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Aliases for PHF1 Gene

Aliases for PHF1 Gene

  • PHD Finger Protein 1 2 3
  • Tudor Domain Containing 19C 2 3
  • Polycomb-Like Protein 1 3 4
  • HPCl1 3 4
  • HPHF1 3 4
  • PCL1 3 4
  • Protein PHF1 4
  • TDRD19C 3
  • MTF2L2 3
  • PHF2 3

External Ids for PHF1 Gene

Previous GeneCards Identifiers for PHF1 Gene

  • GC06P033381
  • GC06P033425
  • GC06P033486
  • GC06Po33518
  • GC06P033120

Summaries for PHF1 Gene

Entrez Gene Summary for PHF1 Gene

  • This gene encodes a Polycomb group protein. The protein is a component of a histone H3 lysine-27 (H3K27)-specific methyltransferase complex, and functions in transcriptional repression of homeotic genes. The protein is also recruited to double-strand breaks, and reduced protein levels results in X-ray sensitivity and increased homologous recombination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

GeneCards Summary for PHF1 Gene

PHF1 (PHD Finger Protein 1) is a Protein Coding gene. Diseases associated with PHF1 include ossifying fibromyxoid tumor. Among its related pathways are Chromatin Regulation / Acetylation. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and methylated histone binding. An important paralog of this gene is PHF19.

UniProtKB/Swiss-Prot for PHF1 Gene

  • Polycomb group (PcG) that specifically binds histone H3 trimethylated at Lys-36 (H3K36me3) and recruits the PRC2 complex. Involved in DNA damage response and is recruited at double-strand breaks (DSBs). Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex: it is however unclear whether recruitment of the PRC2 complex to H3K36me3 leads to enhance or inhibit H3K27me3 methylation mediated by the PRC2 complex. According to some reports, PRC2 recruitment by PHF1 promotes H3K27me3 and subsequent gene silencing by inducing spreading of PRC2 and H3K27me3 into H3K36me3 loci (PubMed:18285464 and PubMed:23273982). According to another report, PHF1 recruits the PRC2 complex at double-strand breaks (DSBs) and inhibits the activity of PRC2 (PubMed:23142980). Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53.

Gene Wiki entry for PHF1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF1 Gene

Genomics for PHF1 Gene

Regulatory Elements for PHF1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PHF1 Gene

Start:
33,410,399 bp from pter
End:
33,416,453 bp from pter
Size:
6,055 bases
Orientation:
Plus strand

Genomic View for PHF1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PHF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF1 Gene

Proteins for PHF1 Gene

  • Protein details for PHF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43189-PHF1_HUMAN
    Recommended name:
    PHD finger protein 1
    Protein Accession:
    O43189
    Secondary Accessions:
    • B1AZX2
    • B1AZX3
    • O60929
    • Q5SU07
    • Q5SU08
    • Q96KM7

    Protein attributes for PHF1 Gene

    Size:
    567 amino acids
    Molecular mass:
    62106 Da
    Quaternary structure:
    • Interacts with CHMP1 (By similarity). Associated component of the PRC2 complex. Interacts with p53/TP53.

    Three dimensional structures from OCA and Proteopedia for PHF1 Gene

    Alternative splice isoforms for PHF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF1 Gene

Proteomics data for PHF1 Gene at MOPED

Post-translational modifications for PHF1 Gene

  • Ubiquitination at Lys172
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF1 Gene

No data available for DME Specific Peptides for PHF1 Gene

Domains for PHF1 Gene

Gene Families for PHF1 Gene

HGNC:
  • PHF :Zinc fingers, PHD-type
  • TDRD :Tudor domain containing

Suggested Antigen Peptide Sequences for PHF1 Gene

Graphical View of Domain Structure for InterPro Entry

O43189

UniProtKB/Swiss-Prot:

PHF1_HUMAN :
  • O43189
Domain:
  • The Tudor domain recognizes and binds H3K36me3 (PubMed:23228662, PubMed:23273982 and PubMed:23142980)
  • Contains 1 Tudor domain.
Family:
  • Belongs to the Polycomblike family.
Similarity:
  • Contains 2 PHD-type zinc fingers.
genes like me logo Genes that share domains with PHF1: view

Function for PHF1 Gene

Molecular function for PHF1 Gene

GENATLAS Biochemistry: PHD finger protein 1,Drosophila polycomb-like homolog,involved in the epigenetic regulation of developmental genes
UniProtKB/Swiss-Prot Function: Polycomb group (PcG) that specifically binds histone H3 trimethylated at Lys-36 (H3K36me3) and recruits the PRC2 complex. Involved in DNA damage response and is recruited at double-strand breaks (DSBs). Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex: it is however unclear whether recruitment of the PRC2 complex to H3K36me3 leads to enhance or inhibit H3K27me3 methylation mediated by the PRC2 complex. According to some reports, PRC2 recruitment by PHF1 promotes H3K27me3 and subsequent gene silencing by inducing spreading of PRC2 and H3K27me3 into H3K36me3 loci (PubMed:18285464 and PubMed:23273982). According to another report, PHF1 recruits the PRC2 complex at double-strand breaks (DSBs) and inhibits the activity of PRC2 (PubMed:23142980). Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53.

Gene Ontology (GO) - Molecular Function for PHF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 sequence-specific DNA binding transcription factor activity TAS 9545646
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0035064 methylated histone binding IDA 23142980
genes like me logo Genes that share ontologies with PHF1: view

Phenotypes for PHF1 Gene

genes like me logo Genes that share phenotypes with PHF1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PHF1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for PHF1 Gene

Localization for PHF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF1 Gene

Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Localizes specifically to the promoters of numerous target genes. Localizes to double-strand breaks (DSBs) sites following DNA damage. Co-localizes with NEK6 in the centrosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PHF1 Gene COMPARTMENTS Subcellular localization image for PHF1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for PHF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 23273982
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton --
genes like me logo Genes that share ontologies with PHF1: view

Pathways for PHF1 Gene

genes like me logo Genes that share pathways with PHF1: view

Pathways by source for PHF1 Gene

1 Cell Signaling Technology pathway for PHF1 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Remodeling Factors in human,mouse,rat
    • Polycomb & Trithorax Complexes in human,mouse,rat

Gene Ontology (GO) - Biological Process for PHF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006974 cellular response to DNA damage stimulus IDA 23142980
GO:0010467 gene expression TAS --
GO:0016568 chromatin modification IEA --
genes like me logo Genes that share ontologies with PHF1: view

Transcripts for PHF1 Gene

Unigene Clusters for PHF1 Gene

PHD finger protein 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PHF1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c · 6d ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c ^ 15a · 15b · 15c ^
SP1: - -
SP2: - - - - - -
SP3: -
SP4: -
SP5: -
SP6: - - - -
SP7:
SP8:
SP9: - -
SP10:
SP11: - - -
SP12:

ExUns: 16 ^ 17a · 17b · 17c · 17d · 17e
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for PHF1 Gene

GeneLoc Exon Structure for
PHF1
ECgene alternative splicing isoforms for
PHF1

Expression for PHF1 Gene

mRNA expression in normal human tissues for PHF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, MOPED, and MaxQB for PHF1 Gene

SOURCE GeneReport for Unigene cluster for PHF1 Gene Hs.166204

mRNA Expression by UniProt/SwissProt for PHF1 Gene

O43189-PHF1_HUMAN
Tissue specificity: Highest levels in heart, skeletal muscle, and pancreas, lower levels in brain, placenta, lung, liver and kidney
genes like me logo Genes that share expressions with PHF1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PHF1 Gene

Orthologs for PHF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF1 35
  • 99.41 (n)
  • 99.29 (a)
PHF1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHF1 35
  • 94.65 (n)
  • 96.65 (a)
PHF1 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF1 35
  • 94.59 (n)
  • 97.35 (a)
PHF1 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Phf1 35
  • 90.04 (n)
  • 93.74 (a)
Phf1 16
Phf1 36
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHF1 36
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 48 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Phf1 35
  • 90.65 (n)
  • 94.29 (a)
lizard
(Anolis carolinensis)
Reptilia PHF1 36
  • 59 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC398142 35
tropical clawed frog
(Silurana tropicalis)
Amphibia phf1 35
  • 60.99 (n)
  • 62.62 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100334345 35
  • 56.16 (n)
  • 52.53 (a)
PHF1 36
  • 46 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Pcl 36
  • 13 (a)
OneToMany
Pcl 37
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6624 36
  • 39 (a)
OneToMany
Species with no ortholog for PHF1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHF1 Gene

ENSEMBL:
Gene Tree for PHF1 (if available)
TreeFam:
Gene Tree for PHF1 (if available)

Paralogs for PHF1 Gene

Paralogs for PHF1 Gene

Selected SIMAP similar genes for PHF1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with PHF1: view

Variants for PHF1 Gene

Sequence variations from dbSNP and Humsavar for PHF1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs442745 -- 33,414,464(-) AAATG(A/G)AGAAA intron-variant
rs761583 -- 33,413,682(-) AACTG(C/T)CCCAA intron-variant
rs1329704 -- 33,412,966(+) GTGGT(A/T)TAACC intron-variant
rs2235982 -- 33,413,027(-) GGACT(C/T)GTCCG intron-variant
rs3106196 -- 33,415,166(+) AACCC(G/T)ATGGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PHF1 Gene

Variant ID Type Subtype PubMed ID
nsv830635 CNV Loss 17160897
nsv830637 CNV Loss 17160897
nsv885769 CNV Loss 21882294

Relevant External Links for PHF1 Gene

HapMap Linkage Disequilibrium report
PHF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF1 Gene

Disorders for PHF1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for PHF1 Gene including...

Search for PHF1 Gene in MalaCards »

UniProtKB/Swiss-Prot

PHF1_HUMAN
  • Note=A chromosomal aberration involving PHF1 may be a cause of endometrial stromal tumors. Translocation t(6;7)(p21;p22) with JAZF1. Translocation t(1;6)(p34;p21) with MEAF6. {ECO:0000269 PubMed:16397222, ECO:0000269 PubMed:22761769}.

(2) University of Copenhagen DISEASES for PHF1 Gene

Relevant External Links for PHF1

Genetic Association Database (GAD)
PHF1
Human Genome Epidemiology (HuGE) Navigator
PHF1
genes like me logo Genes that share disorders with PHF1: view

Publications for PHF1 Gene

  1. The identification and localization of a human gene with sequence similarity to Polycomblike of Drosophila melanogaster. (PMID: 9545646) Coulson M. … Saint R. (Genomics 1998) 2 3 4
  2. A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell. (PMID: 18385154) Hong Z. … Yasui A. (Nucleic Acids Res. 2008) 2 3 4
  3. Role of hPHF1 in H3K27 methylation and Hox gene silencing. (PMID: 18086877) Cao R. … Zhang Y. (Mol. Cell. Biol. 2008) 3 4
  4. Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. (PMID: 18285464) Sarma K. … Reinberg D. (Mol. Cell. Biol. 2008) 3 4
  5. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PMID: 19204726) Chapuis J. … Lambert J.C. (Mol. Psychiatry 2009) 3 48

Products for PHF1 Gene

Sources for PHF1 Gene

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