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H2AFY H2A histone family member Y [ Homo sapiens (human) ]

Gene ID: 9555, updated on 8-May-2016
Official Symbol
H2AFYprovided by HGNC
Official Full Name
H2A histone family member Yprovided by HGNC
Primary source
HGNC:HGNC:4740
See related
Ensembl:ENSG00000113648 HPRD:13624; MIM:610054; Vega:OTTHUMG00000129141
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
H2A.y; H2A/y; mH2A1; H2AF12M; MACROH2A1.1; macroH2A1.2
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. It replaces conventional H2A histones in a subset of nucleosomes where it represses transcription and participates in stable X chromosome inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
Orthologs
Location:
5q31.1
Exon count:
14
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 5 NC_000005.10 (135334381..135400147, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (134670071..134735645, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene chromosome 5 open reading frame 66 Neighboring gene uncharacterized LOC105379188 Neighboring gene C5orf66 antisense RNA 2 Neighboring gene dendritic cell-associated nuclear protein Neighboring gene TIFA inhibitor

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
NHGRI GWA Catalog
Genome-wide association study implicates PARD3B-based AIDS restriction.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

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

  • ATF-2 transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    ATF-2 transcription factor network, organism-specific biosystem
    ATF-2 transcription factor network
  • Alcoholism, organism-specific biosystem (from KEGG)
    Alcoholism, organism-specific biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Alcoholism, conserved biosystem (from KEGG)
    Alcoholism, conserved biosystemAlcoholism, also called dependence on alcohol (ethanol), is a chronic relapsing disorder that is progressive and has serious detrimental health outcomes. As one of the primary mediators of the reward...
  • Systemic lupus erythematosus, organism-specific biosystem (from KEGG)
    Systemic lupus erythematosus, organism-specific biosystemSystemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by the production of IgG autoantibodies that are specific for self-antigens, such as DNA, nuclear proteins and cert...
  • Systemic lupus erythematosus, conserved biosystem (from KEGG)
    Systemic lupus erythematosus, conserved biosystemSystemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by the production of IgG autoantibodies that are specific for self-antigens, such as DNA, nuclear proteins and cert...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
core promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
double-stranded methylated DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
nucleosomal DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleosomal DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein serine/threonine kinase inhibitor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
rDNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
chromatin modification IEA
Inferred from Electronic Annotation
more info
 
chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
 
dosage compensation IDA
Inferred from Direct Assay
more info
PubMed 
establishment of protein localization to chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell cycle G2/M phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H3-K27 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein localization to chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of maintenance of mitotic sister chromatid cohesion IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of cell growth IGI
Inferred from Genetic Interaction
more info
PubMed 
NOT regulation of chromatin silencing at rDNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of lipid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Barr body IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
condensed chromosome IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome NAS
Non-traceable Author Statement
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
pericentric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
sex chromatin TAS
Traceable Author Statement
more info
PubMed 
Preferred Names
core histone macro-H2A.1
Names
H2A histone family, member Y
histone H2A.y
histone macroH2A1
histone macroH2A1.1
histone macroH2A1.2
medulloblastoma antigen MU-MB-50.205

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_001040158.1NP_001035248.1  core histone macro-H2A.1 isoform 2

    See identical proteins and their annotated locations for NP_001035248.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in its coding region, compared to variant 3. This results in a protein (isoform 2) that is a single amino acid shorter than isoform 3. Variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    AC026691, BC095406
    Consensus CDS
    CCDS4183.1
    UniProtKB/Swiss-Prot
    O75367
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:177363
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  2. NM_004893.2NP_004884.1  core histone macro-H2A.1 isoform 2

    See identical proteins and their annotated locations for NP_004884.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has a unique 5' UTR and uses an alternate splice site in its coding region, compared to variant 3. This results in a protein (isoform 2) that is a single amino acid shorter than isoform 3. Variants 2 and 4 encode the same isoform (2).
    Source sequence(s)
    AF054174
    Consensus CDS
    CCDS4183.1
    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000302572, OTTHUMP00000223175, ENST00000304332, OTTHUMT00000371702
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:177363
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  3. NM_138609.2NP_613075.1  core histone macro-H2A.1 isoform 1

    See identical proteins and their annotated locations for NP_613075.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) has multiple differences in the coding region, compared to variant 3. This results in a shorter protein (isoform 1) with a distinct segment in the middle of its coding region, compared to isoform 3.
    Source sequence(s)
    AC026691, BC095406
    Consensus CDS
    CCDS4184.1
    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000310169, OTTHUMP00000223174, ENST00000312469, OTTHUMT00000371700
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:178361
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  4. NM_138610.2NP_613258.2  core histone macro-H2A.1 isoform 3

    See identical proteins and their annotated locations for NP_613258.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is the longest transcript and encodes the longest isoform (3). Isoform 3, also known as macroH2A1.2, differs from isoform 2 by a single amino acid.
    Source sequence(s)
    AC026691, BC095406
    Consensus CDS
    CCDS4185.1
    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000423563, OTTHUMP00000159413, ENST00000511689, OTTHUMT00000251196
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:178364
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p2 Primary Assembly

    Range
    135334381..135400147 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543729.1XP_011542031.1  

    See identical proteins and their annotated locations for XP_011542031.1

    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000424971, OTTHUMP00000223176, ENST00000510038, OTTHUMT00000371703
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:178364
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  2. XM_011543728.1XP_011542030.1  

    See identical proteins and their annotated locations for XP_011542030.1

    UniProtKB/Swiss-Prot
    O75367
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:178364
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  3. XM_011543730.1XP_011542032.1  

    See identical proteins and their annotated locations for XP_011542032.1

    UniProtKB/Swiss-Prot
    O75367
    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:177363
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  4. XM_005272132.1XP_005272189.1  

    See identical proteins and their annotated locations for XP_005272189.1

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cd02904
    Location:177360
    Macro_H2A_like; Macro domain, Macro_H2A_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose ...
  5. XM_011543732.1XP_011542034.1  

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:177264
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  6. XM_011543731.1XP_011542033.1  

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:178265
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  7. XM_011543733.1XP_011542035.1  

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:178225
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  8. XM_011543735.1XP_011542037.1  

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:177195
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  9. XM_011543734.1XP_011542036.1  

    See identical proteins and their annotated locations for XP_011542036.1

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:178196
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  10. XM_005272135.2XP_005272192.1  

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:177195
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...
  11. XM_005272134.2XP_005272191.1  

    See identical proteins and their annotated locations for XP_005272191.1

    Conserved Domains (3) summary
    PTZ00017
    Location:4126
    PTZ00017; histone H2A; Provisional
    cd00074
    Location:5117
    H2A; Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding ...
    cl00019
    Location:178196
    Macro; Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ...

RNA

  1. XR_948311.1 RNA Sequence

  2. XR_948309.1 RNA Sequence

  3. XR_948310.1 RNA Sequence

    Related
    ENST00000360597
  4. XR_948308.1 RNA Sequence

  5. XR_948307.1 RNA Sequence

  6. XR_948306.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 Alternate CHM1_1.1

    Range
    134102741..134168247 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)