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Aliases for PHF2 Gene

Aliases for PHF2 Gene

  • PHD Finger Protein 2 2 3 4 5
  • Jumonji C Domain-Containing Histone Demethylase 1E 2 3
  • Centromere Protein 35 2 3
  • CENP-35 3 4
  • GRC5 3 4
  • EC 1.14.11.- 4
  • KIAA0662 4
  • JHDM1E 3

External Ids for PHF2 Gene

Previous GeneCards Identifiers for PHF2 Gene

  • GC09U990060
  • GC09P088066
  • GC09P089638
  • GC09P091680
  • GC09P093418
  • GC09P095378
  • GC09P096338
  • GC09P066069

Summaries for PHF2 Gene

Entrez Gene Summary for PHF2 Gene

  • This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]

GeneCards Summary for PHF2 Gene

PHF2 (PHD Finger Protein 2) is a Protein Coding gene. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include transcription coactivator activity and methylated histone binding. An important paralog of this gene is KDM2B.

UniProtKB/Swiss-Prot for PHF2 Gene

  • Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated Lys-9 of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated Lys-4 of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF2 Gene

Genomics for PHF2 Gene

Regulatory Elements for PHF2 Gene

Promoters for PHF2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PHF2 on UCSC Golden Path with GeneCards custom track

Genomic Location for PHF2 Gene

Chromosome:
9
Start:
93,576,407 bp from pter
End:
93,679,587 bp from pter
Size:
103,181 bases
Orientation:
Plus strand

Genomic View for PHF2 Gene

Genes around PHF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF2 Gene

Proteins for PHF2 Gene

  • Protein details for PHF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75151-PHF2_HUMAN
    Recommended name:
    Lysine-specific demethylase PHF2
    Protein Accession:
    O75151
    Secondary Accessions:
    • Q4VXG0
    • Q8N3K2
    • Q9Y6N4

    Protein attributes for PHF2 Gene

    Size:
    1096 amino acids
    Molecular mass:
    120775 Da
    Quaternary structure:
    • Component of the PHF2-ARID5B complex, at least composed of PHF2 and ARID5B. Interacts with HNF4A and NR1H4.
    SequenceCaution:
    • Sequence=BAA31637.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF2 Gene

neXtProt entry for PHF2 Gene

Proteomics data for PHF2 Gene at MOPED

Post-translational modifications for PHF2 Gene

  • Phosphorylated by PKA on specific serine residues, leading to the formation of an active lysine demethylase complex.
  • Ubiquitination at Lys 175, Lys 412, and Lys 427
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PHF2 (PHF2)

No data available for DME Specific Peptides for PHF2 Gene

Domains & Families for PHF2 Gene

Gene Families for PHF2 Gene

Protein Domains for PHF2 Gene

Suggested Antigen Peptide Sequences for PHF2 Gene

Graphical View of Domain Structure for InterPro Entry

O75151

UniProtKB/Swiss-Prot:

PHF2_HUMAN :
  • The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
  • Contains 1 PHD-type zinc finger.
Domain:
  • The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.
  • Contains 1 JmjC domain.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
Similarity:
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with PHF2: view

Function for PHF2 Gene

Molecular function for PHF2 Gene

GENATLAS Biochemistry:
PHD finger protein 2,Drosophila polycomb group homolog,PcG,widespread expressed
UniProtKB/Swiss-Prot EnzymeRegulation:
Enzymatically inactive by itself, and become active following phosphorylation by PKA.
UniProtKB/Swiss-Prot Function:
Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated Lys-9 of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated Lys-4 of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA.

Enzyme Numbers (IUBMB) for PHF2 Gene

Gene Ontology (GO) - Molecular Function for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032454 histone demethylase activity (H3-K9 specific) IDA 21532585
GO:0035064 methylated histone binding IDA 20129925
genes like me logo Genes that share ontologies with PHF2: view
genes like me logo Genes that share phenotypes with PHF2: view

Animal Models for PHF2 Gene

MGI Knock Outs for PHF2:

Animal Model Products

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PHF2 Gene

Localization for PHF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF2 Gene

Nucleus, nucleolus. Chromosome, centromere, kinetochore.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PHF2 Gene COMPARTMENTS Subcellular localization image for PHF2 gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with PHF2: view

Pathways & Interactions for PHF2 Gene

genes like me logo Genes that share pathways with PHF2: view

Pathways by source for PHF2 Gene

Interacting Proteins for PHF2 Gene

Gene Ontology (GO) - Biological Process for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006482 protein demethylation IDA 21532585
GO:0033169 histone H3-K9 demethylation IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PHF2: view

No data available for SIGNOR curated interactions for PHF2 Gene

Drugs & Compounds for PHF2 Gene

No Compound Related Data Available

Transcripts for PHF2 Gene

Unigene Clusters for PHF2 Gene

PHD finger protein 2:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PHF2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ·
SP1:
SP2:
SP3:
SP4: -
SP5:
SP6: - - - - - -
SP7:

ExUns: 18c ^ 19a · 19b · 19c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: - -
SP7:

Relevant External Links for PHF2 Gene

GeneLoc Exon Structure for
PHF2
ECgene alternative splicing isoforms for
PHF2

Expression for PHF2 Gene

mRNA expression in normal human tissues for PHF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHF2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (16.4), Placenta (10.9), CD8 Tcells (8.6), and Pancreatic juice (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PHF2 Gene



SOURCE GeneReport for Unigene cluster for PHF2 Gene Hs.211441

mRNA Expression by UniProt/SwissProt for PHF2 Gene

O75151-PHF2_HUMAN
Tissue specificity: Widely expressed, including in liver (at protein level).
genes like me logo Genes that share expression patterns with PHF2: view

Protein tissue co-expression partners for PHF2 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PHF2 Gene

Orthologs for PHF2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PHF2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PHF2 35
  • 88.65 (n)
  • 93.4 (a)
PHF2 36
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF2 35
  • 87.14 (n)
  • 90.7 (a)
PHF2 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Phf2 35
  • 87.3 (n)
  • 92.84 (a)
Phf2 16
Phf2 36
  • 94 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PHF2 35
  • 98.72 (n)
  • 98.72 (a)
PHF2 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phf2 35
  • 86.32 (n)
  • 92.49 (a)
oppossum
(Monodelphis domestica)
Mammalia PHF2 36
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF2 36
  • 96 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF2 35
  • 74.72 (n)
  • 82.58 (a)
PHF2 36
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHF2 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf2 35
  • 71.05 (n)
  • 76.88 (a)
zebrafish
(Danio rerio)
Actinopterygii phf2 35
  • 68.47 (n)
  • 70.34 (a)
wufa14c10 35
phf2 36
  • 67 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F29B9.2a 37
  • 33 (a)
F29B9.2b 37
  • 33 (a)
spt-3 37
  • 27 (a)
jmjd-1.1 36
  • 24 (a)
ManyToMany
jmjd-1.2 36
  • 19 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 36
  • 27 (a)
OneToMany
Species with no ortholog for PHF2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for PHF2 Gene

ENSEMBL:
Gene Tree for PHF2 (if available)
TreeFam:
Gene Tree for PHF2 (if available)

Paralogs for PHF2 Gene

Paralogs for PHF2 Gene

(2) SIMAP similar genes for PHF2 Gene using alignment to 4 proteins:

Pseudogenes.org Pseudogenes for PHF2 Gene

genes like me logo Genes that share paralogs with PHF2: view

Variants for PHF2 Gene

Sequence variations from dbSNP and Humsavar for PHF2 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs34279404 - 93,630,037(+) AGAAA(A/C)CCCAT reference, missense
rs35236745 - 93,676,934(+) CGCAT(C/T)GTCTC reference, missense
rs8690 -- 93,679,468(+) TTTAT(C/T)GTGGC utr-variant-3-prime
rs1123475 -- 93,622,669(-) gctaa(A/G)atcaa intron-variant
rs1132003 -- 93,678,446(+) CTGGC(C/T)ACACT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for PHF2 Gene

Variant ID Type Subtype PubMed ID
nsv824984 CNV Gain 20364138
nsv824985 CNV Gain 20364138
nsv509311 CNV Insertion 20534489
nsv893585 CNV Loss 21882294
nsv893586 CNV Gain 21882294
esv268435 CNV Insertion 20981092
esv274303 CNV Insertion 20981092
esv2738788 CNV Deletion 23290073
esv2738789 CNV Deletion 23290073
esv2738790 CNV Deletion 23290073
esv2738791 CNV Deletion 23290073
nsv512992 CNV Insertion 21212237
esv2631126 CNV Insertion 19546169
nsv519449 CNV Loss 19592680
nsv893587 CNV Loss 21882294
esv28910 CNV Loss 19812545
esv2738792 CNV Deletion 23290073
esv2668862 CNV Deletion 23128226
esv1581383 CNV Deletion 17803354

Variation tolerance for PHF2 Gene

Residual Variation Intolerance Score: 35% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.61; 96.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF2 Gene

HapMap Linkage Disequilibrium report
PHF2
Human Gene Mutation Database (HGMD)
PHF2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF2 Gene

Disorders for PHF2 Gene

Relevant External Links for PHF2

Genetic Association Database (GAD)
PHF2
Human Genome Epidemiology (HuGE) Navigator
PHF2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF2

No disorders were found for PHF2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHF2 Gene

Publications for PHF2 Gene

  1. Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. (PMID: 20129925) Wen H. … Shi X. (J. Biol. Chem. 2010) 2 3 4 67
  2. PHF2, a novel PHD finger gene located on human chromosome 9q22. (PMID: 10051327) Hasenpusch-Theil K. … Frischauf A.M. (Mamm. Genome 1999) 2 3
  3. PHF2 histone demethylase acts as a tumor suppressor in association with p53 in cancer. (PMID: 25043306) Lee K.H. … Chun Y.S. (Oncogene 2015) 3
  4. PHD finger protein 2 (PHF2) represses ribosomal RNA gene transcription by antagonizing PHF finger protein 8 (PHF8) and recruiting methyltransferase SUV39H1. (PMID: 25204660) Shi G. … Wong J. (J. Biol. Chem. 2014) 3
  5. Overexpression of Jumonji AT-rich interactive domain 1B and PHD finger protein 2 is involved in the progression of esophageal squamous cell carcinoma. (PMID: 22534467) Sun L.L. … Xu L.Y. (Acta Histochem. 2013) 3

Products for PHF2 Gene

Sources for PHF2 Gene

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