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    phf2 PHD finger protein 2 [ Danio rerio (zebrafish) ]

    Gene ID: 503778, updated on 9-Dec-2024

    Summary

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    Official Symbol
    phf2provided by ZNC
    Official Full Name
    PHD finger protein 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050302-10
    See related
    Ensembl:ENSDARG00000018691 AllianceGenome:ZFIN:ZDB-GENE-050302-10
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    phf8; im:4200679; wu:fa14c10
    Summary
    Predicted to enable several functions, including histone demethylase activity; transcription coactivator activity; and transition metal ion binding activity. Predicted to be involved in protein demethylation and regulation of gene expression. Predicted to act upstream of or within chromatin organization. Predicted to be located in kinetochore and nucleolus. Orthologous to human PHF2 (PHD finger protein 2). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See phf2 in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (27644474..27702835, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (27397300..27455726, complement)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene BARX homeobox 1 Neighboring gene uncharacterized LOC137496701 Neighboring gene family with sequence similarity 120A Neighboring gene Cas scaffold protein family member 4

    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. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. Tsukada Y, et al. Genes Dev, 2010 Mar 1. PMID 20194436, Free PMC Article
    2. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Fellous A, et al. Gene, 2019 Mar 1. PMID 30458291
    3. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    4. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (8) 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 2-oxoglutarate-dependent dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H4K20 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables iron ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylated histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of rDNA heterochromatin formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein demethylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in kinetochore IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in kinetochore ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase phf2
    Names
    PHD finger protein 8
    NP_001189347.1
    XP_005169348.1
    XP_005169349.1

    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_001202418.1 → NP_001189347.1  lysine-specific demethylase phf2

      Status: VALIDATED

      Source sequence(s)
      BX601648
      UniProtKB/Swiss-Prot
      E7EZ72, Q6P949
      Related
      ENSDARP00000111663.4, ENSDART00000125352.4
      Conserved Domains (3) summary
      smart00558
      Location:201 → 264
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15641
      Location:7 → 56
      PHD_PHF2; PHD finger found in lysine-specific demethylase PHF2
      cl21464
      Location:236 → 336
      cupin_like; Conserved domain found in cupin and related proteins

    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_007122.7 Reference GRCz11 Primary Assembly

      Range
      27644474..27702835 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005169292.5 → XP_005169349.1  lysine-specific demethylase phf2 isoform X2

      UniProtKB/Swiss-Prot
      E7EZ72, Q6P949
      UniProtKB/TrEMBL
      A0A8M2BH62
      Conserved Domains (3) summary
      smart00558
      Location:201 → 264
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15641
      Location:7 → 56
      PHD_PHF2; PHD finger found in lysine-specific demethylase PHF2
      cl21464
      Location:236 → 336
      cupin_like; Conserved domain found in cupin and related proteins

    2. XM_005169291.5 → XP_005169348.1  lysine-specific demethylase phf2 isoform X1

      UniProtKB/Swiss-Prot
      E7EZ72, Q6P949
      UniProtKB/TrEMBL
      A0A8M2BGL0
      Related
      ENSDARP00000045941.6, ENSDART00000045942.8
      Conserved Domains (3) summary
      smart00558
      Location:201 → 264
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15641
      Location:7 → 56
      PHD_PHF2; PHD finger found in lysine-specific demethylase PHF2
      cl21464
      Location:236 → 336
      cupin_like; Conserved domain found in cupin and related proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P949.3 GenPept UniProtKB/Swiss-Prot:Q6P949

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