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H2afy H2A histone family, member Y [ Mus musculus (house mouse) ]

Gene ID: 26914, updated on 8-May-2016
Official Symbol
H2afyprovided by MGI
Official Full Name
H2A histone family, member Yprovided by MGI
Primary source
MGI:MGI:1349392
See related
Ensembl:ENSMUSG00000015937 Vega:OTTMUSG00000020957
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
mH2a1; H2AF12M; macroH2A1
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]
Orthologs
Location:
13; 13 B2
Exon count:
11
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 13 NC_000079.6 (56073622..56135626, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 13 NC_000079.5 (56174983..56236911, complement)

Chromosome 13 - NC_000079.6Genomic Context describing neighboring genes Neighboring gene paired-like homeodomain transcription factor 1 Neighboring gene predicted gene, 31542 Neighboring gene predicted gene, 31485 Neighboring gene predicted gene, 31657 Neighboring gene TRAF-interacting protein with forkhead-associated domain, family member B Neighboring gene RIKEN cDNA 4930550C17 gene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II core promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded methylated DNA binding ISO
Inferred from Sequence Orthology
more info
 
enzyme binding ISO
Inferred from Sequence Orthology
more info
 
nucleosomal DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleosomal DNA binding ISO
Inferred from Sequence Orthology
more info
 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein kinase binding ISO
Inferred from Sequence Orthology
more info
 
protein serine/threonine kinase inhibitor activity ISO
Inferred from Sequence Orthology
more info
 
rDNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
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 ISO
Inferred from Sequence Orthology
more info
PubMed 
establishment of protein localization to chromatin ISO
Inferred from Sequence Orthology
more info
 
negative regulation of cell cycle G2/M phase transition ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
negative regulation of histone H3-K27 methylation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of histone H3-K4 methylation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of histone phosphorylation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of protein localization to chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
 
negative regulation of protein serine/threonine kinase activity ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter ISO
Inferred from Sequence Orthology
more info
 
nucleosome assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
positive regulation of keratinocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
positive regulation of maintenance of mitotic sister chromatid cohesion ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
regulation of histone methylation IBA
Inferred from Biological aspect of Ancestor
more info
 
regulation of lipid metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
regulation of lipid metabolic process ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
Barr body ISO
Inferred from Sequence Orthology
more info
PubMed 
colocalizes_with ESC/E(Z) complex ISO
Inferred from Sequence Orthology
more info
 
centrosome TAS
Traceable Author Statement
more info
PubMed 
chromatin ISO
Inferred from Sequence Orthology
more info
 
chromosome IEA
Inferred from Electronic Annotation
more info
 
condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome ISO
Inferred from Sequence Orthology
more info
 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
nuclear chromatin ISO
Inferred from Sequence Orthology
more info
 
nuclear chromosome ISO
Inferred from Sequence Orthology
more info
 
nuclear chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
 
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleosome ISO
Inferred from Sequence Orthology
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
 
Preferred Names
core histone macro-H2A.1
Names
H2A.y
H2A/y
MACROH2A1.2
histone macroH2A1

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
    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_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
    Q9QZQ8
    UniProtKB/TrEMBL
    Q9CTH9
    Related
    ENSMUSP00000038221, OTTMUSP00000022974, ENSMUST00000045788, OTTMUST00000049547
    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 ...
  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
    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 ...
  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, OTTMUSP00000022973, ENSMUST00000016081, OTTMUST00000049546
    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: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000079.6 Reference GRCm38.p3 C57BL/6J

    Range
    56073622..56135626 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006517258.2XP_006517321.1  

    See identical proteins and their annotated locations for XP_006517321.1

    UniProtKB/TrEMBL
    Q8CA90
    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 ...
  2. XM_006517257.2XP_006517320.1  

    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_382440.2 RNA Sequence

  2. XR_382441.1 RNA Sequence

Alternate Mm_Celera

Genomic

  1. AC_000035.1 Alternate Mm_Celera

    Range
    57128470..57190557 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)