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Protein

Core histone macro-H2A.2

Gene

H2afy2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. May be involved in stable X chromosome inactivation.

GO - Molecular functioni

  1. chromatin DNA binding Source: MGI
  2. transcription regulatory region DNA binding Source: MGI

GO - Biological processi

  1. brain development Source: MGI
  2. chromatin modification Source: UniProtKB-KW
  3. dosage compensation Source: MGI
  4. establishment of protein localization to chromatin Source: MGI
  5. negative regulation of gene expression, epigenetic Source: MGI
  6. negative regulation of transcription from RNA polymerase II promoter Source: MGI
  7. negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter Source: MGI
  8. nucleosome assembly Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiREACT_198626. Meiotic synapsis.
REACT_200667. NoRC negatively regulates rRNA expression.
REACT_214440. NoRC negatively regulates rRNA expression.
REACT_268475. DNA methylation.
REACT_27235. Meiotic Recombination.
REACT_75800. Meiotic Synapsis.

Names & Taxonomyi

Protein namesi
Recommended name:
Core histone macro-H2A.2
Short name:
Histone macroH2A2
Short name:
mH2A2
Gene namesi
Name:H2afy2
Synonyms:H2afy3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 10

Organism-specific databases

MGIiMGI:3037658. H2afy2.

Subcellular locationi

Nucleus 1 Publication. Chromosome 1 Publication
Note: Enriched in inactive X chromosome chromatin and in senescence-associated heterochromatin.

GO - Cellular componenti

  1. Barr body Source: MGI
  2. ESC/E(Z) complex Source: Ensembl
  3. extracellular vesicular exosome Source: MGI
  4. nuclear chromatin Source: MGI
  5. nucleoplasm Source: MGI
  6. nucleosome Source: UniProtKB-KW
  7. nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 372372Core histone macro-H2A.2PRO_0000227906Add
BLAST

Proteomic databases

MaxQBiQ8CCK0.
PaxDbiQ8CCK0.
PRIDEiQ8CCK0.

PTM databases

PhosphoSiteiQ8CCK0.

Expressioni

Tissue specificityi

Present in liver, kidney and adrenal gland (at protein level). In the liver, present in cells of the bile ducts and parenchymal cells, but not in hepatocytes. In the kidney, present in proximal and distal convoluted tubules and in glomeruli. Present at highest levels in the parietal layer of Bowman capsule. In the adrenal gland, present in the outer cells of the capsule.1 Publication

Gene expression databases

BgeeiQ8CCK0.
CleanExiMM_H2AFY2.
ExpressionAtlasiQ8CCK0. baseline and differential.
GenevestigatoriQ8CCK0.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers.

Structurei

3D structure databases

ProteinModelPortaliQ8CCK0.
SMRiQ8CCK0. Positions 12-117, 177-369.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 117116Histone H2AAdd
BLAST
Domaini184 – 370187MacroPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 histone H2A domain.Curated
Contains 1 Macro domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ8CCK0.
KOiK11251.
OMAiKVEGIVH.
OrthoDBiEOG71G9VP.
PhylomeDBiQ8CCK0.
TreeFamiTF332276.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8CCK0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGRSGKKKM SKLSRSARAG VIFPVGRLMR YLKKGTFKYR ISVGAPVYMA
60 70 80 90 100
AVIEYLAAEI LELAGNAARD NKKARIAPRH ILLAVANDEE LNQLLKGVTI
110 120 130 140 150
ASGGVLPRIH PELLAKKRGT KGKSETILSP PPEKRGRKAA SGKKGGKKSK
160 170 180 190 200
ATKPRTSKKS KAKDSDKEGT SNSTSEDGPG DGFTILSSKS LVLGQKLSLT
210 220 230 240 250
QSDISHIGSM RVEGIVHPTT AEIDLKEEIG KALEKAGGKE FLETVKELRK
260 270 280 290 300
SQGPLEVAEA AVSQSSGLAA KFVIHCHIPQ WGSDKCEEQL EETIKNCLSA
310 320 330 340 350
AEDKKLKSVA FPPFPSGRNC FPKQTAAQVT LKAISAHFDD SSSSSLKNVY
360 370
FLLFDSESIG IYVQEMAKLD TK
Length:372
Mass (Da):40,092
Last modified:January 23, 2007 - v3
Checksum:i471E3CDCE28F4A1D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti90 – 901E → D in BAC27963 (PubMed:16141072).Curated
Sequence conflicti239 – 2391K → E in BAE38003 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF336305 mRNA. Translation: AAK52472.1.
AK032636 mRNA. Translation: BAC27963.1.
AK165020 mRNA. Translation: BAE38003.1.
BC045140 mRNA. Translation: AAH45140.1.
BC046794 mRNA. Translation: AAH46794.1.
BC107279 mRNA. Translation: AAI07280.1.
BC107280 mRNA. Translation: AAI07281.1.
BC127144 mRNA. Translation: AAI27145.1.
CCDSiCCDS23885.1.
RefSeqiNP_996883.1. NM_207000.2.
UniGeneiMm.272870.

Genome annotation databases

EnsembliENSMUST00000020283; ENSMUSP00000020283; ENSMUSG00000020086.
GeneIDi404634.
KEGGimmu:404634.
UCSCiuc007fgm.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF336305 mRNA. Translation: AAK52472.1.
AK032636 mRNA. Translation: BAC27963.1.
AK165020 mRNA. Translation: BAE38003.1.
BC045140 mRNA. Translation: AAH45140.1.
BC046794 mRNA. Translation: AAH46794.1.
BC107279 mRNA. Translation: AAI07280.1.
BC107280 mRNA. Translation: AAI07281.1.
BC127144 mRNA. Translation: AAI27145.1.
CCDSiCCDS23885.1.
RefSeqiNP_996883.1. NM_207000.2.
UniGeneiMm.272870.

3D structure databases

ProteinModelPortaliQ8CCK0.
SMRiQ8CCK0. Positions 12-117, 177-369.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ8CCK0.

Proteomic databases

MaxQBiQ8CCK0.
PaxDbiQ8CCK0.
PRIDEiQ8CCK0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000020283; ENSMUSP00000020283; ENSMUSG00000020086.
GeneIDi404634.
KEGGimmu:404634.
UCSCiuc007fgm.1. mouse.

Organism-specific databases

CTDi55506.
MGIiMGI:3037658. H2afy2.

Phylogenomic databases

eggNOGiCOG2110.
GeneTreeiENSGT00760000119217.
HOGENOMiHOG000234653.
HOVERGENiHBG009342.
InParanoidiQ8CCK0.
KOiK11251.
OMAiKVEGIVH.
OrthoDBiEOG71G9VP.
PhylomeDBiQ8CCK0.
TreeFamiTF332276.

Enzyme and pathway databases

ReactomeiREACT_198626. Meiotic synapsis.
REACT_200667. NoRC negatively regulates rRNA expression.
REACT_214440. NoRC negatively regulates rRNA expression.
REACT_268475. DNA methylation.
REACT_27235. Meiotic Recombination.
REACT_75800. Meiotic Synapsis.

Miscellaneous databases

NextBioi407104.
PROiQ8CCK0.
SOURCEiSearch...

Gene expression databases

BgeeiQ8CCK0.
CleanExiMM_H2AFY2.
ExpressionAtlasiQ8CCK0. baseline and differential.
GenevestigatoriQ8CCK0.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR021171. Core_histone_macro-H2A.
IPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
IPR002589. Macro_dom.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF01661. Macro. 1 hit.
[Graphical view]
PIRSFiPIRSF037942. Core_histone_macro-H2A. 1 hit.
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS51154. MACRO. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Histone H2A variants and the inactive X chromosome: identification of a second macroH2A variant."
    Chadwick B.P., Willard H.F.
    Hum. Mol. Genet. 10:1101-1113(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: C57BL/6J.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Cerebellum.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6.
    Tissue: Brain and Olfactory epithelium.
  4. "MACROH2A2, a new member of the MACROH2A core histone family."
    Costanzi C., Pehrson J.R.
    J. Biol. Chem. 276:21776-21784(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiH2AW_MOUSE
AccessioniPrimary (citable) accession number: Q8CCK0
Secondary accession number(s): A0JP36, Q3TNT4, Q925I6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 23, 2007
Last modified: March 4, 2015
This is version 98 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.