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Aliases for PHF21A Gene

Aliases for PHF21A Gene

  • PHD Finger Protein 21A 2 3 5
  • BRAF35-HDAC Complex Protein BHC80 3 4
  • BHC80a 3 4
  • BHC80 3 4
  • BRAF35/HDAC2 Complex (80 KDa) 3
  • KIAA1696 4
  • BM-006 3

External Ids for PHF21A Gene

Previous GeneCards Identifiers for PHF21A Gene

  • GC11M045911
  • GC11M045950
  • GC11M045657
  • GC11M047071
  • GC11M047918

Summaries for PHF21A Gene

Entrez Gene Summary for PHF21A Gene

  • The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]

GeneCards Summary for PHF21A Gene

PHF21A (PHD Finger Protein 21A) is a Protein Coding gene. Diseases associated with PHF21A include potocki-shaffer syndrome and parietal foramina 1. Among its related pathways are Platelet activation, signaling and aggregation and Factors involved in megakaryocyte development and platelet production. GO annotations related to this gene include chromatin binding. An important paralog of this gene is PHF21B.

UniProtKB/Swiss-Prot for PHF21A Gene

  • Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of Lys-4 of histone H3 in vitro, suggesting a role in demethylation regulation.

Gene Wiki entry for PHF21A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF21A Gene

Genomics for PHF21A Gene

Regulatory Elements for PHF21A Gene

Promoters for PHF21A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PHF21A on UCSC Golden Path with GeneCards custom track

Genomic Location for PHF21A Gene

Chromosome:
11
Start:
45,929,319 bp from pter
End:
46,121,434 bp from pter
Size:
192,116 bases
Orientation:
Minus strand

Genomic View for PHF21A Gene

Genes around PHF21A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF21A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF21A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF21A Gene

Proteins for PHF21A Gene

  • Protein details for PHF21A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BD5-PF21A_HUMAN
    Recommended name:
    PHD finger protein 21A
    Protein Accession:
    Q96BD5
    Secondary Accessions:
    • D3DQP5
    • Q6AWA2
    • Q9C0G7
    • Q9H8V9
    • Q9HAK6
    • Q9NZE9

    Protein attributes for PHF21A Gene

    Size:
    680 amino acids
    Molecular mass:
    74854 Da
    Quaternary structure:
    • Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, it interacts directly with HDAC1, HDAC2, HMG20B/BRAF35, KDM1A and RCOR1/CoREST.
    SequenceCaution:
    • Sequence=AAF64262.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=BAB21787.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF21A Gene

    Alternative splice isoforms for PHF21A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF21A Gene

Proteomics data for PHF21A Gene at MOPED

Post-translational modifications for PHF21A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PHF21A Gene

Domains & Families for PHF21A Gene

Gene Families for PHF21A Gene

Suggested Antigen Peptide Sequences for PHF21A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96BD5

UniProtKB/Swiss-Prot:

PF21A_HUMAN :
  • Contains 1 A.T hook DNA-binding domain.
  • Contains 1 PHD-type zinc finger.
Domain:
  • Contains 1 A.T hook DNA-binding domain.
Similarity:
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with PHF21A: view

Function for PHF21A Gene

Molecular function for PHF21A Gene

UniProtKB/Swiss-Prot Function:
Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of Lys-4 of histone H3 in vitro, suggesting a role in demethylation regulation.

Gene Ontology (GO) - Molecular Function for PHF21A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0003682 chromatin binding IEA,IBA --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with PHF21A: view
genes like me logo Genes that share phenotypes with PHF21A: view

Human Phenotype Ontology for PHF21A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHF21A Gene

MGI Knock Outs for PHF21A:

Animal Model Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PHF21A Gene

Localization for PHF21A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF21A Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PHF21A Gene COMPARTMENTS Subcellular localization image for PHF21A gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for PHF21A Gene

Pathways & Interactions for PHF21A Gene

genes like me logo Genes that share pathways with PHF21A: view

Gene Ontology (GO) - Biological Process for PHF21A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 15325272
GO:0006351 transcription, DNA-templated IEA --
GO:0016575 histone deacetylation TAS --
genes like me logo Genes that share ontologies with PHF21A: view

No data available for SIGNOR curated interactions for PHF21A Gene

Drugs & Compounds for PHF21A Gene

No Compound Related Data Available

Transcripts for PHF21A Gene

Unigene Clusters for PHF21A Gene

PHD finger protein 21A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF21A Gene

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

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b · 26c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:

Relevant External Links for PHF21A Gene

GeneLoc Exon Structure for
PHF21A
ECgene alternative splicing isoforms for
PHF21A

Expression for PHF21A Gene

mRNA expression in normal human tissues for PHF21A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PHF21A Gene

This gene is overexpressed in Whole Blood (x7.7).

Protein differential expression in normal tissues from HIPED for PHF21A Gene

This gene is overexpressed in Pancreas (61.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PHF21A Gene



SOURCE GeneReport for Unigene cluster for PHF21A Gene Hs.502458

mRNA Expression by UniProt/SwissProt for PHF21A Gene

Q96BD5-PF21A_HUMAN
Tissue specificity: Highly expressed in brain. Expressed at much lower level in other tissues.
genes like me logo Genes that share expression patterns with PHF21A: view

Protein tissue co-expression partners for PHF21A Gene

Primer Products

In Situ Assay Products

Orthologs for PHF21A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PHF21A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF21A 35
  • 99.9 (n)
  • 100 (a)
PHF21A 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHF21A 36
  • 97 (a)
OneToOne
PHF21A 35
  • 95.28 (n)
  • 96.31 (a)
dog
(Canis familiaris)
Mammalia PHF21A 35
  • 96.07 (n)
  • 97.94 (a)
PHF21A 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Phf21a 16
Phf21a 36
  • 94 (a)
OneToOne
Phf21a 35
  • 92.83 (n)
  • 95.43 (a)
oppossum
(Monodelphis domestica)
Mammalia PHF21A 36
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF21A 36
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phf21a 35
  • 93.03 (n)
  • 95.58 (a)
chicken
(Gallus gallus)
Aves PHF21A 35
  • 85.48 (n)
  • 91.26 (a)
PHF21A 36
  • 87 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHF21A 36
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf21a 35
  • 76.85 (n)
  • 80.69 (a)
zebrafish
(Danio rerio)
Actinopterygii phf21ab 36
  • 48 (a)
OneToOne
phf21ab 35
  • 66.77 (n)
  • 66.61 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RCO1 36
  • 10 (a)
OneToMany
Species with no ortholog for PHF21A:
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PHF21A Gene

ENSEMBL:
Gene Tree for PHF21A (if available)
TreeFam:
Gene Tree for PHF21A (if available)

Paralogs for PHF21A Gene

Paralogs for PHF21A Gene

genes like me logo Genes that share paralogs with PHF21A: view

Variants for PHF21A Gene

Sequence variations from dbSNP and Humsavar for PHF21A Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs3736508 - 45,953,579(+) TGGTG(C/T)GGCTC nc-transcript-variant, reference, missense
rs1132657 -- 46,119,371(-) CTAGA(A/C)TTTCA intron-variant
rs939106 -- 45,954,709(+) TTTTA(A/C)AACAG intron-variant
rs939107 -- 45,960,800(+) ACTCG(A/G)AATTG intron-variant
rs1063809 -- 45,934,030(-) CGCCG(A/G)CCCCT downstream-variant-500B, reference, missense, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for PHF21A Gene

Variant ID Type Subtype PubMed ID
nsv897314 CNV Loss 21882294
nsv516442 CNV Loss 19592680
nsv523952 CNV Gain 19592680
nsv38731 CNV Loss 16902084
nsv522527 CNV Loss 19592680
esv2511558 CNV Deletion 19546169
esv4928 CNV Deletion 18987735
esv2744431 CNV Deletion 23290073
esv8587 CNV Loss 19470904
esv987535 CNV Loss 20482838
esv2672569 CNV Deletion 23128226
esv24317 CNV Gain 19812545

Variation tolerance for PHF21A Gene

Residual Variation Intolerance Score: 20.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.85; 83.58% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF21A Gene

HapMap Linkage Disequilibrium report
PHF21A
Human Gene Mutation Database (HGMD)
PHF21A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF21A Gene

Disorders for PHF21A Gene

MalaCards: The human disease database

(2) MalaCards diseases for PHF21A Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
potocki-shaffer syndrome
  • pss
parietal foramina 1
  • parietal foramina
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PHF21A

Genetic Association Database (GAD)
PHF21A
Human Genome Epidemiology (HuGE) Navigator
PHF21A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF21A
genes like me logo Genes that share disorders with PHF21A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF21A Gene

Publications for PHF21A Gene

  1. A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. (PMID: 12032298) Hakimi M.-A. … Shiekhattar R. (Proc. Natl. Acad. Sci. U.S.A. 2002) 2 3 4 67
  2. The rest repression of the neurosecretory phenotype is negatively modulated by BHC80, a protein of the BRAF/HDAC complex. (PMID: 19439607) Klajn A. … D'Alessandro R. (J. Neurosci. 2009) 3 23
  3. Esco2 is a novel corepressor that associates with various chromatin modifying enzymes. (PMID: 18501190) Kim B.J. … Kim S.T. (Biochem. Biophys. Res. Commun. 2008) 3 23
  4. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T. … Ohara O. (DNA Res. 2000) 2 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for PHF21A Gene

Sources for PHF21A Gene

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