Format

Send to:

Choose Destination

MACROH2A1 macroH2A.1 histone [ Homo sapiens (human) ]

Gene ID: 9555, updated on 9-May-2021

Summary

Official Symbol
MACROH2A1provided by HGNC
Official Full Name
macroH2A.1 histoneprovided by HGNC
Primary source
HGNC:HGNC:4740
See related
Ensembl:ENSG00000113648 MIM:610054
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; H2AFY; 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]
Expression
Ubiquitous expression in bone marrow (RPKM 29.8), esophagus (RPKM 11.4) and 24 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See MACROH2A1 in Genome Data Viewer
Location:
5q31.1
Exon count:
14
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (135334381..135401998, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (134670071..134735577, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PITX1 antisense RNA 1 Neighboring gene uncharacterized LOC105379188 Neighboring gene long intergenic non-protein coding RNA 2900 Neighboring gene VISTA enhancer hs1473 Neighboring gene dendritic cell associated nuclear protein Neighboring gene TIFA inhibitor

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
GeneReviews: Not available
Genome-wide association study implicates PARD3B-based AIDS restriction.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
enables RNA polymerase II core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded methylated DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables nucleosomal DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nucleosomal DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables promoter-specific chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein serine/threonine kinase inhibitor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables rDNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within dosage compensation IDA
Inferred from Direct Assay
more info
 
involved_in establishment of protein localization to chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of cell cycle G2/M phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of histone H3-K27 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of histone H3-K4 methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of histone phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of protein localization to chromosome, telomeric region IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleosome assembly NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of endodermal cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of maintenance of mitotic sister chromatid cohesion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of lipid metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT involved_in regulation of ribosomal DNA heterochromatin assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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 (2) summary
    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:177367
    Macro_H2A-like; macrodomain, macroH2A-like family
  2. NM_004893.3NP_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)
    AC026691
    Consensus CDS
    CCDS4183.1
    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000302572.4, ENST00000304332.8
    Conserved Domains (2) summary
    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:177367
    Macro_H2A-like; macrodomain, macroH2A-like family
  3. NM_138609.3NP_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
    ENSP00000310169.4, ENST00000312469.8
    Conserved Domains (2) summary
    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:178365
    Macro_H2A-like; macrodomain, macroH2A-like family
  4. NM_138610.3NP_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, AF041483
    Consensus CDS
    CCDS4185.1
    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000423563.1, ENST00000511689.5
    Conserved Domains (2) summary
    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:178368
    Macro_H2A-like; macrodomain, macroH2A-like family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    135334381..135401998 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543730.3XP_011542032.1  core histone macro-H2A.1 isoform X2

    See identical proteins and their annotated locations for XP_011542032.1

    UniProtKB/Swiss-Prot
    O75367
    Conserved Domains (2) summary
    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:177367
    Macro_H2A-like; macrodomain, macroH2A-like family
  2. XM_011543729.3XP_011542031.1  core histone macro-H2A.1 isoform X1

    See identical proteins and their annotated locations for XP_011542031.1

    UniProtKB/Swiss-Prot
    O75367
    Related
    ENSP00000424971.1, ENST00000510038.1
    Conserved Domains (2) summary
    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:178368
    Macro_H2A-like; macrodomain, macroH2A-like family
  3. XM_024446264.1XP_024302032.1  core histone macro-H2A.1 isoform X10

    Conserved Domains (2) summary
    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 ...
  4. XM_017010067.2XP_016865556.1  core histone macro-H2A.1 isoform X8

  5. XM_024446263.1XP_024302031.1  core histone macro-H2A.1 isoform X6

    Conserved Domains (2) summary
    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:177261
    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_005272132.2XP_005272189.1  core histone macro-H2A.1 isoform X3

    See identical proteins and their annotated locations for XP_005272189.1

    Conserved Domains (2) summary
    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:177364
    Macro_H2A-like; macrodomain, macroH2A-like family
  7. XM_011543732.2XP_011542034.1  core histone macro-H2A.1 isoform X5

    Conserved Domains (4) summary
    smart00414
    Location:14119
    H2A; Histone 2A
    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 ...
    pfam06959
    Location:130172
    RecQ5; RecQ helicase protein-like 5 (RecQ5)
    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 ...
  8. XM_011543731.2XP_011542033.1  core histone macro-H2A.1 isoform X4

    Conserved Domains (3) summary
    smart00414
    Location:14119
    H2A; Histone 2A
    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 ...
  9. XM_011543733.3XP_011542035.1  core histone macro-H2A.1 isoform X7

    Conserved Domains (3) summary
    smart00414
    Location:14119
    H2A; Histone 2A
    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 ...
  10. XM_017010068.2XP_016865557.1  core histone macro-H2A.1 isoform X9

    Conserved Domains (2) summary
    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:178229
    Macro_SF; macrodomain superfamily
  11. XM_011543735.3XP_011542037.1  core histone macro-H2A.1 isoform X14

    Conserved Domains (2) summary
    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 ...
  12. XM_005272135.4XP_005272192.1  core histone macro-H2A.1 isoform X12

    Conserved Domains (2) summary
    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 ...
  13. XM_011543734.3XP_011542036.1  core histone macro-H2A.1 isoform X13

    See identical proteins and their annotated locations for XP_011542036.1

    Conserved Domains (2) summary
    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_SF; macrodomain superfamily
  14. XM_005272134.4XP_005272191.1  core histone macro-H2A.1 isoform X11

    See identical proteins and their annotated locations for XP_005272191.1

    Conserved Domains (2) summary
    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_SF; macrodomain superfamily

RNA

  1. XR_948311.2 RNA Sequence

  2. XR_001742358.2 RNA Sequence

  3. XR_001742355.2 RNA Sequence

  4. XR_001742353.2 RNA Sequence

  5. XR_948309.2 RNA Sequence

  6. XR_948310.2 RNA Sequence

    Related
    ENST00000360597.8
  7. XR_001742356.2 RNA Sequence

  8. XR_001742357.2 RNA Sequence

  9. XR_001742354.2 RNA Sequence

  10. XR_948306.3 RNA Sequence

  11. XR_948308.2 RNA Sequence

  12. XR_948307.2 RNA Sequence

  13. XR_001742359.2 RNA Sequence

Support Center