enhancer 0.4 Ensembl 4.7 -33.0 -32966 0.4 RXRA HNF4A SP1 DPPA4 ENSG00000241257 HSALNG0027941 HSALNG0027940 lnc-C3orf85-4
GH03J109314 Enhancer 0.2 Ensembl 5.1 +25.4 25434 2.8 DPPA4 DPPA2 RF00017-3674 C3orf85
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DPPA4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DPPA4

Top Transcription factor binding sites by QIAGEN in the DPPA4 gene promoter:
  • AML1a
  • c-Ets-1
  • COUP
  • COUP-TF
  • HNF-1
  • HNF-1A
  • Max1
  • POU2F1
  • POU2F1a
  • S8

Genomic Locations for DPPA4 Gene

Latest Assembly
chr3:109,326,141-109,339,635
(GRCh38/hg38)
Size:
13,495 bases
Orientation:
Minus strand

Previous Assembly
chr3:109,044,988-109,056,419
(GRCh37/hg19 by Entrez Gene)
Size:
11,432 bases
Orientation:
Minus strand

chr3:109,044,988-109,056,419
(GRCh37/hg19 by Ensembl)
Size:
11,432 bases
Orientation:
Minus strand

Genomic View for DPPA4 Gene

Genes around DPPA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DPPA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DPPA4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DPPA4 Gene

Proteins for DPPA4 Gene

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  1. Antibodies for research
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  3. Assay products for research

  • Protein details for DPPA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7L190-DPPA4_HUMAN
    Recommended name:
    Developmental pluripotency-associated protein 4
    Protein Accession:
    Q7L190
    Secondary Accessions:
    • A8K4M7
    • Q9H9N5
    • Q9NVI6

    Protein attributes for DPPA4 Gene

    Size:
    304 amino acids
    Molecular mass:
    33541 Da
    Quaternary structure:
    • Interacts with DPPA2 (By similarity). Interacts with PCGF1 (PubMed:26687479).
    SequenceCaution:
    • Sequence=BAA91765.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB14188.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for DPPA4 Gene

Protein Expression for DPPA4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for DPPA4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DPPA4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DPPA4 Gene

Domains & Families for DPPA4 Gene

Gene Families for DPPA4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for DPPA4 Gene

InterPro:

Suggested Antigen Peptide Sequences for DPPA4 Gene

GenScript: Design optimal peptide antigens:
  • Developmental pluripotency-associated protein 4 (DPPA4_HUMAN)
genes like me logo Genes that share domains with DPPA4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for DPPA4 Gene

Function for DPPA4 Gene

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  6. Cell Lines for research

Molecular function for DPPA4 Gene

UniProtKB/Swiss-Prot Function:
May be involved in the maintenance of active epigenetic status of target genes. May inhibit differentiation of embryonic cells into a primitive ectoderm lineage.

Phenotypes From GWAS Catalog for DPPA4 Gene

Gene Ontology (GO) - Molecular Function for DPPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 16169070
genes like me logo Genes that share ontologies with DPPA4: view
genes like me logo Genes that share phenotypes with DPPA4: view

Animal Models for DPPA4 Gene

MGI Knock Outs for DPPA4:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DPPA4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DPPA4 Gene

Localization for DPPA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DPPA4 Gene

Nucleus. Note=Associated with transcriptionally active chromatin. {ECO:0000250 UniProtKB:Q8CCG4}.

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 DPPA4 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitotic chromosome (2)
  • Nucleoli (2)
  • Nucleoli rim (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DPPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IBA 21873635
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with DPPA4: view

Pathways & Interactions for DPPA4 Gene

genes like me logo Genes that share pathways with DPPA4: view

SIGNOR curated interactions for DPPA4 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for DPPA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0035019 somatic stem cell population maintenance TAS --
GO:0048731 system development IBA 21873635
genes like me logo Genes that share ontologies with DPPA4: view

Drugs & Compounds for DPPA4 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for DPPA4 Gene

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mRNA/cDNA for DPPA4 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DPPA4

Alternative Splicing Database (ASD) splice patterns (SP) for DPPA4 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for DPPA4 Gene

GeneLoc Exon Structure for
DPPA4

Expression for DPPA4 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DPPA4 Gene

mRNA expression in normal human tissues for DPPA4 Gene
mRNA expression by GTEx for DPPA4 GenemRNA expression by BioGPS for DPPA4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DPPA4 Gene

This gene is overexpressed in Testis (x21.1) and Pituitary (x7.6).

Protein differential expression in normal tissues from HIPED for DPPA4 Gene

This gene is overexpressed in Lung (41.4) and Blymphocyte (27.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for DPPA4 Gene



Protein tissue co-expression partners for DPPA4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DPPA4

SOURCE GeneReport for Unigene cluster for DPPA4 Gene:

Hs.317659
genes like me logo Genes that share expression patterns with DPPA4: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for DPPA4 Gene

Orthologs for DPPA4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for DPPA4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia DPPA4 29 30
  • 99.09 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Dppa4 29 16 30
  • 65.49 (n)
 OneToMany
Gm5501 30
  • 49 (a)
 OneToMany
Rat
(Rattus norvegicus)
 Mammalia LOC685378 29
  • 65.38 (n)
Dog
(Canis familiaris)
 Mammalia -- 30
  • 65 (a)
 OneToMany
-- 30
  • 61 (a)
 OneToMany
-- 30
  • 60 (a)
 OneToMany
-- 30
  • 56 (a)
 OneToMany
-- 30
  • 55 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia -- 30
  • 53 (a)
 OneToMany
-- 30
  • 50 (a)
 OneToMany
Oppossum
(Monodelphis domestica)
 Mammalia -- 30
  • 35 (a)
 OneToMany
Species where no ortholog for DPPA4 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)
  • Chicken (Gallus gallus)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for DPPA4 Gene

ENSEMBL:
Gene Tree for DPPA4 (if available)
TreeFam:
Gene Tree for DPPA4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DPPA4: view image
Alliance of Genome Resources:
Additional Orthologs for DPPA4

Paralogs for DPPA4 Gene

Paralogs for DPPA4 Gene

(1) SIMAP similar genes for DPPA4 Gene using alignment to 3 proteins:

  • DPPA4_HUMAN
  • C9J7A7_HUMAN
  • F8WDC6_HUMAN

Pseudogenes.org Pseudogenes for DPPA4 Gene

genes like me logo Genes that share paralogs with DPPA4: view

Variants for DPPA4 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DPPA4 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs193920923 Uncertain Significance: Malignant tumor of prostate 109,327,996(-) A/G
NM_018189.3(DPPA4):c.907T>C (p.Trp303Arg) 		MISSENSE_VARIANT,THREE_PRIME_UTR
rs3762648 -- p.Ile55Val
rs3905734 -- p.Ser226Phe

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for DPPA4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for DPPA4 Gene

Variant ID Type Subtype PubMed ID
esv2421541 CNV deletion 20811451
esv2725758 CNV deletion 23290073
esv2725759 CNV deletion 23290073
esv2725760 CNV deletion 23290073
nsv1002080 CNV loss 25217958
nsv829665 CNV gain 17160897

Variation tolerance for DPPA4 Gene

Residual Variation Intolerance Score: 56.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.41; 42.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DPPA4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DPPA4
Leiden Open Variation Database (LOVD)
DPPA4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DPPA4 Gene

Disorders for DPPA4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for DPPA4 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
germ cell and embryonal cancer
  • germ cell and embryonal neoplasm
astigmatism
- elite association - COSMIC cancer census association via MalaCards
Search DPPA4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DPPA4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with DPPA4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DPPA4 Gene

Publications for DPPA4 Gene

  1. The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis. (PMID: 26687479) Oliviero G … Cagney G (Scientific reports 2015) 2 3 4
  2. Identification of DPPA4 and DPPA2 as a novel family of pluripotency-related oncogenes. (PMID: 23963736) Tung PY … Knoepfler PS (Stem cells (Dayton, Ohio) 2013) 2 3
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

ExternalLinks

View latest publications for DPPA4 gene in Mastermind

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Sources for DPPA4 Gene