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

Gene ID: 21652, updated on 11-Apr-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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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
  • 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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Related articles in PubMed

  1. PHF1 is required for chromosome alignment and asymmetric division during mouse meiotic oocyte maturation. Qu Y, et al. Cell Cycle, 2018. PMID 30382790, Free PMC Article
  2. Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19. Dong C, et al. Elife, 2020 Sep 1. PMID 32869745, Free PMC Article
  3. Role of hPHF1 in H3K27 methylation and Hox gene silencing. Cao R, et al. Mol Cell Biol, 2008 Mar. PMID 18086877, Free PMC Article
  4. Misexpression of Polycomb-group proteins in Xenopus alters anterior neural development and represses neural target genes. Yoshitake Y, et al. Dev Biol, 1999 Nov 15. PMID 10545244
  5. Xenopus Polycomblike 2 (XPcl2) controls anterior to posterior patterning of the neural tissue. Kitaguchi T, et al. Dev Genes Evol, 2001 Jun. PMID 11466526

See all (36) citations in PubMed

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
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair-dependent chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
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
  
colocalizes_with centrosome ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton 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 site of double-strand break ISO
Inferred from Sequence Orthology
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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