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

Gene ID: 360550, updated on 2-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 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

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