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

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; AllianceGenome:HGNC:4740
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: mouse all
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Genomic context

Location:: 5q31.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (135334381..135399887, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (135861569..135927059, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (134670071..134735577, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.
Title: Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.
macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast.
Title: macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast.
MacroH2A1.1 as a crossroad between epigenetics, inflammation and metabolism of mesenchymal stromal cells in myelodysplastic syndromes.
Title: MacroH2A1.1 as a crossroad between epigenetics, inflammation and metabolism of mesenchymal stromal cells in myelodysplastic syndromes.
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.
Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs.
Title: Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs.
High expression of H2A histone family member Y promotes the proliferation and autophagy of hepatocellular carcinoma cells.
Title: High expression of H2A histone family member Y promotes the proliferation and autophagy of hepatocellular carcinoma cells.
Exploring the Prognostic Value, Immune Implication and Biological Function of H2AFY Gene in Hepatocellular Carcinoma.
Title: Exploring the Prognostic Value, Immune Implication and Biological Function of H2AFY Gene in Hepatocellular Carcinoma.
Evolution of a histone variant involved in compartmental regulation of NAD metabolism.
Title: Evolution of a histone variant involved in compartmental regulation of NAD metabolism.
LSH catalyzes ATP-driven exchange of histone variants macroH2A1 and macroH2A2.
Title: LSH catalyzes ATP-driven exchange of histone variants macroH2A1 and macroH2A2.
Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions.
Title: Poly(ADP-ribose) binding and macroH2A mediate recruitment and functions of KDM5A at DNA lesions.

Submit: New GeneRIF Correction See all GeneRIFs (52)

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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5S2212E (e-PCR)
- UniSTS:154418

H2AFY_976 (e-PCR)
- UniSTS:277304

H2AFY_V251 (e-PCR)
- UniSTS:277304

RH44864 (e-PCR)
- UniSTS:23155

WI-19826 (e-PCR)
- UniSTS:64388

D5S2115 (e-PCR), detects polymorphism
- UniSTS:52628

SHGC-53813 (e-PCR)
- UniSTS:59808

RH46205 (e-PCR)
- UniSTS:74409

G19965 (e-PCR)
- UniSTS:56014

A002D42 (e-PCR)
- UniSTS:56015

bac51472T (e-PCR)
- UniSTS:181467

RH80062 (e-PCR)
- UniSTS:89829

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ADP-D-ribose binding	IDA Inferred from Direct Assay more info	PubMed
enables ADP-D-ribose modification-dependent protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	NAS Non-traceable Author Statement 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 poly-ADP-D-ribose modification-dependent protein 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 structural constituent of chromatin	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of chromatin	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 DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of protein localization to chromatin	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
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 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 response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
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	IBA Inferred from Biological aspect of Ancestor more info
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 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 positive regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of NAD metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of lipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of oxidative phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in regulation of rDNA heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sex-chromosome dosage compensation	IDA Inferred from Direct Assay more info
involved_in transcription initiation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Barr body	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	HDA more info	PubMed
located_in condensed chromosome	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in nuclear chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
part_of nucleosome	IBA Inferred from Biological aspect of Ancestor more info
part_of nucleosome	NAS Non-traceable Author Statement more info	PubMed
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in pericentric heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in sex chromatin	TAS Traceable Author Statement more info	PubMed
is_active_in site of DNA damage	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

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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)

NM_001040158.2 → NP_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

Consensus CDS

CCDS4183.1

UniProtKB/TrEMBL

A0A8I5KRC6

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:177 → 367

Macro_H2A-like; macrodomain, macroH2A-like family
NM_001400401.1 → NP_001387330.1 core histone macro-H2A.1 isoform 3

Status: REVIEWED

Source sequence(s)

AC026691

Consensus CDS

CCDS4185.1

Related

ENSP00000424971.1, ENST00000510038.1
NM_001400402.1 → NP_001387331.1 core histone macro-H2A.1 isoform 3

Status: REVIEWED

Source sequence(s)

AC026691

Consensus CDS

CCDS4185.1
NM_001400403.1 → NP_001387332.1 core histone macro-H2A.1 isoform 4

Status: REVIEWED

Source sequence(s)

AC026691
NM_001400404.1 → NP_001387333.1 core histone macro-H2A.1 isoform 5

Status: REVIEWED

Source sequence(s)

AC026691

Consensus CDS

CCDS93784.1

UniProtKB/TrEMBL

B4DJC3

Related

ENSP00000415121.2, ENST00000423969.6
NM_004893.3 → NP_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/TrEMBL

A0A8I5KRC6

Related

ENSP00000302572.4, ENST00000304332.8

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:177 → 367

Macro_H2A-like; macrodomain, macroH2A-like family
NM_138609.3 → NP_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, O75377, Q503A8, Q7Z5E3, Q96D41, Q9H8P3, Q9UP96

UniProtKB/TrEMBL

A0A8I5KRC6

Related

ENSP00000310169.4, ENST00000312469.8

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:178 → 365

Macro_H2A-like; macrodomain, macroH2A-like family
NM_138610.3 → NP_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/TrEMBL

A0A8I5KRC6

Related

ENSP00000423563.1, ENST00000511689.6

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:178 → 368

Macro_H2A-like; macrodomain, macroH2A-like family

RNA

NR_174483.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174484.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174485.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174486.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174487.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174488.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174489.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174490.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691

Related

ENST00000687629.1
NR_174491.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174492.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174493.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174494.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174495.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174496.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174497.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691

Related

ENST00000688649.1
NR_174498.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174499.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174500.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691
NR_174501.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC026691

Related

ENST00000360597.8

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

135334381..135399887 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011543730.4 → XP_011542032.1 core histone macro-H2A.1 isoform X1

See identical proteins and their annotated locations for XP_011542032.1

UniProtKB/TrEMBL

A0A8I5KRC6

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:177 → 367

Macro_H2A-like; macrodomain, macroH2A-like family
XM_011543735.4 → XP_011542037.1 core histone macro-H2A.1 isoform X5

UniProtKB/TrEMBL

D6RCF2

Related

ENST00000508785.5

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:177 → 195

Macro_SF; macrodomain superfamily
XM_005272135.5 → XP_005272192.1 core histone macro-H2A.1 isoform X3

UniProtKB/TrEMBL

D6RCF2

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:177 → 195

Macro_SF; macrodomain superfamily
XM_011543734.4 → XP_011542036.1 core histone macro-H2A.1 isoform X4

See identical proteins and their annotated locations for XP_011542036.1

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:178 → 196

Macro_SF; macrodomain superfamily
XM_005272134.5 → XP_005272191.1 core histone macro-H2A.1 isoform X2

See identical proteins and their annotated locations for XP_005272191.1

UniProtKB/TrEMBL

A0A994J4J7

Related

ENSP00000515857.1, ENST00000513210.6

Conserved Domains (2) summary

cd00074
Location:5 → 117

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:178 → 196

Macro_SF; macrodomain superfamily

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

135861569..135927059 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054353833.1 → XP_054209808.1 core histone macro-H2A.1 isoform X1
XM_054353837.1 → XP_054209812.1 core histone macro-H2A.1 isoform X5
XM_054353836.1 → XP_054209811.1 core histone macro-H2A.1 isoform X4
XM_054353835.1 → XP_054209810.1 core histone macro-H2A.1 isoform X3
XM_054353834.1 → XP_054209809.1 core histone macro-H2A.1 isoform X2

UniProtKB/TrEMBL

A0A994J4J7