Macroh2a1 macroH2A.1 histone [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Macroh2a1provided by RGD
Official Full Name: macroH2A.1 histoneprovided by RGD
Primary source: RGD:621462
See related: Ensembl:ENSRNOG00000011523 AllianceGenome:RGD:621462
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: H2A.y; H2A/y; H2afy; mH2A1
Summary: Predicted to enable several functions, including DNA binding activity; promoter-specific chromatin binding activity; and protein serine/threonine kinase inhibitor activity. Predicted to be involved in several processes, including negative regulation of macromolecule metabolic process; positive regulation of cell differentiation; and regulation of response to oxidative stress. Predicted to act upstream of or within dosage compensation; negative regulation of transcription by RNA polymerase II; and regulation of lipid metabolic process. Located in chromatin and nucleus. Part of nucleosome. Orthologous to human MACROH2A1 (macroH2A.1 histone). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 102.3), Spleen (RPKM 94.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 17p14

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (8484340..8547268)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	17	NC_051352.1 (8479331..8542071)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	17	NC_005116.4 (9282109..9344698)

Chromosome 17 - NC_086035.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ADP-D-ribose binding	ISO Inferred from Sequence Orthology more info
enables ADP-D-ribose binding	ISS Inferred from Sequence or Structural Similarity more info
enables ADP-D-ribose modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables ADP-D-ribose modification-dependent protein binding	ISS Inferred from Sequence or Structural Similarity more info
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	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation 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
involved_in biological_process	ND No biological Data available 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 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	ISO Inferred from Sequence Orthology more info
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	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	ISO Inferred from Sequence Orthology more info
involved_in regulation of NAD metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of NAD metabolic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of lipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of oxidative phosphorylation	ISO Inferred from Sequence Orthology more info
NOT involved_in regulation of rDNA heterochromatin formation	ISO Inferred from Sequence Orthology more info
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
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
part_of nucleosome	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
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

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Preferred Names: core histone macro-H2A.1

Names: H2A histone family, member Y; 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)

NM_017182.3 → NP_058878.1 core histone macro-H2A.1

See identical proteins and their annotated locations for NP_058878.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000017

UniProtKB/Swiss-Prot

O09140, Q02874, Q63325

UniProtKB/TrEMBL

A6KAN9

Related

ENSRNOP00000049143.4, ENSRNOT00000051702.7

Conserved Domains (4) summary

smart00414
Location:14 → 119

H2A; Histone 2A

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 → 363

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:130 → 172

RecQ5; RecQ helicase protein-like 5 (RecQ5)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086035.1 Reference GRCr8

Range

8484340..8547268

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006253576.5 → XP_006253638.1 core histone macro-H2A.1 isoform X3

See identical proteins and their annotated locations for XP_006253638.1

UniProtKB/Swiss-Prot

O09140, Q02874, Q63325

UniProtKB/TrEMBL

A6KAP1

Conserved Domains (4) summary

smart00414
Location:14 → 119

H2A; Histone 2A

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 → 360

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:130 → 172

RecQ5; RecQ helicase protein-like 5 (RecQ5)
XM_006253573.5 → XP_006253635.1 core histone macro-H2A.1 isoform X1

See identical proteins and their annotated locations for XP_006253635.1

Conserved Domains (3) summary

smart00414
Location:14 → 119

H2A; Histone 2A

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:179 → 364

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 ...
XM_006253575.5 → XP_006253637.1 core histone macro-H2A.1 isoform X2

UniProtKB/Swiss-Prot

O09140, Q02874, Q63325

UniProtKB/TrEMBL

A0A140TAB4

Related

ENSRNOP00000015632.5

Conserved Domains (3) summary

smart00414
Location:14 → 119

H2A; Histone 2A

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:179 → 361

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 ...
XM_039095579.2 → XP_038951507.1 core histone macro-H2A.1 isoform X4

UniProtKB/TrEMBL

A6KAP2

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_039095580.2 → XP_038951508.1 core histone macro-H2A.1 isoform X5

UniProtKB/TrEMBL

A0A8I5ZW79, A6KAP2

Related

ENSRNOP00000083083.1

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:177 → 195

Macro_SF; macrodomain superfamily