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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
  • Lysine-Specific Demethylase PHF2 3
  • EC 1.14.11.- 4
  • KIAA0662 4
  • JHDM1E 3
  • KDM7C 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. Diseases associated with PHF2 include Decubitus Ulcer. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity and methylated histone binding. An important paralog of this gene is PHF8.

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.

Additional gene information for PHF2 Gene

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

Genomics for PHF2 Gene

GeneHancer (GH) Regulatory Elements for PHF2 Gene

Promoters and enhancers for PHF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I093574 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.4 396 4.3 HDGF HDAC1 CLOCK NFRKB SIN3A YY1 ZNF335 ZNF766 GLIS2 EGR1 GC09M093574 PHF2 ENSG00000227603 MFSD14B MIR548AU
GH09I092607 Enhancer 1.2 Ensembl ENCODE dbSUPER 47.1 -966.2 -966214 5.6 SMAD1 MLX ZNF195 THRB RARA ZNF350 RCOR1 ZNF214 ZNF174 REST LINC00475 PHF2 NOL8 CENPP IARS ZNF484 MTND4P15 IPPK CARD19 PIR58934
GH09I092946 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 19.3 -629.0 -628977 1.1 HDGF ZNF473 NFIB ZSCAN4 ZNF133 SIN3A YBX1 ZNF335 GLIS2 ZNF202 FGD3 NOL8 MTND4P15 IARS PHF2 FAM120A ZNF484 LINC00475 SUSD3 MTCO3P29
GH09I092608 Enhancer 0.9 ENCODE dbSUPER 42.8 -969.2 -969153 0.2 SMAD1 NFIB ZNF195 ZNF776 ZNF350 ZNF214 ZNF174 ZNF571 ZNF621 ZNF398 LINC00475 PHF2 NOL8 CENPP IARS ZNF484 MTND4P15 PIR58934 GC09P092539
GH09I093449 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 14.4 -123.7 -123723 5.4 HDGF PKNOX1 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B ZNF766 FAM120A FAM120AOS PIR40533 PIR42067 PIR60796 ENSG00000227603 PHF2 LOC100132077 RNU6-829P PIR45755
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHF2 gene promoter:

Genomic Locations for PHF2 Gene

Genomic Locations for PHF2 Gene
chr9:93,576,407-93,679,587
(GRCh38/hg38)
Size:
103,181 bases
Orientation:
Plus strand
chr9:96,338,689-96,441,869
(GRCh37/hg19)

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

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 Lys175, isoforms=412, and isoforms=427

Other Protein References for PHF2 Gene

No data available for DME Specific Peptides for PHF2 Gene

Domains & Families for PHF2 Gene

Gene Families 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.
Domain:
  • The PHD-type zinc finger mediates the binding to H3K4me2 and H3K4me3.
Family:
  • Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.
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

Phenotypes From GWAS Catalog for PHF2 Gene

Gene Ontology (GO) - Molecular Function for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 contributes_to transcription coactivator activity IDA 21532585
GO:0005506 iron ion binding IDA 21167174
GO:0005515 protein binding IPI 21532585
GO:0008270 zinc ion binding IDA 20129925
GO:0016491 oxidoreductase activity IEA --
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:

Clone Products

  • Addgene plasmids for PHF2

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
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 PHF2 gene
Compartment Confidence
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000776 kinetochore IEA,IDA 20813266
GO:0000777 condensed chromosome kinetochore IEA --
GO:0005634 nucleus TAS 10051327
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with PHF2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PHF2 Gene

Pathways & Interactions for PHF2 Gene

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

Pathways by source for PHF2 Gene

1 Cell Signaling Technology pathway for PHF2 Gene

Gene Ontology (GO) - Biological Process for PHF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001889 liver development TAS 21532585
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006482 protein demethylation IDA 21532585
GO:0016569 covalent chromatin modification 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:

Clone Products

  • Addgene plasmids for PHF2

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PHF2 Gene



Protein tissue co-expression partners for PHF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF2 Gene:

PHF2

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).

Evidence on tissue expression from TISSUES for PHF2 Gene

  • Nervous system(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with PHF2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia PHF2 33 34
  • 98.72 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PHF2 34
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHF2 33 34
  • 88.65 (n)
mouse
(Mus musculus)
Mammalia Phf2 33 16 34
  • 87.3 (n)
dog
(Canis familiaris)
Mammalia PHF2 33 34
  • 87.14 (n)
rat
(Rattus norvegicus)
Mammalia Phf2 33
  • 86.32 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF2 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF2 33 34
  • 74.72 (n)
lizard
(Anolis carolinensis)
Reptilia PHF2 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf2 33
  • 71.05 (n)
zebrafish
(Danio rerio)
Actinopterygii phf2 33 34
  • 68.47 (n)
wufa14c10 33
worm
(Caenorhabditis elegans)
Secernentea F29B9.2a 35
  • 33 (a)
F29B9.2b 35
  • 33 (a)
spt-3 35
  • 27 (a)
jmjd-1.1 34
  • 24 (a)
ManyToMany
jmjd-1.2 34
  • 19 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 34
  • 27 (a)
OneToMany
Species where no ortholog for PHF2 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs193921057 uncertain-significance, Malignant tumor of prostate 93,673,799(+) G/A/C coding_sequence_variant, missense_variant
rs1000095901 -- 93,579,686(+) G/C intron_variant
rs1000111733 -- 93,678,873(+) A/T 3_prime_UTR_variant
rs1000163363 -- 93,578,411(+) G/T intron_variant
rs1000164269 -- 93,583,983(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
nsv824985 CNV gain 20364138
nsv824984 CNV gain 20364138
nsv519449 CNV loss 19592680
nsv512992 CNV insertion 21212237
nsv509311 CNV insertion 20534489
nsv1149043 CNV duplication 26484159
nsv1145256 CNV deletion 24896259
nsv1139996 CNV duplication 24896259
nsv1137483 CNV deletion 24896259
nsv1110039 CNV deletion 24896259
nsv1076192 CNV deletion 25765185
nsv1036609 CNV gain 25217958
esv3573292 CNV loss 25503493
esv3440136 CNV duplication 20981092
esv3421237 CNV duplication 20981092
esv3358961 CNV duplication 20981092
esv3350789 CNV duplication 20981092
esv28910 CNV loss 19812545
esv2738792 CNV deletion 23290073
esv2738791 CNV deletion 23290073
esv2738790 CNV deletion 23290073
esv2738789 CNV deletion 23290073
esv2738788 CNV deletion 23290073
esv2668862 CNV deletion 23128226
esv2631126 CNV insertion 19546169
esv1581383 CNV deletion 17803354
dgv7688n100 CNV gain 25217958
dgv4485e59 CNV duplication 20981092

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)

Additional Variant Information for PHF2 Gene

Human Gene Mutation Database (HGMD)
PHF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF2

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

Disorders for PHF2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PHF2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
decubitus ulcer
  • bedsore
- elite association - COSMIC cancer census association via MalaCards
Search PHF2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PHF2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PHF2: view

No data available for 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 (The Journal of biological chemistry 2010) 2 3 4 58
  2. PHF2, a novel PHD finger gene located on human chromosome 9q22. (PMID: 10051327) Hasenpusch-Theil K … Frischauf AM (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 4 58
  3. PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B. (PMID: 21532585) Baba A … Kato S (Nature cell biology 2011) 3 4 58
  4. Structural basis for human PHF2 Jumonji domain interaction with metal ions. (PMID: 21167174) Horton JR … Cheng X (Journal of molecular biology 2011) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for PHF2 Gene

  • Addgene plasmids for PHF2

Sources for PHF2 Gene

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