U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Dpf3 double PHD fingers 3 [ Mus musculus (house mouse) ]

    Gene ID: 70127, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Dpf3provided by MGI
    Official Full Name
    double PHD fingers 3provided by MGI
    Primary source
    MGI:MGI:1917377
    See related
    Ensembl:ENSMUSG00000021221 AllianceGenome:MGI:1917377
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CERD4; BAF45C; cer-d4; Gm18872; 2810403B03Rik; 6530402L11Rik
    Summary
    Predicted to enable metal ion binding activity. Involved in muscle cell differentiation and nervous system development. Part of nBAF complex. Is expressed in several structures, including central nervous system; gonad; heart; retina; and urinary system. Orthologous to human DPF3 (double PHD fingers 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis adult (RPKM 4.7), cerebellum adult (RPKM 3.8) and 24 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Dpf3 in Genome Data Viewer
    Location:
    12 D1; 12 38.64 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (83260525..83534510, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (83213751..83487736, complement)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene regulator of G-protein signaling 6 Neighboring gene predicted gene, 51988 Neighboring gene predicted gene, 53731 Neighboring gene CapStarr-seq enhancer MGSCv37_chr12:84716828-84716981 Neighboring gene STARR-positive B cell enhancer ABC_E3060 Neighboring gene STARR-positive B cell enhancer ABC_E9860 Neighboring gene STARR-seq mESC enhancer starr_32707 Neighboring gene STARR-seq mESC enhancer starr_32708 Neighboring gene STARR-seq mESC enhancer starr_32712 Neighboring gene STARR-positive B cell enhancer ABC_E1444 Neighboring gene DDB1 and CUL4 associated factor 4 Neighboring gene zinc finger, FYVE domain containing 1 Neighboring gene H2A histone family, member Z pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. CCR7 Chemokine Receptor-Inducible lnc-Dpf3 Restrains Dendritic Cell Migration by Inhibiting HIF-1α-Mediated Glycolysis. Liu J, et al. Immunity, 2019 Mar 19. PMID 30824325
    2. EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex. Shapira SN, et al. Genes Dev, 2017 Apr 1. PMID 28428261, Free PMC Article
    3. The d4 gene family in the human genome. Chestkov AV, et al. Genomics, 1996 Aug 15. PMID 8812431
    4. Cerd4, third member of the d4 gene family: expression and organization of genomic locus. Ninkina NN, et al. Mamm Genome, 2001 Nov. PMID 11845289
    5. HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription. Zhu X, et al. Nucleic Acids Res, 2020 Jul 9. PMID 32459350, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription.
      Title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription.
    2. Lnc-Dpf3 directly bound to HIF-1alpha.
      Title: CCR7 Chemokine Receptor-Inducible lnc-Dpf3 Restrains Dendritic Cell Migration by Inhibiting HIF-1α-Mediated Glycolysis.
    3. DPF3 adds a further layer of complexity to the BAF complex by representing a tissue-specific anchor between histone acetylations as well as methylations and chromatin remodeling.
      Title: Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (6) 
    • Targeted (1) 

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in muscle cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of myoblast differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G0 to G1 transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of mitotic metaphase/anaphase transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of nucleotide-excision repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of brahma complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of nBAF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    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

    Go to the top of the page Help
    Preferred Names
    zinc finger protein DPF3
    Names
    BRG1-associated factor 45C
    D4 zinc and double PHD finger family 3
    cerebellum D4
    zinc finger protein cer-d4

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001267625.1 → NP_001254554.1  zinc finger protein DPF3 isoform 1

      See identical proteins and their annotated locations for NP_001254554.1

      Status: VALIDATED

      Source sequence(s)
      AK012970, AK039011
      Consensus CDS
      CCDS59574.1
      UniProtKB/Swiss-Prot
      P58269, Q80W78, Q8CAD8
      UniProtKB/TrEMBL
      F7CPB1
      Related
      ENSMUSP00000136280.2, ENSMUST00000178756.8
      Conserved Domains (4) summary
      COG5189
      Location:195 → 222
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:318 → 363
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15692
      Location:261 → 317
      PHD1_DPF3; PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3)
      pfam14051
      Location:13 → 84
      Requiem_N; N-terminal domain of DPF2/REQ

    2. NM_001267626.2 → NP_001254555.1  zinc finger protein DPF3 isoform 2

      See identical proteins and their annotated locations for NP_001254555.1

      Status: VALIDATED

      Source sequence(s)
      AC139382, AC205767, CT025545
      UniProtKB/TrEMBL
      B5TZD5, F7CL41
      Related
      ENSMUSP00000122004.2, ENSMUST00000144237.8
      Conserved Domains (2) summary
      pfam14051
      Location:13 → 84
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:261 → 292
      PHD_SF; PHD finger superfamily

    3. NM_058212.3 → NP_478119.1  zinc finger protein DPF3 isoform 3

      See identical proteins and their annotated locations for NP_478119.1

      Status: VALIDATED

      Source sequence(s)
      AC139382, AC205767, CT025545
      Consensus CDS
      CCDS56846.1
      UniProtKB/TrEMBL
      F6T820
      Related
      ENSMUSP00000137477.2, ENSMUST00000177959.8
      Conserved Domains (2) summary
      pfam14051
      Location:13 → 84
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:260 → 291
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      83260525..83534510 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NG_018261.2: Suppressed sequence

      Description
      NG_018261.2: This RefSeq was removed because it is now thought that this gene does encode a protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P58269.2 GenPept UniProtKB/Swiss-Prot:P58269

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools