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Aliases for PHF20 Gene

Aliases for PHF20 Gene

  • PHD Finger Protein 20 2 3 3 5
  • Hepatocellular Carcinoma-Associated Antigen 58 3 4
  • Tudor Domain Containing 20A 2 3
  • Glioma-Expressed Antigen 2 3 4
  • Novel Zinc Finger Protein 3 4
  • Transcription Factor TZP 3 4
  • C20orf104 3 4
  • GLEA2 3 4
  • HCA58 3 4
  • NZF 3 4
  • TZP 3 4
  • Chromosome 20 Open Reading Frame 104 2
  • TDRD20A 3

External Ids for PHF20 Gene

Previous HGNC Symbols for PHF20 Gene

  • C20orf104

Previous GeneCards Identifiers for PHF20 Gene

  • GC20P033824
  • GC20P034359
  • GC20P031137

Summaries for PHF20 Gene

GeneCards Summary for PHF20 Gene

PHF20 (PHD Finger Protein 20) is a Protein Coding gene. Diseases associated with PHF20 include Actinomycosis. Among its related pathways are Gene Expression and Chromatin organization. Gene Ontology (GO) annotations related to this gene include histone acetyltransferase activity (H4-K5 specific) and histone acetyltransferase activity (H4-K16 specific). An important paralog of this gene is PHF20L1.

UniProtKB/Swiss-Prot for PHF20 Gene

  • Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. Not required for maintaining the global histone H4 Lys-16 acetylation (H4K16ac) levels or locus specific histone acetylation, but instead works downstream in transcriptional regulation of MOF target genes (By similarity). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. Contributes to methyllysine-dependent p53/TP53 stabilization and up-regulation after DNA damage.

Gene Wiki entry for PHF20 Gene

Additional gene information for PHF20 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF20 Gene

Genomics for PHF20 Gene

GeneHancer (GH) Regulatory Elements for PHF20 Gene

Promoters and enhancers for PHF20 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
GH20J035764 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 674.7 -2.4 -2429 9.2 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF416 ZNF548 SP3 PHF20 ENSG00000283527 CPNE1 RBM12 RBM39 NCOA6 ERGIC3 TRPC4AP AAR2 DLGAP4-AS1
GH20J035738 Promoter/Enhancer 3.3 UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 21.6 -30.3 -30251 7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 RBM39 CPNE1 RBM12 ERGIC3 AAR2 TRPC4AP RPL36P4 EDEM2 PHF20 EIF6
GH20J035791 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 28.7 +20.4 20438 1.7 SOX6 ATM JUND GATA3 ZNF366 POLR2A RCOR2 ADNP IKZF1 ESR1 CPNE1 PHF20 RBM39 RPF2P1 ROMO1 NFS1 SPAG4 GC20M035824
GH20J035659 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.8 -109.1 -109141 5.9 HDGF PKNOX1 SMAD1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 CPNE1 RBM12 RBM39 EIF6 ERGIC3 ROMO1 NFS1 TRPC4AP GGT7 PHF20
GH20J035795 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 17.9 +24.8 24827 3.5 HLF ZNF507 CPNE1 PHF20 SPAG4 RBM39 SCAND1 GC20M035824
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHF20 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHF20 gene promoter:
  • Pax-4a
  • Meis-1b
  • Meis-1
  • HOXA9B
  • HOXA9
  • Egr-3
  • Pbx1a
  • Egr-4
  • Egr-2
  • ATF6

Genomic Locations for PHF20 Gene

Genomic Locations for PHF20 Gene
chr20:35,771,974-35,950,381
(GRCh38/hg38)
Size:
178,408 bases
Orientation:
Plus strand
chr20:34,359,896-34,538,303
(GRCh37/hg19)
Size:
178,408 bases
Orientation:
Plus strand

Genomic View for PHF20 Gene

Genes around PHF20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF20 Gene

Proteins for PHF20 Gene

  • Protein details for PHF20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BVI0-PHF20_HUMAN
    Recommended name:
    PHD finger protein 20
    Protein Accession:
    Q9BVI0
    Secondary Accessions:
    • A7E235
    • B2RB56
    • E1P5S3
    • Q566Q2
    • Q5JWY9
    • Q66K49
    • Q9BWV4
    • Q9BXA3
    • Q9BZW3
    • Q9H421
    • Q9H4J6
    • Q9NZ22

    Protein attributes for PHF20 Gene

    Size:
    1012 amino acids
    Molecular mass:
    115386 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Component of some MLL1/MLL complex, at least composed of the core components KMT2A/MLL1, ASH2L, HCFC1, WDR5 and RBBP5, as well as the facultative components BAP18, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, KAT8/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1.
    Miscellaneous:
    • Antibodies against PHF20 are present in sera from patients with hepatocellular carcinoma, glioblastoma and childhood medulloblastula.
    SequenceCaution:
    • Sequence=AAF34184.1; Type=Frameshift; Positions=260; Evidence={ECO:0000305}; Sequence=AAK19748.1; Type=Frameshift; Positions=635, 653, 655; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF20 Gene

    Alternative splice isoforms for PHF20 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF20 Gene

Post-translational modifications for PHF20 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PHF20 Gene

Domains & Families for PHF20 Gene

Gene Families for PHF20 Gene

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

Suggested Antigen Peptide Sequences for PHF20 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BVI0

UniProtKB/Swiss-Prot:

PHF20_HUMAN :
  • The Tudor domain 2 mediates reading of dimethyl-lysine residues.
Domain:
  • The Tudor domain 2 mediates reading of dimethyl-lysine residues.
  • The Tudor domain 1 doesnt bind dimethyl-lysine residues, due to an atypical and occluded aromatic cage.
genes like me logo Genes that share domains with PHF20: view

Function for PHF20 Gene

Molecular function for PHF20 Gene

UniProtKB/Swiss-Prot Function:
Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. Not required for maintaining the global histone H4 Lys-16 acetylation (H4K16ac) levels or locus specific histone acetylation, but instead works downstream in transcriptional regulation of MOF target genes (By similarity). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. Contributes to methyllysine-dependent p53/TP53 stabilization and up-regulation after DNA damage.

Phenotypes From GWAS Catalog for PHF20 Gene

Gene Ontology (GO) - Molecular Function for PHF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16415788
GO:0043995 contributes_to histone acetyltransferase activity (H4-K5 specific) IDA 20018852
genes like me logo Genes that share ontologies with PHF20: view
genes like me logo Genes that share phenotypes with PHF20: view

Animal Model Products

Clone Products

  • Addgene plasmids for PHF20

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF20 Gene

Localization for PHF20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF20 Gene

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 PHF20 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Nuclear membrane (3)
  • Cytosol (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PHF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000123 histone acetyltransferase complex IDA 20018852
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005829 cytosol TAS --
GO:0031965 nuclear membrane IDA --
genes like me logo Genes that share ontologies with PHF20: view

Pathways & Interactions for PHF20 Gene

genes like me logo Genes that share pathways with PHF20: view

Pathways by source for PHF20 Gene

SIGNOR curated interactions for PHF20 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for PHF20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0043981 histone H4-K5 acetylation IDA 20018852
genes like me logo Genes that share ontologies with PHF20: view

Drugs & Compounds for PHF20 Gene

No Compound Related Data Available

Transcripts for PHF20 Gene

Unigene Clusters for PHF20 Gene

PHD finger protein 20:
Representative Sequences:

Clone Products

  • Addgene plasmids for PHF20

Alternative Splicing Database (ASD) splice patterns (SP) for PHF20 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a ·
SP1: -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - -
SP5: - - -
SP6: -
SP7:
SP8: - -
SP9:
SP10:
SP11: - -
SP12:

ExUns: 20b ^ 21a · 21b ^ 22
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for PHF20 Gene

GeneLoc Exon Structure for
PHF20
ECgene alternative splicing isoforms for
PHF20

Expression for PHF20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF20 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHF20 Gene

This gene is overexpressed in Blymphocyte (40.7) and CD8 Tcells (22.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PHF20 Gene



Protein tissue co-expression partners for PHF20 Gene

NURSA nuclear receptor signaling pathways regulating expression of PHF20 Gene:

PHF20

SOURCE GeneReport for Unigene cluster for PHF20 Gene:

Hs.517044

mRNA Expression by UniProt/SwissProt for PHF20 Gene:

Q9BVI0-PHF20_HUMAN
Tissue specificity: Expressed in heart, kidney, liver, lung, pancreas, placenta, spleen and testis. Not expressed in brain, skeletal muscle, colon, ovary, prostate, small intestine and thymus. Expressed in colon and ovary cancer cell lines while it is not expressed in the respective normal tissues.

Evidence on tissue expression from TISSUES for PHF20 Gene

  • Nervous system(4.7)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with PHF20: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF20 Gene

Orthologs for PHF20 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF20 34 33
  • 99.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PHF20 34 33
  • 92.57 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PHF20 34 33
  • 92.25 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phf20 33
  • 88.05 (n)
mouse
(Mus musculus)
Mammalia Phf20 16 34 33
  • 87.82 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF20 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF20 34
  • 51 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF20 34 33
  • 72.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHF20 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf20 33
  • 65.15 (n)
Str.20328 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.17757 33
zebrafish
(Danio rerio)
Actinopterygii phf20a 34
  • 39 (a)
OneToMany
phf20b 34
  • 38 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta MBD-R2 34
  • 9 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
ManyToMany
-- 34
  • 22 (a)
ManyToMany
Species where no ortholog for PHF20 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)
  • 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 PHF20 Gene

ENSEMBL:
Gene Tree for PHF20 (if available)
TreeFam:
Gene Tree for PHF20 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PHF20: view image

Paralogs for PHF20 Gene

Paralogs for PHF20 Gene

(1) SIMAP similar genes for PHF20 Gene using alignment to 6 proteins:

  • PHF20_HUMAN
  • B0QYY0_HUMAN
  • B0QZ19_HUMAN
  • F8WCQ1_HUMAN
  • Q5JWZ0_HUMAN
  • Q5JXL1_HUMAN
genes like me logo Genes that share paralogs with PHF20: view

Variants for PHF20 Gene

Sequence variations from dbSNP and Humsavar for PHF20 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000047511 -- 35,936,654(+) G/T intron_variant
rs1000053582 -- 35,939,365(+) G/T intron_variant
rs1000063960 -- 35,881,597(+) CATTC/CATTCATTC intron_variant
rs1000079151 -- 35,874,742(+) A/C intron_variant
rs1000088540 -- 35,783,427(+) TTTCTTT/TTTCTTTCTTT genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PHF20 Gene

Variant ID Type Subtype PubMed ID
nsv979431 CNV duplication 23825009
nsv965874 CNV duplication 23825009
nsv833964 CNV loss 17160897
nsv526188 CNV gain 19592680
nsv522947 CNV gain 19592680
nsv3367 CNV insertion 18451855
nsv3366 CNV insertion 18451855
nsv1138955 CNV deletion 24896259
nsv1138954 CNV deletion 24896259
nsv1136539 CNV deletion 24896259
nsv1131590 CNV deletion 24896259
nsv1127835 CNV deletion 24896259
nsv1125869 CNV deletion 24896259
nsv1116863 CNV deletion 24896259
nsv1116862 CNV deletion 24896259
nsv1067230 CNV gain 25217958
nsv1066673 CNV loss 25217958
nsv1056503 CNV gain 25217958
esv3645728 CNV loss 21293372
esv3645725 CNV loss 21293372
esv3645722 CNV loss 21293372
esv3645721 CNV loss 21293372
esv3557030 CNV deletion 23714750
esv3337522 CNV insertion 20981092
esv2722368 CNV deletion 23290073
esv2722367 CNV deletion 23290073
esv2353057 CNV deletion 18987734
esv2096453 CNV deletion 18987734
dgv4303n100 CNV gain 25217958

Variation tolerance for PHF20 Gene

Residual Variation Intolerance Score: 12.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.94; 74.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF20 Gene

Human Gene Mutation Database (HGMD)
PHF20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF20

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF20 Gene

Disorders for PHF20 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PHF20 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
actinomycosis
  • actinomycetoma
- elite association - COSMIC cancer census association via MalaCards
Search PHF20 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PHF20

genes like me logo Genes that share disorders with PHF20: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF20 Gene

Publications for PHF20 Gene

  1. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PMID: 12800201) Behrends U … Mautner J (International journal of cancer 2003) 3 4 22 58
  2. Glioma-expressed antigen 2 (GLEA2): a novel protein that can elicit immune responses in glioblastoma patients and some controls. (PMID: 11703362) Fischer U … Meese E (Clinical and experimental immunology 2001) 3 4 22 58
  3. PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53. (PMID: 22864287) Cui G … Mer G (Nature structural & molecular biology 2012) 3 4 58
  4. Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins. (PMID: 22449972) Adams-Cioaba MA … Min J (FEBS letters 2012) 3 4 58
  5. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. (PMID: 20018852) Cai Y … Conaway RC (The Journal of biological chemistry 2010) 3 4 58

Products for PHF20 Gene

  • Addgene plasmids for PHF20

Sources for PHF20 Gene

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