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Aliases for PHF3 Gene

Aliases for PHF3 Gene

  • PHD Finger Protein 3 2 3 5
  • KIAA0244 4

External Ids for PHF3 Gene

Previous GeneCards Identifiers for PHF3 Gene

  • GC06P064338
  • GC06P064353
  • GC06P064403
  • GC06P061536

Summaries for PHF3 Gene

Entrez Gene Summary for PHF3 Gene

  • This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

GeneCards Summary for PHF3 Gene

PHF3 (PHD Finger Protein 3) is a Protein Coding gene. Diseases associated with PHF3 include Alcohol Dependence. An important paralog of this gene is DIDO1.

Gene Wiki entry for PHF3 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF3 Gene

Genomics for PHF3 Gene

Regulatory Elements for PHF3 Gene

Enhancers for PHF3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PHF3 on UCSC Golden Path with GeneCards custom track

Promoters for PHF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PHF3 on UCSC Golden Path with GeneCards custom track

Genomic Location for PHF3 Gene

63,635,802 bp from pter
63,779,336 bp from pter
143,535 bases
Plus strand

Genomic View for PHF3 Gene

Genes around PHF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF3 Gene

Proteins for PHF3 Gene

  • Protein details for PHF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PHD finger protein 3
    Protein Accession:
    Secondary Accessions:
    • A3KFI8
    • Q14CR5
    • Q5CZI1
    • Q5T1T6
    • Q9NQ16
    • Q9UI45

    Protein attributes for PHF3 Gene

    2039 amino acids
    Molecular mass:
    229481 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA13438.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF3 Gene

    Alternative splice isoforms for PHF3 Gene


neXtProt entry for PHF3 Gene

Proteomics data for PHF3 Gene at MOPED

Post-translational modifications for PHF3 Gene

  • Ubiquitination at Lys 964 and Lys 1220
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHF3 Gene

Domains & Families for PHF3 Gene

Gene Families for PHF3 Gene

Suggested Antigen Peptide Sequences for PHF3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 TFIIS central domain.
  • Contains 1 PHD-type zinc finger.
  • Contains 1 TFIIS central domain.
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with PHF3: view

Function for PHF3 Gene

Gene Ontology (GO) - Molecular Function for PHF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with PHF3: view
genes like me logo Genes that share phenotypes with PHF3: view

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF3 Gene

Localization for PHF3 Gene

Subcellular locations from

Jensen Localization Image for PHF3 Gene COMPARTMENTS Subcellular localization image for PHF3 gene
Compartment Confidence
nucleus 5

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PHF3 Gene

Pathways & Interactions for PHF3 Gene

SuperPathways for PHF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHF3 Gene


No data available for Pathways by source and SIGNOR curated interactions for PHF3 Gene

Drugs & Compounds for PHF3 Gene

No Compound Related Data Available

Transcripts for PHF3 Gene

Unigene Clusters for PHF3 Gene

PHD finger protein 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PHF3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17 ^
SP1: - - - - -
SP3: -
SP4: -
SP6: - - - -
SP9: - -
SP10: - -
SP11: - - - - - -
SP13: - - - - - - - -

ExUns: 18a · 18b · 18c · 18d ^ 19 ^ 20 ^ 21a · 21b · 21c ^ 22

Relevant External Links for PHF3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHF3 Gene

mRNA expression in normal human tissues for PHF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PHF3 Gene

This gene is overexpressed in Blymphocyte (15.1), CD8 Tcells (9.4), Peripheral blood mononuclear cells (8.9), and Liver (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PHF3 Gene

SOURCE GeneReport for Unigene cluster for PHF3 Gene Hs.348921

mRNA Expression by UniProt/SwissProt for PHF3 Gene

Tissue specificity: Ubiquitous. Expression is significantly reduced or lost in glioblastomas, glioblastoma cell lines, anaplastic astrocytomas, and astrocytomas.
genes like me logo Genes that share expression patterns with PHF3: view

Protein tissue co-expression partners for PHF3 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues for PHF3 Gene

Orthologs for PHF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PHF3 35
  • 87.69 (n)
  • 83.79 (a)
PHF3 36
  • 81 (a)
(Canis familiaris)
Mammalia PHF3 35
  • 91.38 (n)
  • 88.35 (a)
PHF3 36
  • 86 (a)
(Mus musculus)
Mammalia Phf3 35
  • 83.05 (n)
  • 79.62 (a)
Phf3 16
Phf3 36
  • 75 (a)
(Pan troglodytes)
Mammalia PHF3 35
  • 99.72 (n)
  • 99.51 (a)
PHF3 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Phf3 35
  • 83.19 (n)
  • 79.79 (a)
(Monodelphis domestica)
Mammalia PHF3 36
  • 69 (a)
(Ornithorhynchus anatinus)
Mammalia PHF3 36
  • 71 (a)
(Gallus gallus)
Aves PHF3 35
  • 68.54 (n)
  • 62.96 (a)
PHF3 36
  • 52 (a)
(Anolis carolinensis)
Reptilia PHF3 36
  • 49 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phf3 35
  • 59.72 (n)
  • 49.36 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.30130 35
(Danio rerio)
Actinopterygii phf3 36
  • 30 (a)
fruit fly
(Drosophila melanogaster)
Insecta pps 36
  • 10 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 36 (a)
Species with no ortholog for PHF3:
  • 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 PHF3 Gene

Gene Tree for PHF3 (if available)
Gene Tree for PHF3 (if available)

Paralogs for PHF3 Gene

Paralogs for PHF3 Gene

(3) SIMAP similar genes for PHF3 Gene using alignment to 9 proteins:

genes like me logo Genes that share paralogs with PHF3: view

Variants for PHF3 Gene

Sequence variations from dbSNP and Humsavar for PHF3 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs3734881 - 63,713,088(-) CAAAT(A/G)TGGTG reference, missense
rs34288820 - 63,685,295(+) TTAAT(A/G/T)TCAAA intron-variant, reference, missense
rs1045943 -- 63,714,895(+) TGAAA(A/C)CTATT utr-variant-3-prime
rs1050512 -- 63,714,281(+) ATTAC(C/T)ATATA utr-variant-3-prime
rs1197982 -- 63,654,177(+) tggaa(G/T)aattt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PHF3 Gene

Variant ID Type Subtype PubMed ID
nsv830674 CNV Gain+Loss 17160897

Variation tolerance for PHF3 Gene

Residual Variation Intolerance Score: 0.512% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.45; 71.51% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF3 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF3 Gene

Disorders for PHF3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PHF3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
alcohol dependence
  • alcohol dependence, protection against
- elite association - COSMIC cancer census association via MalaCards
Search PHF3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PHF3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PHF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF3 Gene

Publications for PHF3 Gene

  1. PHF3 expression is frequently reduced in glioma. (PMID: 11856869) Fischer U. … Meese E. (Cytogenet. Cell Genet. 2001) 2 3 4 23 67
  2. PHF3-specific antibody responses in over 60% of patients with glioblastoma multiforme. (PMID: 11464277) Struss A.K. … Meese E. (Oncogene 2001) 3 23
  3. SR protein kinases promote splicing of nonconsensus introns. (PMID: 26167880) Lipp J.J. … Guthrie C. (Nat. Struct. Mol. Biol. 2015) 3
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3
  5. The central role of EED in the orchestration of polycomb group complexes. (PMID: 24457600) Cao Q. … Chinnaiyan A.M. (Nat Commun 2014) 3

Products for PHF3 Gene

Sources for PHF3 Gene