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

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

    Summary

    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
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    Genomic context

    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

    Expression

    • 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

    General gene information

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity  
    enables dioxygenase activity  
    enables histone H3K9 demethylase activity  
    enables histone H4K20 demethylase activity  
    enables histone demethylase activity  
    enables iron ion binding  
    enables metal ion binding  
    enables methylated histone binding  
    enables oxidoreductase activity  
    enables transcription coactivator activity  
    enables transcription coregulator activity  
    enables zinc ion binding  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization  
    involved_in chromatin remodeling  
    involved_in negative regulation of rDNA heterochromatin formation  
    involved_in protein demethylation  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in transcription initiation-coupled chromatin remodeling  
    Component Evidence Code Pubs
    located_in chromosome  
    located_in chromosome, centromeric region  
    located_in kinetochore  
    located_in kinetochore  
    located_in nucleolus  
    located_in nucleus  

    General protein information

    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
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