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Macroh2a1 macroH2A.1 histone [ Mus musculus (house mouse) ]

Gene ID: 26914, updated on 12-May-2024

Summary

Official Symbol
Macroh2a1provided by MGI
Official Full Name
macroH2A.1 histoneprovided by MGI
Primary source
MGI:MGI:1349392
See related
Ensembl:ENSMUSG00000015937 AllianceGenome:MGI:1349392
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
H2afy; mH2a1; H2AF12M
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, Nov 2015]
Expression
Ubiquitous expression in thymus adult (RPKM 36.0), CNS E11.5 (RPKM 35.6) and 28 other tissues See more
Orthologs
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Genomic context

See Macroh2a1 in Genome Data Viewer
Location:
13 B1; 13 30.06 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (56221435..56283439, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (56073622..56135626, complement)

Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 31542 Neighboring gene predicted gene, 47072 Neighboring gene STARR-seq mESC enhancer starr_34629 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:56206540-56206649 Neighboring gene STARR-seq mESC enhancer starr_34633 Neighboring gene predicted gene, 31485 Neighboring gene STARR-seq mESC enhancer starr_34635 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:56277360-56277561 Neighboring gene predicted gene, 31657 Neighboring gene predicted gene, 25148 Neighboring gene TRAF-interacting protein with forkhead-associated domain, family member B

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ADP-D-ribose binding IDA
Inferred from Direct Assay
more info
PubMed 
enables ADP-D-ribose binding ISO
Inferred from Sequence Orthology
more info
 
enables ADP-D-ribose modification-dependent protein binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded methylated DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables nucleosomal DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables nucleosomal DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nucleosomal DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables promoter-specific chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein kinase binding ISO
Inferred from Sequence Orthology
more info
 
enables protein serine/threonine kinase inhibitor activity ISO
Inferred from Sequence Orthology
more info
 
enables rDNA binding ISO
Inferred from Sequence Orthology
more info
 
enables structural constituent of chromatin ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in DNA repair ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in epigenetic regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in establishment of protein localization to chromatin ISO
Inferred from Sequence Orthology
more info
 
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of cell cycle G2/M phase transition ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of protein localization to chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of protein serine/threonine kinase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of response to oxidative stress ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription of nucleolar large rRNA by RNA polymerase I ISO
Inferred from Sequence Orthology
more info
 
involved_in nucleosome assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of endodermal cell differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of keratinocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of maintenance of mitotic sister chromatid cohesion ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of response to oxidative stress ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of NAD metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of lipid metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of oxidative phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of response to oxidative stress ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within sex-chromosome dosage compensation ISO
Inferred from Sequence Orthology
more info
 
involved_in transcription initiation-coupled chromatin remodeling ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in Barr body ISO
Inferred from Sequence Orthology
more info
PubMed 
located_in centrosome TAS
Traceable Author Statement
more info
PubMed 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear chromosome ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
part_of nucleosome IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of nucleosome ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
 
is_active_in site of DNA damage ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
core histone macro-H2A.1
Names
H2A histone family, member Y
H2A.y
H2A/y
MACROH2A1.2
histone macroH2A1

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_001159513.1NP_001152985.1  core histone macro-H2A.1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks one internal residue, compared to isoform 1.
    Source sequence(s)
    AB071988, AK003531, BB633156, BE988321, CJ095488, CV561613
    UniProtKB/Swiss-Prot
    Q9QZQ8
    UniProtKB/TrEMBL
    Q9CTH9
    Conserved Domains (3) 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: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 ...
    pfam06959
    Location:130172
    RecQ5; RecQ helicase protein-like 5 (RecQ5)
  2. NM_001159514.1NP_001152986.1  core histone macro-H2A.1 isoform 3

    See identical proteins and their annotated locations for NP_001152986.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate exon in the central coding region, compared to variant 1. The resulting isoform (3) differs in one internal segment, compared to isoform 1.
    Source sequence(s)
    AB071988, AK003531, AW990415, BB633156, BE988321, CJ095488
    Consensus CDS
    CCDS49278.1
    UniProtKB/Swiss-Prot
    Q91VZ2, Q9QZQ7, Q9QZQ8
    Related
    ENSMUSP00000038221.8, ENSMUST00000045788.9
    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: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 ...
  3. NM_001159515.1NP_001152987.1  core histone macro-H2A.1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site and an alternate exon in the central coding region, compared to variant 1. The resulting isoform (4) lacks an internal residue and differs in an internal segment, compared to isoform 1.
    Source sequence(s)
    AB071988, AK003531, BB633156, BE988321, CB574813, CJ095488
    UniProtKB/Swiss-Prot
    Q9QZQ8
    UniProtKB/TrEMBL
    Q9CTH9
    Conserved Domains (3) 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: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 ...
    pfam06959
    Location:130172
    RecQ5; RecQ helicase protein-like 5 (RecQ5)
  4. NM_012015.2NP_036145.1  core histone macro-H2A.1 isoform 1

    See identical proteins and their annotated locations for NP_036145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB071988, AK003531, BB633156, BE988321, CJ095488
    Consensus CDS
    CCDS26557.1
    UniProtKB/Swiss-Prot
    Q9QZQ8
    UniProtKB/TrEMBL
    Q9CTH9
    Related
    ENSMUSP00000016081.7, ENSMUST00000016081.13
    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: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: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000079.7 Reference GRCm39 C57BL/6J

    Range
    56221435..56283439 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006517258.3XP_006517321.1  core histone macro-H2A.1 isoform X2

    See identical proteins and their annotated locations for XP_006517321.1

    UniProtKB/TrEMBL
    Q8CA90
    Conserved Domains (3) 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 ...
    pfam06959
    Location:130172
    RecQ5; RecQ helicase protein-like 5 (RecQ5)
    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 ...
  2. XM_006517257.3XP_006517320.1  core histone macro-H2A.1 isoform X1

    Conserved Domains (1) 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 ...

RNA

  1. XR_003950457.1 RNA Sequence

  2. XR_001780786.1 RNA Sequence

  3. XR_003950458.1 RNA Sequence

  4. XR_001780784.1 RNA Sequence

  5. XR_001780785.1 RNA Sequence

  6. XR_382440.2 RNA Sequence

  7. XR_003950456.1 RNA Sequence

  8. XR_003950455.1 RNA Sequence