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    Dpf2 double PHD fingers 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361711, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Dpf2provided by RGD
    Official Full Name
    double PHD fingers 2provided by RGD
    Primary source
    RGD:1311699
    See related
    EnsemblRapid:ENSRNOG00000020892 AllianceGenome:RGD:1311699
    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 H3K9me3 modified histone binding activity and lysine-acetylated histone binding activity. Predicted to be involved in negative regulation of myeloid progenitor cell differentiation and nervous system development. Predicted to be located in several cellular components, including centrosome; chromatin; and nucleoplasm. Predicted to be part of nBAF complex. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 7. Orthologous to human DPF2 (double PHD fingers 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 180.1), Lung (RPKM 152.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Dpf2 in Genome Data Viewer
    Location:
    1q43
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (212612986..212628376, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (203183674..203199037, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (221253764..221269043, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 25, member 45 Neighboring gene U2 spliceosomal RNA Neighboring gene tigger transposable element derived 3 Neighboring gene CDC42 effector protein 2 Neighboring gene 40S ribosomal protein S27-like

    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
    • 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. Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome. Vasileiou G, et al. Am J Hum Genet, 2018 Mar 1. PMID 29429572, Free PMC Article
    2. Expression and chromosomal localization of the Requiem gene. Gabig TG, et al. Mamm Genome, 1998 Aug. PMID 9680388
    3. The spectrum of SWI/SNF mutations, ubiquitous in human cancers. Shain AH, et al. PLoS One, 2013. PMID 23355908, Free PMC Article
    4. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Hargreaves DC, et al. Cell Res, 2011 Mar. PMID 21358755, Free PMC Article
    5. Heterogeneous nuclear ribonucleoprotein C1/C2, MeCP1, and SWI/SNF form a chromatin remodeling complex at the beta-globin locus control region. Mahajan MC, et al. Proc Natl Acad Sci U S A, 2005 Oct 18. PMID 16217013, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables H3K9me3 modified histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables lysine-acetylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 negative regulation of myeloid progenitor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein ubi-d4
    Names
    D4, zinc and double PHD fingers family 2

    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_001108516.1 → NP_001101986.1  zinc finger protein ubi-d4

      See identical proteins and their annotated locations for NP_001101986.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473953
      UniProtKB/TrEMBL
      A6HZB0, B2RYI3
      Related
      ENSRNOP00000028363.7, ENSRNOT00000028363.7
      Conserved Domains (4) summary
      COG5189
      Location:201 → 233
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:329 → 374
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:272 → 327
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:13 → 75
      Requiem_N; N-terminal domain of DPF2/REQ

    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_086019.1 Reference GRCr8

      Range
      212612986..212628376 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006230850.4 → XP_006230912.1  zinc finger protein ubi-d4 isoform X1

      UniProtKB/TrEMBL
      B2RYI3
      Related
      ENSRNOP00000100880.1, ENSRNOT00000130117.1
      Conserved Domains (4) summary
      COG5189
      Location:201 → 247
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:343 → 388
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:286 → 341
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:13 → 75
      Requiem_N; N-terminal domain of DPF2/REQ

    2. XM_039083942.2 → XP_038939870.1  zinc finger protein ubi-d4 isoform X2

      UniProtKB/TrEMBL
      B2RYI3
      Conserved Domains (4) summary
      COG5189
      Location:181 → 227
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:323 → 368
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15691
      Location:266 → 321
      PHD1_DPF2_like; PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2)
      pfam14051
      Location:1 → 55
      Requiem_N; N-terminal domain of DPF2/REQ
    Nucleotide Protein Strain
    Heading Accession and Version

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