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    phf3 PHD finger protein 3 [ Danio rerio (zebrafish) ]

    Gene ID: 553518, updated on 4-Jan-2025

    Summary

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    Official Symbol
    phf3provided by ZNC
    Official Full Name
    PHD finger protein 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-090313-207
    See related
    Ensembl:ENSDARG00000034768 AllianceGenome:ZFIN:ZDB-GENE-090313-207
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    si:dkey-188i13.1
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within DNA-templated transcription. Predicted to be active in nucleus. Is expressed in telencephalon. Orthologous to human PHF3 (PHD finger protein 3). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See phf3 in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (37653953..37673494)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (37528012..37547823)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene interferon alpha inducible protein 27.7 Neighboring gene interferon alpha inducible protein 27.8 Neighboring gene eyes shut homolog Neighboring gene zgc:171579

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    2. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. Diotel N, et al. J Comp Neurol, 2015 Jun 1. PMID 25556858, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007124.7 Reference GRCz11 Primary Assembly

      Range
      37653953..37673494
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068213095.1 → XP_068069196.1  PHD finger protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M6Z9N0

    2. XM_017358845.3 → XP_017214334.2  PHD finger protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M6Z9N0

    3. XM_005157030.5 → XP_005157087.1  PHD finger protein 3 isoform X3

      See identical proteins and their annotated locations for XP_005157087.1

      UniProtKB/TrEMBL
      A0A8M2B347, A0A8M6Z9N0, B8A483
      Related
      ENSDARP00000091125.4, ENSDART00000100352.6
      Conserved Domains (6) summary
      cd15638
      Location:625 → 675
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:755 → 863
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1027 → 1176
      SPOC; SPOC domain
      cl25495
      Location:1271 → 1449
      Endomucin; Endomucin
      cl25751
      Location:341 → 732
      DUF4045; Domain of unknown function (DUF4045)
      cl25887
      Location:1605 → 1690
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

    4. XM_681308.10 → XP_686400.6  PHD finger protein 3 isoform X3

      See identical proteins and their annotated locations for XP_686400.6

      UniProtKB/TrEMBL
      A0A8M2B347, A0A8M6Z9N0, B8A483
      Related
      ENSDARP00000148563.1, ENSDART00000193251.1
      Conserved Domains (6) summary
      cd15638
      Location:625 → 675
      PHD_PHF3; PHD finger found in PHD finger protein 3 (PHF3)
      pfam07500
      Location:755 → 863
      TFIIS_M; Transcription factor S-II (TFIIS), central domain
      pfam07744
      Location:1027 → 1176
      SPOC; SPOC domain
      cl25495
      Location:1271 → 1449
      Endomucin; Endomucin
      cl25751
      Location:341 → 732
      DUF4045; Domain of unknown function (DUF4045)
      cl25887
      Location:1605 → 1690
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    Nucleotide Protein Strain
    Heading Accession and Version

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