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    DPPA4 developmental pluripotency associated 4 [ Homo sapiens (human) ]

    Gene ID: 55211, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DPPA4provided by HGNC
    Official Full Name
    developmental pluripotency associated 4provided by HGNC
    Primary source
    HGNC:HGNC:19200
    See related
    Ensembl:ENSG00000121570 MIM:614125; AllianceGenome:HGNC:19200
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    2410091M23Rik
    Summary
    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]
    Expression
    Biased expression in testis (RPKM 2.8), bone marrow (RPKM 2.1) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DPPA4 in Genome Data Viewer
    Location:
    3q13.13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (109326144..109339636, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (112046432..112059906, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (109044991..109056393, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene BRD7 pseudogene 7 Neighboring gene developmental pluripotency associated 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:109043097-109043597 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:109054673-109055281 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:109055282-109055890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:109055891-109056498 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:109057717-109058324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:109066679-109067180 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:109074429-109075164 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:109075165-109075898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:109075899-109076634 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:109085761-109085928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:109114646-109115452 Neighboring gene RLIG1 pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 1205 Neighboring gene H3 histone pseudogene 12

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells. Abu-Dawud R, et al. Tissue Cell, 2022 Oct. PMID 36007377
    2. Differentiation of human embryonal carcinomas in vitro and in vivo reveals expression profiles relevant to normal development. Skotheim RI, et al. Cancer Res, 2005 Jul 1. PMID 15994931
    3. Gene expression profiling differentiates germ cell tumors from other cancers and defines subtype-specific signatures. Juric D, et al. Proc Natl Acad Sci U S A, 2005 Dec 6. PMID 16306258, Free PMC Article
    4. Comparisons between transcriptional regulation and RNA expression in human embryonic stem cell lines. Player A, et al. Stem Cells Dev, 2006 Jun. PMID 16846370
    5. Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. Galán A, et al. PLoS One, 2010 Oct 26. PMID 21049019, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders.
      Title: Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders.
    2. Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells.
      Title: Dynamic cytosolic foci of DPPA4 in human pluripotent stem cells.
    3. Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region.
      Title: Dppa2/4 as a trigger of signaling pathways to promote zygote genome activation by binding to CG-rich region.
    4. Dppa4 promotes nonsmallcell lung cancer progression, partly through glycolysis by lactate dehydrogenase B.
      Title: High developmental pluripotency‑associated 4 expression promotes cell proliferation and glycolysis, and predicts poor prognosis in non‑small‑cell lung cancer.
    5. identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1
      Title: ERBB3-Binding Protein 1 (EBP1) Is a Novel Developmental Pluripotency-Associated-4 (DPPA4) Cofactor in Human Pluripotent Cells.
    6. Across cell types Dppa4 shows a preference for binding to regions with active chromatin signatures, and can influence chromatin modifications at target genes. Data provide novel insights into Dppa4 function in both pluripotent and oncogenic contexts.
      Title: Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer.
    7. knockdown of PCGF1 results in reduced expression of DPPA4 and other subunits of the variant PRC1 complex at both mRNA and protein levels
      Title: The variant Polycomb Repressor Complex 1 component PCGF1 interacts with a pluripotency sub-network that includes DPPA4, a regulator of embryogenesis.
    8. Results identified a new family of pluripotency-related oncogenes consisting of DPPA2 and DPPA4.
      Title: Identification of DPPA4 and DPPA2 as a novel family of pluripotency-related oncogenes.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality.
    EBI GWAS Catalog
    Interrogation of the platelet-derived growth factor receptor alpha locus and corneal astigmatism in Australians of Northern European ancestry: results of a genome-wide association study.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10713

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in lung-associated mesenchyme development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    developmental pluripotency-associated protein 4

    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.

    Genomic

    1. NG_053021.1 RefSeqGene

      Range
      5027..16429
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001348928.3 → NP_001335857.1  developmental pluripotency-associated protein 4 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC076971
      Conserved Domains (2) summary
      pfam14047
      Location:175 → 242
      DCR; Dppa2/4 conserved region
      pfam14049
      Location:79 → 170
      Dppa2_A; Dppa2/4 conserved region in higher vertebrates

    2. NM_001348929.2 → NP_001335858.1  developmental pluripotency-associated protein 4 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC076971
      UniProtKB/TrEMBL
      B7Z595

    3. NM_018189.4 → NP_060659.3  developmental pluripotency-associated protein 4 isoform 1

      See identical proteins and their annotated locations for NP_060659.3

      Status: REVIEWED

      Source sequence(s)
      AC076971
      Consensus CDS
      CCDS33814.1
      UniProtKB/Swiss-Prot
      A8K4M7, Q7L190, Q9H9N5, Q9NVI6
      UniProtKB/TrEMBL
      B7Z5Q7
      Related
      ENSP00000335306.6, ENST00000335658.7
      Conserved Domains (2) summary
      pfam14047
      Location:227 → 294
      DCR; Dppa2/4 conserved region
      pfam14049
      Location:131 → 222
      Dppa2_A; Dppa2/4 conserved region in higher vertebrates

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      109326144..109339636 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453622.2 → XP_024309390.1  developmental pluripotency-associated protein 4 isoform X1

      Conserved Domains (2) summary
      pfam14047
      Location:175 → 242
      DCR; Dppa2/4 conserved region
      pfam14049
      Location:79 → 170
      Dppa2_A; Dppa2/4 conserved region in higher vertebrates

    2. XM_011512954.4 → XP_011511256.1  developmental pluripotency-associated protein 4 isoform X1

      Conserved Domains (2) summary
      pfam14047
      Location:175 → 242
      DCR; Dppa2/4 conserved region
      pfam14049
      Location:79 → 170
      Dppa2_A; Dppa2/4 conserved region in higher vertebrates

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      112046432..112059906 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347157.1 → XP_054203132.1  developmental pluripotency-associated protein 4 isoform X1

    2. XM_054347156.1 → XP_054203131.1  developmental pluripotency-associated protein 4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7L190.2 GenPept UniProtKB/Swiss-Prot:Q7L190

    Gene LinkOut

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