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Aliases for PHF3 Gene

Aliases for PHF3 Gene

  • PHD Finger Protein 3 2 3 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. An important paralog of this gene is DIDO1.

Gene Wiki entry for PHF3 Gene

Additional gene information for PHF3 Gene

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

Genomics for PHF3 Gene

GeneHancer (GH) Regulatory Elements for PHF3 Gene

Promoters and enhancers for PHF3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J063634 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 665 +0.7 730 3.8 MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 PHF3 GC06M063647
GH06J063569 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 30.2 -62.7 -62662 7.3 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC SSRP1 ENSG00000266680 PTP4A1 PHF3 LGSN ENSG00000236345 GC06M063587
GH06J063597 Enhancer 1.2 Ensembl ENCODE 24.4 -37.2 -37239 1.5 HDGF FOXA2 ARNT ARID4B SIN3A ZNF2 IRF4 YY1 ZNF207 ZNF143 PHF3 ENSG00000236345 GC06M063602 GC06M063595
GH06J063536 Enhancer 1.2 Ensembl ENCODE dbSUPER 12.3 -97.9 -97946 1.7 PKNOX1 SMAD1 NFIB BMI1 FEZF1 KLF5 ZNF350 RCOR1 ATF7 IKZF2 LGSN PHF3 GC06P063532 RPL7AP34 PTP4A1
GH06J063676 Enhancer 1 FANTOM5 ENCODE 14.7 +41.5 41548 1.1 FOXA2 RAD21 YY1 SLC30A9 MIXL1 RXRA CEBPB REST NR2F2 NFIL3 PHF3 GC06M063647 GC06P063737
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PHF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHF3 gene promoter:
  • Nkx2-5
  • GATA-2
  • HNF-1A
  • HNF-1
  • XBP-1
  • Evi-1
  • GATA-6
  • Max
  • c-Myc
  • Egr-2

Genomic Locations for PHF3 Gene

Genomic Locations for PHF3 Gene
143,535 bases
Plus strand
143,505 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

Post-translational modifications for PHF3 Gene

  • Ubiquitination at isoforms=21220 and Lys964
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHF3 Gene

Domains & Families for PHF3 Gene

Gene Families for PHF3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PHF3 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

Function for PHF3 Gene

Gene Ontology (GO) - Molecular Function for PHF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0046872 metal ion 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

Clone Products

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

Localization for PHF3 Gene

Subcellular locations from

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 PHF3 gene
Compartment Confidence
nucleus 4

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with PHF3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PHF3 Gene

Pathways & Interactions for PHF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0007275 multicellular organism development NAS 11856869
genes like me logo Genes that share ontologies with PHF3: view

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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PHF3 Gene

Protein tissue co-expression partners for PHF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF3 Gene:


SOURCE GeneReport for Unigene cluster for PHF3 Gene:


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.

Evidence on tissue expression from TISSUES for PHF3 Gene

  • Nervous system(4.6)
  • Liver(4.3)
  • Bone marrow(4.2)
  • Adrenal gland(2.4)
  • Spleen(2)
genes like me logo Genes that share expression patterns with PHF3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia PHF3 34 33
  • 99.72 (n)
(Canis familiaris)
Mammalia PHF3 34 33
  • 91.38 (n)
(Bos Taurus)
Mammalia PHF3 34 33
  • 87.69 (n)
(Rattus norvegicus)
Mammalia Phf3 33
  • 83.19 (n)
(Mus musculus)
Mammalia Phf3 16 34 33
  • 83.05 (n)
(Ornithorhynchus anatinus)
Mammalia PHF3 34
  • 71 (a)
(Monodelphis domestica)
Mammalia PHF3 34
  • 69 (a)
(Gallus gallus)
Aves PHF3 34 33
  • 68.54 (n)
(Anolis carolinensis)
Reptilia PHF3 34
  • 49 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phf3 33
  • 59.72 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.30130 33
(Danio rerio)
Actinopterygii phf3 34
  • 30 (a)
fruit fly
(Drosophila melanogaster)
Insecta pps 34
  • 10 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
Species where no ortholog for PHF3 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 PHF3 Gene

Gene Tree for PHF3 (if available)
Gene Tree for PHF3 (if available)
Evolutionary constrained regions (ECRs) for PHF3: view image

Paralogs for PHF3 Gene

Paralogs for PHF3 Gene

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

  • B3KP41_HUMAN
  • D6R9X2_HUMAN
  • E7ER40_HUMAN
  • E9PE34_HUMAN
  • H0Y8L0_HUMAN
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 Variation AA Info Type
rs1000033724 -- 63,682,839(+) G/A intron_variant
rs1000039362 -- 63,659,977(+) A/T intron_variant
rs1000045758 -- 63,642,892(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000117434 -- 63,641,581(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000184409 -- 63,688,612(+) G/A genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
esv3429676 CNV insertion 20981092
nsv1146820 CNV insertion 26484159
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)

Additional Variant Information for PHF3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PHF3 Gene

Additional Disease Information for PHF3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PHF3 Gene.

No data available for MalaCards , 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 (Cytogenetics and cell genetics 2001) 2 3 4 22 58
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58
  5. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D … Nagase T (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4 58

Products for PHF3 Gene

Sources for PHF3 Gene

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