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    PHF21A PHD finger protein 21A [ Homo sapiens (human) ]

    Gene ID: 51317, updated on 20-Feb-2017
    Official Symbol
    PHF21Aprovided by HGNC
    Official Full Name
    PHD finger protein 21Aprovided by HGNC
    Primary source
    HGNC:HGNC:24156
    See related
    Ensembl:ENSG00000135365 MIM:608325; Vega:OTTHUMG00000167038
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BHC80; BM-006
    Summary
    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]
    Orthologs
    Location:
    11p11.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (45929319..46121434, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45950870..46142985, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene peroxisomal biogenesis factor 16 Neighboring gene LARGE xylosyl- and glucuronyltransferase 2 Neighboring gene uncharacterized LOC105376661 Neighboring gene filamin binding LIM protein 1 pseudogene

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated (2015-02-12)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated (2015-02-12)

    ClinGen Genome Curation Page

    NHGRI GWAS Catalog

    Description
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    NHGRI GWA Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    NHGRI GWA Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    NHGRI GWA Catalog
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Factors involved in megakaryocyte development and platelet production, organism-specific biosystem (from REACTOME)
      Factors involved in megakaryocyte development and platelet production, organism-specific biosystemMegakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they underg...
    • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
      HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...
    • Hemostasis, organism-specific biosystem (from REACTOME)
      Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA1696

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA polymerase II regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    histone deacetylase activity TAS
    Traceable Author Statement
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription cofactor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    blood coagulation TAS
    Traceable Author Statement
    more info
     
    histone deacetylation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-templated IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    DNA repair complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone deacetylase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    PHD finger protein 21A
    Names
    BHC80a
    BRAF35-HDAC complex protein BHC80
    BRAF35/HDAC2 complex (80 kDa)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001101802.1NP_001095272.1  PHD finger protein 21A isoform a

      See identical proteins and their annotated locations for NP_001095272.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AB051483, AC068385, AK023258, AL359608, BC015714, CB266669
      Consensus CDS
      CCDS44578.1
      UniProtKB/Swiss-Prot
      Q96BD5
      Related
      ENSP00000398824, OTTHUMP00000234842, ENST00000418153, OTTHUMT00000392583
      Conserved Domains (3) summary
      COG5034
      Location:374536
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:490532
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    2. NM_016621.3NP_057705.3  PHD finger protein 21A isoform b

      See identical proteins and their annotated locations for NP_057705.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, and includes an alternate in-frame exon in the 3' coding region, but lacks a different alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting protein (isoform b) is shorter than isoform a.
      Source sequence(s)
      AB051483, AC068385, AK023258, AL359608, CB266669
      Consensus CDS
      CCDS31474.1
      UniProtKB/Swiss-Prot
      Q96BD5
      Related
      ENSP00000323152, OTTHUMP00000234841, ENST00000323180, OTTHUMT00000392581
      Conserved Domains (2) summary
      cd15523
      Location:444486
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      45929319..46121434 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017017901.1XP_016873390.1  PHD finger protein 21A isoform X13

    2. XM_011520158.2XP_011518460.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518460.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    3. XM_017017893.1XP_016873382.1  PHD finger protein 21A isoform X8

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    4. XM_011520179.2XP_011518481.1  PHD finger protein 21A isoform X14

      See identical proteins and their annotated locations for XP_011518481.1

      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (2) summary
      cd15523
      Location:444486
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    5. XM_017017897.1XP_016873386.1  PHD finger protein 21A isoform X12

      Conserved Domains (2) summary
      COG5034
      Location:330492
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:446488
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    6. XM_017017905.1XP_016873394.1  PHD finger protein 21A isoform X18

      Conserved Domains (2) summary
      COG5034
      Location:298460
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:414456
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    7. XM_017017890.1XP_016873379.1  PHD finger protein 21A isoform X4

    8. XM_017017889.1XP_016873378.1  PHD finger protein 21A isoform X3

      Conserved Domains (2) summary
      COG5034
      Location:381543
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:497539
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    9. XM_017017896.1XP_016873385.1  PHD finger protein 21A isoform X11

    10. XM_017017888.1XP_016873377.1  PHD finger protein 21A isoform X2

      Conserved Domains (2) summary
      COG5034
      Location:381543
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:497539
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    11. XM_017017895.1XP_016873384.1  PHD finger protein 21A isoform X10

    12. XM_017017894.1XP_016873383.1  PHD finger protein 21A isoform X9

      Conserved Domains (1) summary
      cd15523
      Location:451493
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    13. XM_017017908.1XP_016873397.1  PHD finger protein 21A isoform X21

    14. XM_017017886.1XP_016873375.1  PHD finger protein 21A isoform X1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    15. XM_017017900.1XP_016873389.1  PHD finger protein 21A isoform X12

      Conserved Domains (2) summary
      COG5034
      Location:330492
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:446488
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    16. XM_011520164.2XP_011518466.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518466.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    17. XM_011520167.2XP_011518469.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518469.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    18. XM_011520161.2XP_011518463.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518463.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    19. XM_017017907.1XP_016873396.1  PHD finger protein 21A isoform X20

      Conserved Domains (3) summary
      COG5034
      Location:291453
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:407449
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    20. XM_017017892.1XP_016873381.1  PHD finger protein 21A isoform X7

      Conserved Domains (3) summary
      COG5034
      Location:374536
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:490532
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    21. XM_017017902.1XP_016873391.1  PHD finger protein 21A isoform X15

    22. XM_017017891.1XP_016873380.1  PHD finger protein 21A isoform X6

      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (3) summary
      COG5034
      Location:374536
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:490532
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    23. XM_011520173.2XP_011518475.1  PHD finger protein 21A isoform X5

      See identical proteins and their annotated locations for XP_011518475.1

      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (3) summary
      COG5034
      Location:375537
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:491533
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    24. XM_011520157.2XP_011518459.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518459.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    25. XM_017017887.1XP_016873376.1  PHD finger protein 21A isoform X1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    26. XM_011520166.2XP_011518468.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518468.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    27. XM_017017885.1XP_016873374.1  PHD finger protein 21A isoform X1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    28. XM_011520162.2XP_011518464.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518464.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    29. XM_011520160.2XP_011518462.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518462.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    30. XM_011520169.2XP_011518471.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518471.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    31. XM_005252965.4XP_005253022.1  PHD finger protein 21A isoform X5

      See identical proteins and their annotated locations for XP_005253022.1

      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (3) summary
      COG5034
      Location:375537
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:491533
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    32. XM_017017899.1XP_016873388.1  PHD finger protein 21A isoform X12

      Conserved Domains (2) summary
      COG5034
      Location:330492
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:446488
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    33. XM_011520168.2XP_011518470.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518470.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    34. XM_011520175.2XP_011518477.1  PHD finger protein 21A isoform X7

      See identical proteins and their annotated locations for XP_011518477.1

      Conserved Domains (3) summary
      COG5034
      Location:374536
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:490532
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    35. XM_011520174.2XP_011518476.1  PHD finger protein 21A isoform X5

      See identical proteins and their annotated locations for XP_011518476.1

      UniProtKB/Swiss-Prot
      Q96BD5
      Conserved Domains (3) summary
      COG5034
      Location:375537
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:491533
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
      pfam01017
      Location:362
      STAT_alpha; STAT protein, all-alpha domain
    36. XM_011520165.2XP_011518467.1  PHD finger protein 21A isoform X1

      See identical proteins and their annotated locations for XP_011518467.1

      Conserved Domains (2) summary
      COG5034
      Location:382544
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:498540
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    37. XM_017017898.1XP_016873387.1  PHD finger protein 21A isoform X12

      Conserved Domains (2) summary
      COG5034
      Location:330492
      TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
      cd15523
      Location:446488
      PHD_PHF21A; PHD finger found in PHD finger protein 21A (PHF21A)
    38. XM_017017903.1XP_016873392.1  PHD finger protein 21A isoform X16

    39. XM_017017906.1XP_016873395.1  PHD finger protein 21A isoform X19

    40. XM_017017904.1XP_016873393.1  PHD finger protein 21A isoform X17

    RNA

    1. XR_001747900.1 RNA Sequence

    2. XR_001747901.1 RNA Sequence

    3. XR_001747902.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      45949282..46141198 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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