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    Phf1 PHD finger protein 1 [ Mus musculus (house mouse) ]

    Gene ID: 21652, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Phf1provided by MGI
    Official Full Name
    PHD finger protein 1provided by MGI
    Primary source
    MGI:MGI:98647
    See related
    Ensembl:ENSMUSG00000024193 AllianceGenome:MGI:98647
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Pcl1; Phf2; Tctex3; D17Ertd455e
    Summary
    The protein encoded by this gene belongs to the polycomb-like protein family, which is a component of polycomb repressive complex-2. This complex represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 and is required for the regulation of developmental genes including homeotic genes. The gene is expressed primarily in testis tissue. Small interfering RNA-mediated knockdown in cultured cell lines results in changes in homeotic gene expression coincident with alterations in promoter methylation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 74.8), spleen adult (RPKM 55.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Phf1 in Genome Data Viewer
    Location:
    17 A3.3; 17 13.6 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (27152101..27156882)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (26933127..26937908)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 41555 Neighboring gene STARR-seq mESC enhancer starr_42135 Neighboring gene STARR-seq mESC enhancer starr_42137 Neighboring gene kinesin family member C5B Neighboring gene microRNA 6967-1 Neighboring gene STARR-positive B cell enhancer ABC_E487 Neighboring gene microRNA 6968 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene synaptic Ras GTPase activating protein 1 homolog (rat) Neighboring gene microRNA 3083b Neighboring gene microRNA 3083

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19.
      Title: Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19.
    2. PHF1 is necessary for the accurate alignment of chromosomes and oocyte euploidy, as well for the regulation of the asymmetric division of oocytes in mouse.
      Title: PHF1 is required for chromosome alignment and asymmetric division during mouse meiotic oocyte maturation.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (2) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone methyltransferase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA repair-dependent chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair-dependent chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of ESC/E(Z) complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ESC/E(Z) complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ESC/E(Z) complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 1
    Names
    polycomb-like protein 1
    t-complex testis-expressed 3

    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_001302397.1 → NP_001289326.1  PHD finger protein 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
      Source sequence(s)
      AC144621, AK133474, AK139088
      Consensus CDS
      CCDS89030.1
      UniProtKB/TrEMBL
      A0A494B9I3, A0A494BBE6
      Related
      ENSMUSP00000158483.2, ENSMUST00000237412.2
      Conserved Domains (4) summary
      smart00333
      Location:29 → 80
      TUDOR; Tudor domain
      cd15500
      Location:89 → 139
      PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
      cd15582
      Location:188 → 239
      PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
      pfam14061
      Location:530 → 555
      Mtf2_C; Polycomb-like MTF2 factor 2

    2. NM_009343.3 → NP_033369.2  PHD finger protein 1 isoform 1

      See identical proteins and their annotated locations for NP_033369.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC144621, AK133474, AK139088
      Consensus CDS
      CCDS37518.1
      UniProtKB/Swiss-Prot
      O54808, Q9Z1B8
      UniProtKB/TrEMBL
      A0A494B9I3
      Related
      ENSMUSP00000073402.6, ENSMUST00000073724.7
      Conserved Domains (4) summary
      smart00333
      Location:29 → 80
      TUDOR; Tudor domain
      cd15500
      Location:89 → 139
      PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
      cd15582
      Location:188 → 239
      PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
      pfam14061
      Location:531 → 556
      Mtf2_C; Polycomb-like MTF2 factor 2

    RNA

    1. NR_126158.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, which results in a frameshift compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC144621, AK133474, AK139088

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      27152101..27156882
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Z1B8.2 GenPept UniProtKB/Swiss-Prot:Q9Z1B8

    Gene LinkOut

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

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