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Aliases for DPF3 Gene

Aliases for DPF3 Gene

  • Double PHD Fingers 3 2 3 5
  • D4, Zinc And Double PHD Fingers, Family 3 2 3
  • Zinc Finger Protein Cer-D4 3 4
  • BRG1-Associated Factor 45C 3 4
  • BAF45C 3 4
  • CERD4 3 4
  • Zinc Finger Protein DPF3 3

External Ids for DPF3 Gene

Previous GeneCards Identifiers for DPF3 Gene

  • GC14M066871
  • GC14M071065
  • GC14M072145
  • GC14M073086
  • GC14M053303

Summaries for DPF3 Gene

Entrez Gene Summary for DPF3 Gene

  • This gene encodes a member of the D4 protein family. The encoded protein is a transcription regulator that binds acetylated histones and is a component of the BAF chromatin remodeling complex. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

GeneCards Summary for DPF3 Gene

DPF3 (Double PHD Fingers 3) is a Protein Coding gene. Among its related pathways are Gastric cancer and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.. An important paralog of this gene is DPF1.

UniProtKB/Swiss-Prot for DPF3 Gene

  • Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.

Additional gene information for DPF3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DPF3 Gene

Genomics for DPF3 Gene

GeneHancer (GH) Regulatory Elements for DPF3 Gene

Promoters and enhancers for DPF3 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
GH14J073456 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650 -566.2 -566222 7.9 HDGF PKNOX1 FOXA2 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZBTB7B YY1 NUMB DPF3 ZNF410 LOC100420966 ELMSAN1 DCAF4 ENSG00000258891 ENSG00000258695 ENSG00000258944 RBM25
GH14J072891 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 656.3 +0.5 518 3.9 PKNOX1 ATF1 ARID4B SIN3A ZNF2 YY1 GLIS2 ZFP91 ATF7 FOS DPF3 DCAF4 PSEN1 RBM25 ZNF410 ELMSAN1 ACOT2 LOC101928123 ENSG00000206751 GC14M072854
GH14J072662 Enhancer 1.2 Ensembl ENCODE dbSUPER 45.7 +228.8 228817 4.7 BMI1 RFX5 ZNF143 ATF7 FOS IKZF2 RUNX3 CREM CEBPB JUNB DPF3 GC14M072609 GC14P072612 GC14M072730
GH14J072606 Enhancer 0.9 Ensembl ENCODE 21.4 +285.1 285079 4.1 JUN FOSL1 ZNF335 ZFHX2 VEZF1 FOSL2 NFE2 FOS EGR2 NRF1 DPF3 GC14M072609 GC14P072612 GC14M072593
GH14J072780 Enhancer 1.2 Ensembl ENCODE dbSUPER 15.6 +112.5 112547 2.3 ELF3 SOX13 FOXA2 JUN ZNF384 BATF RARA ETS1 EED FOSL2 DPF3 ACOT2 GC14M072730 GC14M072854 ENSG00000206751
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DPF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DPF3 gene promoter:

Genomic Locations for DPF3 Gene

Genomic Locations for DPF3 Gene
chr14:72,609,032-72,894,116
(GRCh38/hg38)
Size:
285,085 bases
Orientation:
Minus strand
chr14:73,086,004-73,360,809
(GRCh37/hg19)

Genomic View for DPF3 Gene

Genes around DPF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DPF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DPF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DPF3 Gene

Proteins for DPF3 Gene

  • Protein details for DPF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92784-DPF3_HUMAN
    Recommended name:
    Zinc finger protein DPF3
    Protein Accession:
    Q92784
    Secondary Accessions:
    • A8MSI3
    • B7Z276
    • F5H575
    • Q32UJ0
    • Q6P9E6
    • Q6ZT41
    • Q9H7Y5

    Protein attributes for DPF3 Gene

    Size:
    378 amino acids
    Molecular mass:
    43084 Da
    Quaternary structure:
    • Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Interacts with acetylated histones H3 and H4. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity).

    Three dimensional structures from OCA and Proteopedia for DPF3 Gene

    Alternative splice isoforms for DPF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DPF3 Gene

Post-translational modifications for DPF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for DPF3 Gene

Domains & Families for DPF3 Gene

Gene Families for DPF3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for DPF3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92784

UniProtKB/Swiss-Prot:

DPF3_HUMAN :
  • The PHD-type zinc fingers mediate the binding to acetylated histones.
  • Belongs to the requiem/DPF family.
Domain:
  • The PHD-type zinc fingers mediate the binding to acetylated histones.
Family:
  • Belongs to the requiem/DPF family.
genes like me logo Genes that share domains with DPF3: view

Function for DPF3 Gene

Molecular function for DPF3 Gene

UniProtKB/Swiss-Prot Function:
Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development.

Phenotypes From GWAS Catalog for DPF3 Gene

Gene Ontology (GO) - Molecular Function for DPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0008270 zinc ion binding NAS 8812431
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with DPF3: view
genes like me logo Genes that share phenotypes with DPF3: view

Animal Models for DPF3 Gene

MGI Knock Outs for DPF3:
  • Dpf3 Dpf3<tm1.1Grc>

Animal Model Products

Clone Products

  • Addgene plasmids for DPF3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DPF3 Gene

Localization for DPF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DPF3 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 DPF3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for DPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0071565 nBAF complex ISS --
genes like me logo Genes that share ontologies with DPF3: view

Pathways & Interactions for DPF3 Gene

genes like me logo Genes that share pathways with DPF3: view

Pathways by source for DPF3 Gene

2 KEGG pathways for DPF3 Gene

Gene Ontology (GO) - Biological Process for DPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007399 nervous system development IEA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with DPF3: view

No data available for SIGNOR curated interactions for DPF3 Gene

Drugs & Compounds for DPF3 Gene

No Compound Related Data Available

Transcripts for DPF3 Gene

Unigene Clusters for DPF3 Gene

D4, zinc and double PHD fingers, family 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for DPF3

Alternative Splicing Database (ASD) splice patterns (SP) for DPF3 Gene

No ASD Table

Relevant External Links for DPF3 Gene

GeneLoc Exon Structure for
DPF3
ECgene alternative splicing isoforms for
DPF3

Expression for DPF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DPF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for DPF3 Gene

This gene is overexpressed in Muscle - Skeletal (x6.6), Brain - Cerebellar Hemisphere (x5.0), Heart - Left Ventricle (x4.6), and Brain - Cerebellum (x4.3).

Protein differential expression in normal tissues from HIPED for DPF3 Gene

This gene is overexpressed in Retina (29.8), Fetal Brain (26.9), and Blymphocyte (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DPF3 Gene



Protein tissue co-expression partners for DPF3 Gene

NURSA nuclear receptor signaling pathways regulating expression of DPF3 Gene:

DPF3

SOURCE GeneReport for Unigene cluster for DPF3 Gene:

Hs.162868

Evidence on tissue expression from TISSUES for DPF3 Gene

  • Nervous system(4.7)
  • Heart(4.2)
genes like me logo Genes that share expression patterns with DPF3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DPF3 Gene

Orthologs for DPF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for DPF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DPF3 34 33
  • 99.89 (n)
OneToOne
cow
(Bos Taurus)
Mammalia DPF3 34 33
  • 93.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Dpf3 16 34 33
  • 92.15 (n)
dog
(Canis familiaris)
Mammalia DPF3 34 33
  • 87.85 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DPF3 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DPF3 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves DPF3 34 33
  • 82.72 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DPF3 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100125167 33
  • 74.38 (n)
Str.19639 33
zebrafish
(Danio rerio)
Actinopterygii dpf3 34 33
  • 71.07 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6137 33
fruit fly
(Drosophila melanogaster)
Insecta d4 34
  • 22 (a)
ManyToMany
tth 34
  • 18 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea dpff-1 34 33
  • 46.1 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToMany
Species where no ortholog for DPF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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)
  • rat (Rattus norvegicus)
  • 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 DPF3 Gene

ENSEMBL:
Gene Tree for DPF3 (if available)
TreeFam:
Gene Tree for DPF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DPF3: view image

Paralogs for DPF3 Gene

Paralogs for DPF3 Gene

(2) SIMAP similar genes for DPF3 Gene using alignment to 3 proteins:

  • DPF3_HUMAN
  • F5H575_HUMAN
  • F8W7T1_HUMAN
genes like me logo Genes that share paralogs with DPF3: view

Variants for DPF3 Gene

Sequence variations from dbSNP and Humsavar for DPF3 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000026477 -- 72,850,334(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000046776 -- 72,755,771(-) G/C intron_variant
rs1000051360 -- 72,677,658(-) G/C genic_downstream_transcript_variant, intron_variant
rs1000054329 -- 72,609,180(-) A/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000060532 -- 72,877,875(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for DPF3 Gene

Variant ID Type Subtype PubMed ID
esv2675309 CNV deletion 23128226
esv2748861 CNV deletion 23290073
esv29194 CNV loss 19812545
esv29330 CNV gain 19812545
esv32878 CNV loss 17666407
esv3303051 CNV tandem duplication 20981092
esv3551754 CNV deletion 23714750
esv3581286 CNV loss 25503493
esv3634891 CNV loss 21293372
esv3634892 CNV loss 21293372
esv3634894 CNV loss 21293372
esv3892558 CNV gain 25118596
esv3892560 CNV gain 25118596
nsv1035460 CNV gain 25217958
nsv1048734 CNV gain 25217958
nsv1108909 CNV deletion 24896259
nsv456337 CNV loss 19166990
nsv456338 CNV loss 19166990
nsv517683 CNV gain 19592680
nsv520843 CNV loss 19592680
nsv565046 CNV loss 21841781
nsv565049 CNV loss 21841781
nsv85673 CNV deletion 16902084

Variation tolerance for DPF3 Gene

Residual Variation Intolerance Score: 57.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.54; 44.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DPF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DPF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DPF3 Gene

Disorders for DPF3 Gene

Additional Disease Information for DPF3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for DPF3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DPF3 Gene

Publications for DPF3 Gene

  1. Cerd4, third member of the d4 gene family: expression and organization of genomic locus. (PMID: 11845289) Ninkina NN … Buchman VL (Mammalian genome : official journal of the International Mammalian Genome Society 2001) 2 3 22 58
  2. The d4 gene family in the human genome. (PMID: 8812431) Chestkov AV … Buchman VL (Genomics 1996) 2 3 4 58
  3. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. (PMID: 20613843) Zeng L … Zhou MM (Nature 2010) 3 4 58
  4. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira AR … Marazita ML (Genetics in medicine : official journal of the American College of Medical Genetics 2008) 3 44 58
  5. Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. (PMID: 18765789) Lange M … Sperling S (Genes & development 2008) 3 4 58

Products for DPF3 Gene

  • Addgene plasmids for DPF3

Sources for DPF3 Gene

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