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Aliases for PHF13 Gene

Aliases for PHF13 Gene

  • PHD Finger Protein 13 2 3 5
  • Survival Time-Associated PHD Finger Protein In Ovarian Cancer 1 3 4
  • SPOC1 3 4
  • Survival Time-Associated PHD Protein In Ovarian Cancer 3
  • PHD Zinc Finger Protein PHF5 3
  • PHF5 3

External Ids for PHF13 Gene

Previous GeneCards Identifiers for PHF13 Gene

  • GC01P006270
  • GC01P006383
  • GC01P006608
  • GC01P006596
  • GC01P006673
  • GC01P005821

Summaries for PHF13 Gene

GeneCards Summary for PHF13 Gene

PHF13 (PHD Finger Protein 13) is a Protein Coding gene. GO annotations related to this gene include chromatin binding and methylated histone binding. An important paralog of this gene is PHF23.

UniProtKB/Swiss-Prot for PHF13 Gene

  • Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.

Additional gene information for PHF13 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF13 Gene

Genomics for PHF13 Gene

Regulatory Elements for PHF13 Gene

Enhancers for PHF13 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H005990 1.7 FANTOM5 ENCODE dbSUPER 21.1 -620.5 -620518 4.6 HDGF PKNOX1 ARID4B SIN3A ZNF143 ZNF207 FOS SP3 CEBPZ MXD4 THAP3 TNFRSF25 PHF13 NPHP4 NOL9 RPL22 ZBTB48 KCNAB2 CHD5 GC01M006038
GH01H006197 1.1 ENCODE 31.5 -414.3 -414342 3.2 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 PHF13 THAP3 NOL9 RNF207 ZBTB48 GC01M006194
GH01H006024 1.7 FANTOM5 ENCODE dbSUPER 13.8 -586.3 -586327 5.3 HDGF PKNOX1 MLX SIN3A ARID4B DMAP1 ELK1 ZNF143 FOS ATF7 KCNAB2 PHF13 ZBTB48 NPHP4 TNFRSF25 GC01M006038
GH01H006783 1.1 ENCODE 21.2 +171.5 171503 3.6 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 PHF13 ZBTB48 NOL9 CAMTA1-DT CAMTA1
GH01H006404 1 ENCODE 21.9 -208.9 -208850 0.2 ZNF493 ZFP64 ARID4B FEZF1 ZNF121 GLIS2 ZNF302 ZNF143 KLF7 ZNF548 THAP3 NOL9 RPL22 PHF13 CAMTA1 NPHP4 CAMTA1-DT ZBTB48 LOC102724450 GC01M006398
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHF13 on UCSC Golden Path with GeneCards custom track

Promoters for PHF13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000000710 315 3601 HDGF ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 SP3 SP5

Genomic Locations for PHF13 Gene

Genomic Locations for PHF13 Gene
chr1:6,613,685-6,624,033
(GRCh38/hg38)
Size:
10,349 bases
Orientation:
Plus strand
chr1:6,673,745-6,684,093
(GRCh37/hg19)

Genomic View for PHF13 Gene

Genes around PHF13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF13 Gene

Proteins for PHF13 Gene

  • Protein details for PHF13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86YI8-PHF13_HUMAN
    Recommended name:
    PHD finger protein 13
    Protein Accession:
    Q86YI8
    Secondary Accessions:
    • B3KUQ7
    • Q59FB6
    • Q5TH65
    • Q8N551
    • Q9UJP2

    Protein attributes for PHF13 Gene

    Size:
    300 amino acids
    Molecular mass:
    33582 Da
    Quaternary structure:
    • Interacts with histone H3 that is trimethylated at Lys-4 (H3K4me3). Interacts with GSK3B.
    SequenceCaution:
    • Sequence=AAH32792.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAD92781.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF13 Gene

neXtProt entry for PHF13 Gene

Post-translational modifications for PHF13 Gene

  • Subject to proteasomal degradation. Stable when bound to chromatin. The soluble form is rapidly degraded.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PHF13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PHF13 Gene

Domains & Families for PHF13 Gene

Gene Families for PHF13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHF13 Gene

Suggested Antigen Peptide Sequences for PHF13 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PHF13: view

No data available for UniProtKB/Swiss-Prot for PHF13 Gene

Function for PHF13 Gene

Molecular function for PHF13 Gene

UniProtKB/Swiss-Prot Function:
Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.
UniProtKB/Swiss-Prot Induction:
Expression levels are tightly regulated during the cell cycle. Strongly up-regulated during late G2 phase and M phase of the mitotic cell cycle. Down-regulated at the G1-S phase transition of the cell cycle.

Phenotypes From GWAS Catalog for PHF13 Gene

Gene Ontology (GO) - Molecular Function for PHF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 19638409
GO:0035064 methylated histone binding NAS 19638409
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF13: view
genes like me logo Genes that share phenotypes with PHF13: view

Animal Model Products

CRISPR Products

miRNA for PHF13 Gene

miRTarBase miRNAs that target PHF13

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PHF13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF13 Gene

Localization for PHF13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF13 Gene

Nucleus. Nucleus, nucleoplasm. Note=Predominantly bound to chromatin, but a minor proportion is also detected in the nucleoplasm.

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 PHF13 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for PHF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 19638409
GO:0005654 nucleoplasm IEA --
genes like me logo Genes that share ontologies with PHF13: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PHF13 Gene

Pathways & Interactions for PHF13 Gene

SuperPathways for PHF13 Gene

No Data Available

Interacting Proteins for PHF13 Gene

Gene Ontology (GO) - Biological Process for PHF13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 19638409
GO:0007049 cell cycle IEA --
GO:0007059 chromosome segregation IMP 19638409
GO:0007076 mitotic chromosome condensation IMP 19638409
GO:0016569 covalent chromatin modification IEA --
genes like me logo Genes that share ontologies with PHF13: view

No data available for Pathways by source and SIGNOR curated interactions for PHF13 Gene

Drugs & Compounds for PHF13 Gene

No Compound Related Data Available

Transcripts for PHF13 Gene

mRNA/cDNA for PHF13 Gene

Unigene Clusters for PHF13 Gene

PHD finger protein 13:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PHF13

Alternative Splicing Database (ASD) splice patterns (SP) for PHF13 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6
SP1: -
SP2: - - - - - -
SP3:
SP4:

Relevant External Links for PHF13 Gene

GeneLoc Exon Structure for
PHF13
ECgene alternative splicing isoforms for
PHF13

Expression for PHF13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PHF13 Gene:

PHF13

SOURCE GeneReport for Unigene cluster for PHF13 Gene:

Hs.516079

Evidence on tissue expression from TISSUES for PHF13 Gene

  • Nervous system(4.5)
  • Lung(4.4)
genes like me logo Genes that share expression patterns with PHF13: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF13 Gene

Orthologs for PHF13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PHF13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF13 33 34
  • 99.67 (n)
dog
(Canis familiaris)
Mammalia PHF13 33
  • 90.78 (n)
-- 34
  • 9 (a)
ManyToMany
cow
(Bos Taurus)
Mammalia PHF13 33 34
  • 89.33 (n)
rat
(Rattus norvegicus)
Mammalia Phf13 33
  • 88.51 (n)
mouse
(Mus musculus)
Mammalia Phf13 33 16 34
  • 88.4 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF13 34
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF13 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF13 33 34
  • 73.38 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 35 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia phf13 33
  • 64.88 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100537300 33
  • 58.14 (n)
PHF13 34
  • 52 (a)
OneToOne
Species where no ortholog for PHF13 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)
  • 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PHF13 Gene

ENSEMBL:
Gene Tree for PHF13 (if available)
TreeFam:
Gene Tree for PHF13 (if available)

Paralogs for PHF13 Gene

Paralogs for PHF13 Gene

genes like me logo Genes that share paralogs with PHF13: view

Variants for PHF13 Gene

Sequence variations from dbSNP and Humsavar for PHF13 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000349690 -- 6,611,735(+) TTTTT(-/G)GTATT intron-variant, upstream-variant-2KB
rs1000489825 -- 6,615,094(+) GGGTG(C/G)GGGCC intron-variant, upstream-variant-2KB
rs1000626728 -- 6,618,609(+) CCATC(C/T)GCTAC intron-variant
rs1000696729 -- 6,619,911(+) CCTTG(C/T)CAGTC reference, missense
rs1000747780 -- 6,614,675(+) GGGCC(C/T)CACCC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PHF13 Gene

Variant ID Type Subtype PubMed ID
nsv955152 CNV deletion 24416366
nsv826253 CNV gain 20364138
nsv545269 CNV loss 21841781
nsv1076992 CNV deletion 25765185
dgv29n106 CNV deletion 24896259

Variation tolerance for PHF13 Gene

Residual Variation Intolerance Score: 20.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.46; 28.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF13 Gene

Disorders for PHF13 Gene

Relevant External Links for PHF13

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF13

No disorders were found for PHF13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHF13 Gene

Publications for PHF13 Gene

  1. SPOC1: a novel PHD-containing protein modulating chromatin structure and mitotic chromosome condensation. (PMID: 19638409) Kinkley S … Will H (Journal of cell science 2009) 3 4 60
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 60

Products for PHF13 Gene

  • Addgene plasmids for PHF13

Sources for PHF13 Gene

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