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    Phf23 PHD finger protein 23 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360550, updated on 27-Nov-2024

    Summary

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    Symbol
    Phf23provided by RGD
    Full Name
    PHD finger protein 23provided by RGD
    Primary source
    RGD:1302969
    See related
    EnsemblRapid:ENSRNOG00000017657 AllianceGenome:RGD:1302969
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of protein ubiquitination. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human PHF23 (PHD finger protein 23). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 82.0), Thymus (RPKM 73.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Phf23 in Genome Data Viewer
    Location:
    10q24
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (55217351..55221471)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (54718663..54722784)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (56605078..56609236)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene CTD nuclear envelope phosphatase 1 Neighboring gene GABA type A receptor-associated protein Neighboring gene dishevelled segment polarity protein 2 Neighboring gene acyl-CoA dehydrogenase, very long chain Neighboring gene microRNA 324

    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. PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1. Wang Z, et al. Autophagy, 2014. PMID 25484098, Free PMC Article
    2. 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
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC94192

    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 autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of autophagosome maturation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    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
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 23
    Names
    PDH-containing protein JUNE-1
    PHD zinc finger containing protein JUNE1

    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_001004272.2 → NP_001004272.1  PHD finger protein 23 isoform 2

      See identical proteins and their annotated locations for NP_001004272.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/Swiss-Prot
      Q6AY75
      UniProtKB/TrEMBL
      A0A8I5ZTH2
      Related
      ENSRNOP00000082050.1, ENSRNOT00000104234.2
      Conserved Domains (1) summary
      cd15631
      Location:272 → 315
      PHD_PHF23; PHD finger found in PHD finger protein 23 (PHF23)

    2. NM_001399559.1 → NP_001386488.1  PHD finger protein 23 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8L2QDN5, A6HFZ9
      Related
      ENSRNOP00000024079.5, ENSRNOT00000024079.7

    3. NM_001399560.1 → NP_001386489.1  PHD finger protein 23 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A6HG04

    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_086028.1 Reference GRCr8

      Range
      55217351..55221471
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269337.1 → XP_063125407.1  PHD finger protein 23 isoform X1

      UniProtKB/TrEMBL
      A6HG04

    2. XM_063269336.1 → XP_063125406.1  PHD finger protein 23 isoform X1

      UniProtKB/TrEMBL
      A6HG04

    3. XM_063269338.1 → XP_063125408.1  PHD finger protein 23 isoform X1

      UniProtKB/TrEMBL
      A6HG04

    4. XM_063269335.1 → XP_063125405.1  PHD finger protein 23 isoform X1

      UniProtKB/TrEMBL
      A6HG04
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6AY75.1 GenPept UniProtKB/Swiss-Prot:Q6AY75

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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