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Aliases for PHF1 Gene

Aliases for PHF1 Gene

  • PHD Finger Protein 1 2 3 5
  • Tudor Domain Containing 19C 2 3
  • Polycomb-Like Protein 1 3 4
  • Polycomb-Like 1 2 3
  • HPCl1 3 4
  • HPHF1 3 4
  • PCL1 3 4
  • Testicular Tissue Protein Li 140 3
  • 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 Endometrial Stromal Sarcoma and Heart Sarcoma. Among its related pathways are Gene Expression and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

Additional gene information for PHF1 Gene

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

Genomics for PHF1 Gene

Regulatory Elements for PHF1 Gene

Enhancers for PHF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H033270 1.5 ENCODE dbSUPER 48.2 -135.3 -135271 8 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D BRD2 LEMD2 VPS52 DAXX RXRB WDR46 RPS18 RING1 PHF1 RGL2
GH06H032965 1.5 ENCODE dbSUPER 37.7 -439.7 -439731 10 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC ZC3H11A PPARGC1A BRD2 LEMD2 VPS52 RXRB ATF6B HCG25 RING1 DAXX WDR46 PPT2
GH06H033430 1.5 FANTOM5 ENCODE dbSUPER 31 +22.0 22021 4 HDGF ATF1 FOXA2 ARID4B SIN3A GLIS2 ELK1 ZNF143 FOS RUNX3 RING1 HCG25 DAXX ZBTB9 PHF1 RXRB BRD2 LEMD2 SYNGAP1 LOC105375022
GH06H034390 1.4 ENCODE dbSUPER 32.8 +981.7 981738 3 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 MEF2D ZNF610 RPS10 TAF11 ENSG00000272374 LEMD2 PHF1 ITPR3 ZNF76 NUDT3 SYNGAP1 ANKS1A
GH06H033569 2 FANTOM5 Ensembl ENCODE dbSUPER 19.1 +160.9 160916 2 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 ZNF143 ZNF207 BAK1 PHF1 VPS52 LINC00336 HCG25 RING1 ITPR3 TAPBP LEMD2 RPS18
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHF1 on UCSC Golden Path with GeneCards custom track

Promoters for PHF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195791 401 2001 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF766

Genomic Location for PHF1 Gene

Chromosome:
6
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

Genes around PHF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for PHF1 Gene

  • Ubiquitination at posLast=172172
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHF1 Gene

Domains & Families for PHF1 Gene

Gene Families for PHF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PHF1 Gene

Graphical View of Domain Structure for InterPro Entry

O43189

UniProtKB/Swiss-Prot:

PHF1_HUMAN :
  • The Tudor domain recognizes and binds H3K36me3 (PubMed:23228662, PubMed:23273982 and PubMed:23142980).
  • Belongs to the Polycomblike family.
Domain:
  • The Tudor domain recognizes and binds H3K36me3 (PubMed:23228662, PubMed:23273982 and PubMed:23142980).
Family:
  • Belongs to the Polycomblike family.
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.

Phenotypes From GWAS Catalog for PHF1 Gene

Gene Ontology (GO) - Molecular Function for PHF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 9545646
GO:0005515 protein binding IPI 11571280
GO:0035064 methylated histone binding IEA,IDA 23142980
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF1: view
genes like me logo Genes that share phenotypes with PHF1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHF1 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 23273982
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0005813 colocalizes_with centrosome IDA 20873783
GO:0005815 microtubule organizing center IEA --
genes like me logo Genes that share ontologies with PHF1: view

Pathways & Interactions for PHF1 Gene

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

Pathways by source for PHF1 Gene

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 IEA,IDA 23142980
GO:0016569 covalent chromatin modification IEA --
GO:0031060 regulation of histone methylation IEA --
genes like me logo Genes that share ontologies with PHF1: view

No data available for SIGNOR curated interactions for PHF1 Gene

Drugs & Compounds for PHF1 Gene

No Compound Related Data Available

Transcripts for PHF1 Gene

Unigene Clusters for PHF1 Gene

PHD finger protein 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHF1 Gene

This gene is overexpressed in Bone marrow stromal cell (33.3), Peripheral blood mononuclear cells (12.7), and Retina (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHF1 Gene



Protein tissue co-expression partners for PHF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF1 Gene:

PHF1

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.

Evidence on tissue expression from TISSUES for PHF1 Gene

  • Liver(4.2)
  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with PHF1: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.41 (n)
cow
(Bos Taurus)
Mammalia PHF1 33 34
  • 94.65 (n)
dog
(Canis familiaris)
Mammalia PHF1 33 34
  • 94.59 (n)
rat
(Rattus norvegicus)
Mammalia Phf1 33
  • 90.65 (n)
mouse
(Mus musculus)
Mammalia Phf1 33 16 34
  • 90.04 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF1 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 48 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia PHF1 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf1 33
  • 60.99 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398142 33
zebrafish
(Danio rerio)
Actinopterygii LOC100334345 33
  • 56.16 (n)
PHF1 34
  • 46 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Pcl 35 34
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6624 34
  • 39 (a)
OneToMany
Species where no ortholog for PHF1 was found in the sources mined by GeneCards:
  • 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

(2) 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
rs1000806306 -- 33,410,217(+) CCGGA(C/T)CCCAG intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-3-prime
rs1000881131 -- 33,412,978(+) TTGCA(A/G)GCAGA intron-variant
rs1001202102 -- 33,414,172(+) ATGCC(A/C)CAACC intron-variant
rs1001792307 -- 33,413,790(+) GAGGC(C/T)TGCAC intron-variant, nc-transcript-variant, reference, synonymous-codon
rs1002353031 -- 33,410,997(+) CTCCC(C/T)CCCTC intron-variant, nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime

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

Variant ID Type Subtype PubMed ID
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv602832 CNV loss 21841781
nsv830635 CNV loss 17160897
nsv830637 CNV loss 17160897

Variation tolerance for PHF1 Gene

Residual Variation Intolerance Score: 54.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.45; 43.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF1

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

Disorders for PHF1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PHF1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
endometrial stromal sarcoma
  • endometrial stromal sarcoma, high grade
heart sarcoma
  • cardiac sarcoma
- elite association - COSMIC cancer census association via MalaCards
Search PHF1 in MalaCards View complete list of genes associated with diseases

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}.

Relevant External Links for PHF1

Genetic Association Database (GAD)
PHF1
Human Genome Epidemiology (HuGE) Navigator
PHF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF1
genes like me logo Genes that share disorders with PHF1: view

No data available for Genatlas for PHF1 Gene

Publications for PHF1 Gene

  1. 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 research 2008) 2 3 4 60
  2. 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 60
  3. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. (PMID: 23273982) Cai L … Wang GG (Molecular cell 2013) 3 4 60
  4. Tudor domains of the PRC2 components PHF1 and PHF19 selectively bind to histone H3K36me3. (PMID: 23228662) Qin S … Min J (Biochemical and biophysical research communications 2013) 3 4 60
  5. Polycomb group protein PHF1 regulates p53-dependent cell growth arrest and apoptosis. (PMID: 23150668) Yang Y … Yu L (The Journal of biological chemistry 2013) 3 4 60

Products for PHF1 Gene

Sources for PHF1 Gene

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