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    H2AZ2 H2A.Z variant histone 2 [ Homo sapiens (human) ]

    Gene ID: 94239, updated on 27-Nov-2024

    Summary

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    Official Symbol
    H2AZ2provided by HGNC
    Official Full Name
    H2A.Z variant histone 2provided by HGNC
    Primary source
    HGNC:HGNC:20664
    See related
    Ensembl:ENSG00000105968 MIM:620008; AllianceGenome:HGNC:20664
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    H2AV; H2AFV; H2A.Z-2
    Summary
    Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H2A family. Several transcript variants encoding different isoforms, have been identified for this gene. [provided by RefSeq, Oct 2015]
    Expression
    Ubiquitous expression in bone marrow (RPKM 39.7), brain (RPKM 29.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See H2AZ2 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44826889..44848126, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44987408..45008612, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44866488..44887725, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18154 Neighboring gene peptidylprolyl isomerase A Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44887269-44887826 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44887827-44888385 Neighboring gene H2AZ2 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12861 Neighboring gene purine rich element binding protein B Neighboring gene microRNA 4657

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification and characterization of the two isoforms of the vertebrate H2A.Z histone variant. Matsuda R, et al. Nucleic Acids Res, 2010 Jul. PMID 20299344, Free PMC Article
    2. Analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes: H2AFY2, H2AFZ, H2AFY, H2AFV, H1F0. Lubin E, et al. Hum Genet, 2022 Aug. PMID 35072799
    3. Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates. Dryhurst D, et al. BMC Biol, 2009 Dec 14. PMID 20003410, Free PMC Article
    4. A comprehensive view of the epigenetic landscape part I: DNA methylation, passive and active DNA demethylation pathways and histone variants. Sadakierska-Chudy A, et al. Neurotox Res, 2015 Jan. PMID 25362550, Free PMC Article
    5. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Shaytan AK, et al. Curr Opin Struct Biol, 2015 Jun. PMID 25731851, Free PMC Article

    See all (120) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes: H2AFY2, H2AFZ, H2AFY, H2AFV, H1F0.
      Title: Analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes: H2AFY2, H2AFZ, H2AFY, H2AFV, H1F0.
    2. A mutational analysis revealed that the amino-acid difference at position 38 is at least partially responsible for the structural polymorphism in the L1 loop region of H2A.Z.1 and H2A.Z.2.
      Title: Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC1947, FLJ26479, MGC10170, MGC10831

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables structural constituent of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    part_of nucleosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of nucleosome IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone H2A.V
    Names
    H2A histone family member V
    H2A.F/Z
    histone H2A.F/Z
    purine-rich binding element protein B

    NCBI Reference Sequences (RefSeq)

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    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_012412.5 → NP_036544.1  histone H2A.V isoform 1

      See identical proteins and their annotated locations for NP_036544.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AC004854
      Consensus CDS
      CCDS5496.1
      UniProtKB/Swiss-Prot
      A6NFA8, A6NKY0, A6NN01, A8MQC5, Q59GV8, Q6PK98, Q71UI9
      UniProtKB/TrEMBL
      C9J0D1
      Related
      ENSP00000308405.5, ENST00000308153.9
      Conserved Domains (1) summary
      PLN00154
      Location:6 → 121
      PLN00154; histone H2A; Provisional

    2. NM_138635.3 → NP_619541.1  histone H2A.V isoform 2

      See identical proteins and their annotated locations for NP_619541.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) utilizes an alternate exon in the 3' coding region and 3' UTR, compared to variant 1. It encodes a shorter protein (isoform 2) compared to that encoded by variant 1.
      Source sequence(s)
      AB209001, AC004854, AK023973, DA456475, DB460745
      Consensus CDS
      CCDS5495.1
      UniProtKB/TrEMBL
      C9J0D1
      Related
      ENSP00000222690.6, ENST00000222690.10
      Conserved Domains (1) summary
      PLN00154
      Location:6 → 108
      PLN00154; histone H2A; Provisional

    3. NM_201436.3 → NP_958844.1  histone H2A.V isoform 3

      See identical proteins and their annotated locations for NP_958844.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 3) compared to isoform 1.
      Source sequence(s)
      AB209001, AC004854, BM850777, DB460745
      Consensus CDS
      CCDS5497.1
      UniProtKB/Swiss-Prot
      Q71UI9
      Related
      ENSP00000340708.3, ENST00000350771.7
      Conserved Domains (1) summary
      PLN00154
      Location:2 → 95
      PLN00154; histone H2A; Provisional

    4. NM_201516.3 → NP_958924.1  histone H2A.V isoform 4

      See identical proteins and their annotated locations for NP_958924.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks a 3' exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 4) compared to isoform 1.
      Source sequence(s)
      AB209001, AC004854, BM850777, DB460745
      Consensus CDS
      CCDS47581.1
      UniProtKB/Swiss-Prot
      Q71UI9
      Related
      ENSP00000370516.5, ENST00000381124.9
      Conserved Domains (1) summary
      PLN00154
      Location:6 → 66
      PLN00154; histone H2A; Provisional

    5. NM_201517.3 → NP_958925.1  histone H2A.V isoform 5

      See identical proteins and their annotated locations for NP_958925.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an internal exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 5) compared to isoform 1.
      Source sequence(s)
      AB209001, AC004854, BM850777, DB460745
      Consensus CDS
      CCDS5498.1
      UniProtKB/Swiss-Prot
      Q71UI9
      Related
      ENSP00000342714.3, ENST00000349299.7
      Conserved Domains (1) summary
      PTZ00017
      Location:3 → 90
      PTZ00017; histone H2A; Provisional

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44826889..44848126 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44987408..45008612 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q71UI9.3 GenPept UniProtKB/Swiss-Prot:Q71UI9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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