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

Gene ID: 94239, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44826889..44848126, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44987408..45008612, complement)
105.20220307 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. PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection. Zhang Y, et al. Nat Immunol, 2015 Dec. PMID 26479788, Free PMC Article

See all (101) 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)

Genotypes

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 molecular adaptor activity EXP
Inferred from Experiment
more info
 PubMed 
enables molecular_function ND
No biological Data available
more info
  
enables nucleosomal DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables structural constituent of chromatin IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
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_2023_10

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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