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    Dpf3 double PHD fingers 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 299186, updated on 17-Aug-2024

    Summary

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    Official Symbol
    Dpf3provided by RGD
    Official Full Name
    double PHD fingers 3provided by RGD
    Primary source
    RGD:1309052
    See related
    EnsemblRapid:ENSRNOG00000008086 AllianceGenome:RGD:1309052
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable histone binding activity and transcription coregulator activity. Predicted to be involved in negative regulation of transcription, DNA-templated; nervous system development; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of nBAF complex. Orthologous to human DPF3 (double PHD fingers 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 30.7), Brain (RPKM 29.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dpf3 in Genome Data Viewer
    Location:
    6q31
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (108577792..108856724, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (102841403..103125558, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (106660569..106971310, complement)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene regulator of G-protein signaling 6 Neighboring gene uncharacterized LOC120093216 Neighboring gene uncharacterized LOC120093217 Neighboring gene uncharacterized LOC134479225 Neighboring gene uncharacterized LOC134479227 Neighboring gene uncharacterized LOC134479226 Neighboring gene DDB1 and CUL4 associated factor 4 Neighboring gene zinc finger FYVE-type containing 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH, et al. PLoS One, 2013. PMID 23355908, Free PMC Article
    2. Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA. Cui H, et al. Nucleic Acids Res, 2016 Apr 7. PMID 26582913, Free PMC Article
    3. Readout of epigenetic modifications. Patel DJ, et al. Annu Rev Biochem, 2013. PMID 23642229, Free PMC Article
    4. Kinetic analysis of npBAF to nBAF switching reveals exchange of SS18 with CREST and integration with neural developmental pathways. Staahl BT, et al. J Neurosci, 2013 Jun 19. PMID 23785148, Free PMC Article
    5. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Lessard J, et al. Neuron, 2007 Jul 19. PMID 17640523, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Activation of DPF3a upon hypertrophic stimuli in cardiac hypertrophy switches cardiac fetal gene expression from being silenced by HEY to being activated by BRG1.
      Title: Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of nBAF complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein DPF3
    Names
    D4, zinc and double PHD fingers, family 3
    RGD1563913
    zinc finger protein DPF3-like

    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.

    mRNA and Protein(s)

    1. NM_001191818.1 → NP_001178747.1  zinc finger protein DPF3

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000006
      UniProtKB/TrEMBL
      D3Z9E7
      Conserved Domains (3) summary
      COG5189
      Location:195 → 222
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:261 → 292
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086024.1 Reference GRCr8

      Range
      108577792..108856724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008764749.4 → XP_008762971.1  zinc finger protein DPF3 isoform X2

      See identical proteins and their annotated locations for XP_008762971.1

      UniProtKB/TrEMBL
      A0A8I6AL27
      Related
      ENSRNOP00000093966.1, ENSRNOT00000097275.2
      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 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    2. XM_008764747.3 → XP_008762969.1  zinc finger protein DPF3 isoform X1

      See identical proteins and their annotated locations for XP_008762969.1

      Conserved Domains (3) summary
      cd15530
      Location:341 → 386
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15692
      Location:284 → 340
      PHD1_DPF3; PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3)
      pfam14051
      Location:36 → 107
      Requiem_N; N-terminal domain of DPF2/REQ

    3. XM_039112021.2 → XP_038967949.1  zinc finger protein DPF3 isoform X4

      Conserved Domains (4) summary
      COG5189
      Location:139 → 166
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:262 → 307
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15692
      Location:205 → 261
      PHD1_DPF3; PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ

    4. XM_008764751.4 → XP_008762973.1  zinc finger protein DPF3 isoform X4

      See identical proteins and their annotated locations for XP_008762973.1

      Conserved Domains (4) summary
      COG5189
      Location:139 → 166
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:262 → 307
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15692
      Location:205 → 261
      PHD1_DPF3; PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3)
      pfam14051
      Location:1 → 23
      Requiem_N; N-terminal domain of DPF2/REQ

    5. XM_063261728.1 → XP_063117798.1  zinc finger protein DPF3 isoform X6

    6. XM_039112020.2 → XP_038967948.1  zinc finger protein DPF3 isoform X3

      Conserved Domains (3) summary
      COG5189
      Location:218 → 245
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      pfam14051
      Location:36 → 102
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:284 → 315
      PHD_SF; PHD finger superfamily

    7. XM_039112022.2 → XP_038967950.1  zinc finger protein DPF3 isoform X5

      Related
      ENSRNOP00000099978.1, ENSRNOT00000153738.1
      Conserved Domains (3) summary
      COG5189
      Location:218 → 245
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      pfam14051
      Location:36 → 102
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:284 → 314
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_010052069.1 RNA Sequence

    2. XR_010052068.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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