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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. 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.

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

Regulatory Elements for DPF3 Gene

Enhancers for DPF3 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
GH14G072662 1.3 Ensembl ENCODE dbSUPER 45.7 +228.8 228817 4.7 CBX3 JUN ETV1 BMI1 EBF1 RFX5 CTBP1 GATA3 GATA2 CBX5 DPF3 GC14M072609 GC14M072730
GH14G072557 1.9 FANTOM5 Ensembl ENCODE dbSUPER 14.9 +335.0 335014 3.1 HDGF FOXA2 PKNOX1 CREB3L1 MLX ARNT ARID4B SIN3A YY1 ZNF766 DPF3 GC14P072564 MIR7843
GH14G072780 1.5 Ensembl ENCODE dbSUPER 15.6 +112.5 112547 2.3 HDGF ATF1 FOXA2 YBX1 TCF12 GATA2 ZNF207 FOS KLF13 MCM3 DPF3 ACOT2 GC14M072730 GC14M072854 ENSG00000206751
GH14G072606 1 Ensembl ENCODE 21.3 +285.1 285079 4.1 JUN FOSL1 ZFHX2 SMC3 NFE2 FOS MAFK NFE2L2 EGR2 PAF1 DPF3 GC14P072612 GC14M072593
GH14G072677 1 ENCODE dbSUPER 20.6 +215.0 215023 2.8 SOX13 MXI1 FOXA2 JUN MAX ZNF384 BMI1 TEAD3 RARA RERE DPF3 GC14M072609 GC14M072730
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DPF3 on UCSC Golden Path with GeneCards custom track

Promoters for DPF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000070585 716 2801 PKNOX1 ATF1 ARID4B SIN3A ZNF2 YY1 GLIS2 FOS ZNF263 ZHX2

Genomic Location for DPF3 Gene

Chromosome:
14
Start:
72,609,032 bp from pter
End:
72,894,116 bp from pter
Size:
285,085 bases
Orientation:
Minus strand

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

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.

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:

Animal Model Products

CRISPR Products

Inhibitory RNA 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

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

No Data Available

Gene Ontology (GO) - Biological Process for DPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0016569 covalent chromatin modification IEA --
genes like me logo Genes that share ontologies with DPF3: view

No data available for Pathways by source and 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:

CRISPR Products

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 35
  • 99.89 (n)
cow
(Bos Taurus)
Mammalia DPF3 34 35
  • 93.56 (n)
mouse
(Mus musculus)
Mammalia Dpf3 34 16 35
  • 92.15 (n)
dog
(Canis familiaris)
Mammalia DPF3 34 35
  • 87.85 (n)
oppossum
(Monodelphis domestica)
Mammalia DPF3 35
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DPF3 35
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves DPF3 34 35
  • 82.72 (n)
lizard
(Anolis carolinensis)
Reptilia DPF3 35
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100125167 34
  • 74.38 (n)
Str.19639 34
zebrafish
(Danio rerio)
Actinopterygii dpf3 34 35
  • 71.07 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6137 34
fruit fly
(Drosophila melanogaster)
Insecta d4 35
  • 22 (a)
ManyToMany
tth 35
  • 18 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea dpff-1 34 35
  • 46.1 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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)

Paralogs for DPF3 Gene

Paralogs for DPF3 Gene

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

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 Sequence Context AA Info Type
rs1000026477 -- 72,850,334(+) CCCTA(C/T)TCTTC intron-variant
rs1000046776 -- 72,755,771(+) GCTTT(C/G)AATCC intron-variant
rs1000051360 -- 72,677,658(+) TAGTG(C/G)GTGGC intron-variant
rs1000054329 -- 72,609,180(+) CTTTG(A/T)GAACG intron-variant, utr-variant-3-prime
rs1000060532 -- 72,877,875(+) TATGT(A/G)TAAGT 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)

Relevant External Links for DPF3 Gene

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

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

Disorders for DPF3 Gene

Relevant External Links for DPF3

Genetic Association Database (GAD)
DPF3
Human Genome Epidemiology (HuGE) Navigator
DPF3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DPF3

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 N.N. … Buchman V.L. (Mamm. Genome 2001) 2 3 22 64
  2. The d4 gene family in the human genome. (PMID: 8812431) Chestkov A.V. … Buchman V.L. (Genomics 1996) 2 3 4 64
  3. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. (PMID: 20613843) Zeng L. … Zhou M.M. (Nature 2010) 3 4 64
  4. 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 Dev. 2008) 3 4 64
  5. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira A.R. … Marazita M.L. (Genet. Med. 2008) 3 46 64

Products for DPF3 Gene

  • Addgene plasmids for DPF3

Sources for DPF3 Gene

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