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Protein

Histone H2A.V

Gene

H2AFV

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. 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 the formation of constitutive heterochromatin. May be required for chromosome segregation during cell division (By similarity).By similarity

GO - Molecular functioni

  • DNA binding Source: GO_Central
  • protein heterodimerization activity Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632 Meiotic synapsis
R-HSA-171306 Packaging Of Telomere Ends
R-HSA-1912408 Pre-NOTCH Transcription and Translation
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-5334118 DNA methylation
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-73728 RNA Polymerase I Promoter Opening
R-HSA-73777 RNA Polymerase I Chain Elongation
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-912446 Meiotic recombination

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A.V
Alternative name(s):
H2A.F/Z
Gene namesi
Name:H2AFV
Synonyms:H2AV
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

EuPathDBiHostDB:ENSG00000105968.18
HGNCiHGNC:20664 H2AFV
neXtProtiNX_Q71UI9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000105968
PharmGKBiPA134895050

Polymorphism and mutation databases

BioMutaiH2AFV
DMDMi74749787

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCurated
ChainiPRO_00002390682 – 128Histone H2A.VAdd BLAST127

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei5N6-acetyllysineBy similarity1
Modified residuei8N6-acetyllysineBy similarity1
Modified residuei12N6-acetyllysineBy similarity1

Post-translational modificationi

Monoubiquitination of Lys-122 gives a specific tag for epigenetic transcriptional repression.By similarity
Acetylated on Lys-5, Lys-8 and Lys-12 during interphase. Acetylation disappears at mitosis (By similarity).By similarity

Keywords - PTMi

Acetylation, Ubl conjugation

Proteomic databases

EPDiQ71UI9
MaxQBiQ71UI9
PaxDbiQ71UI9
PeptideAtlasiQ71UI9
PRIDEiQ71UI9
ProteomicsDBi68632
68633 [Q71UI9-2]
TopDownProteomicsiQ71UI9-1 [Q71UI9-1]
Q71UI9-3 [Q71UI9-3]
Q71UI9-4 [Q71UI9-4]

PTM databases

iPTMnetiQ71UI9
PhosphoSitePlusiQ71UI9
SwissPalmiQ71UI9

Expressioni

Gene expression databases

BgeeiENSG00000105968 Expressed in 231 organ(s), highest expression level in substantia nigra
CleanExiHS_H2AFV
ExpressionAtlasiQ71UI9 baseline and differential
GenevisibleiQ71UI9 HS

Organism-specific databases

HPAiHPA057236

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. The octamer wraps approximately 147 bp of DNA. H2A or its variant H2AFV forms a heterodimer with H2B (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi125150, 48 interactors
IntActiQ71UI9, 16 interactors
MINTiQ71UI9
STRINGi9606.ENSP00000308405

Structurei

Secondary structure

1128
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ71UI9
SMRiQ71UI9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2A family.Curated

Phylogenomic databases

eggNOGiKOG1757 Eukaryota
COG5262 LUCA
GeneTreeiENSGT00900000140979
HOGENOMiHOG000234652
HOVERGENiHBG009342
InParanoidiQ71UI9
KOiK11251
OMAiIHRYLMN
OrthoDBiEOG091G0XGD
PhylomeDBiQ71UI9
TreeFamiTF354232

Family and domain databases

CDDicd00074 H2A, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR002119 Histone_H2A
IPR007125 Histone_H2A/H2B/H3
IPR032454 Histone_H2A_C
IPR032458 Histone_H2A_CS
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PF16211 Histone_H2A_C, 1 hit
PRINTSiPR00620 HISTONEH2A
SMARTiView protein in SMART
SM00414 H2A, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00046 HISTONE_H2A, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q71UI9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAGGKAGKDS GKAKAKAVSR SQRAGLQFPV GRIHRHLKTR TTSHGRVGAT
60 70 80 90 100
AAVYSAAILE YLTAEVLELA GNASKDLKVK RITPRHLQLA IRGDEELDSL
110 120
IKATIAGGGV IPHIHKSLIG KKGQQKTA
Length:128
Mass (Da):13,509
Last modified:January 23, 2007 - v3
Checksum:i1F3C388F6854041C
GO
Isoform 2 (identifier: Q71UI9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     109-128: GVIPHIHKSLIGKKGQQKTA → EKRRCS

Note: No experimental confirmation available.
Show »
Length:114
Mass (Da):12,146
Checksum:i4CF80C91A39397B4
GO
Isoform 3 (identifier: Q71UI9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     28-65: Missing.

Note: No experimental confirmation available.
Show »
Length:90
Mass (Da):9,375
Checksum:i34DA01283B7A93F1
GO
Isoform 4 (identifier: Q71UI9-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-27: MAGGKAGKDSGKAKAKAVSRSQRAGLQ → M

Note: No experimental confirmation available.
Show »
Length:102
Mass (Da):10,999
Checksum:i0E6071539B4139F9
GO
Isoform 5 (identifier: Q71UI9-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     67-128: Missing.

Note: No experimental confirmation available.
Show »
Length:66
Mass (Da):6,892
Checksum:i90DA3A9820A88CB0
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9J0D1C9J0D1_HUMAN
Histone H2A
H2AFV
122Annotation score:
C9J386C9J386_HUMAN
Histone H2A
H2AFV
76Annotation score:
E5RJU1E5RJU1_HUMAN
Histone H2A.V
H2AFV
40Annotation score:

Sequence cautioni

The sequence BAD92238 differs from that shown. Reason: Erroneous initiation.Curated

Mass spectrometryi

Molecular mass is 13369.4 Da from positions 2 - 128. Determined by ESI. Monoisotopic, not modified.1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059312125Q → R. Corresponds to variant dbSNP:rs1802437Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0452321 – 27MAGGK…RAGLQ → M in isoform 4. 1 PublicationAdd BLAST27
Alternative sequenceiVSP_04463328 – 65Missing in isoform 3. 1 PublicationAdd BLAST38
Alternative sequenceiVSP_04678367 – 128Missing in isoform 5. CuratedAdd BLAST62
Alternative sequenceiVSP_042855109 – 128GVIPH…QQKTA → EKRRCS in isoform 2. 1 PublicationAdd BLAST20

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081192 mRNA Translation: AAC31938.1
AK023973 mRNA Translation: BAG51243.1
AB209001 mRNA Translation: BAD92238.1 Different initiation.
AC004854 Genomic DNA Translation: AAS00365.1
CH471128 Genomic DNA Translation: EAW61075.1
CH471128 Genomic DNA Translation: EAW61077.1
BC000098 mRNA Translation: AAH00098.1
BC004274 mRNA Translation: AAH04274.3
BC014885 mRNA Translation: AAH14885.1
BC070169 mRNA Translation: AAH70169.1
BE742590 mRNA No translation available.
BU543626 mRNA No translation available.
CCDSiCCDS47581.1 [Q71UI9-5]
CCDS5495.1 [Q71UI9-2]
CCDS5496.1 [Q71UI9-1]
CCDS5497.1 [Q71UI9-4]
CCDS5498.1 [Q71UI9-3]
RefSeqiNP_036544.1, NM_012412.4 [Q71UI9-1]
NP_619541.1, NM_138635.3 [Q71UI9-2]
NP_958844.1, NM_201436.2 [Q71UI9-4]
NP_958924.1, NM_201516.2 [Q71UI9-5]
NP_958925.1, NM_201517.2 [Q71UI9-3]
UniGeneiHs.488189

Genome annotation databases

EnsembliENST00000222690; ENSP00000222690; ENSG00000105968 [Q71UI9-2]
ENST00000308153; ENSP00000308405; ENSG00000105968 [Q71UI9-1]
ENST00000349299; ENSP00000342714; ENSG00000105968 [Q71UI9-3]
ENST00000350771; ENSP00000340708; ENSG00000105968 [Q71UI9-4]
ENST00000381124; ENSP00000370516; ENSG00000105968 [Q71UI9-5]
GeneIDi94239
KEGGihsa:94239
UCSCiuc003tlz.3 human [Q71UI9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF081192 mRNA Translation: AAC31938.1
AK023973 mRNA Translation: BAG51243.1
AB209001 mRNA Translation: BAD92238.1 Different initiation.
AC004854 Genomic DNA Translation: AAS00365.1
CH471128 Genomic DNA Translation: EAW61075.1
CH471128 Genomic DNA Translation: EAW61077.1
BC000098 mRNA Translation: AAH00098.1
BC004274 mRNA Translation: AAH04274.3
BC014885 mRNA Translation: AAH14885.1
BC070169 mRNA Translation: AAH70169.1
BE742590 mRNA No translation available.
BU543626 mRNA No translation available.
CCDSiCCDS47581.1 [Q71UI9-5]
CCDS5495.1 [Q71UI9-2]
CCDS5496.1 [Q71UI9-1]
CCDS5497.1 [Q71UI9-4]
CCDS5498.1 [Q71UI9-3]
RefSeqiNP_036544.1, NM_012412.4 [Q71UI9-1]
NP_619541.1, NM_138635.3 [Q71UI9-2]
NP_958844.1, NM_201436.2 [Q71UI9-4]
NP_958924.1, NM_201516.2 [Q71UI9-5]
NP_958925.1, NM_201517.2 [Q71UI9-3]
UniGeneiHs.488189

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3WAAX-ray3.20C/G1-128[»]
ProteinModelPortaliQ71UI9
SMRiQ71UI9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125150, 48 interactors
IntActiQ71UI9, 16 interactors
MINTiQ71UI9
STRINGi9606.ENSP00000308405

PTM databases

iPTMnetiQ71UI9
PhosphoSitePlusiQ71UI9
SwissPalmiQ71UI9

Polymorphism and mutation databases

BioMutaiH2AFV
DMDMi74749787

Proteomic databases

EPDiQ71UI9
MaxQBiQ71UI9
PaxDbiQ71UI9
PeptideAtlasiQ71UI9
PRIDEiQ71UI9
ProteomicsDBi68632
68633 [Q71UI9-2]
TopDownProteomicsiQ71UI9-1 [Q71UI9-1]
Q71UI9-3 [Q71UI9-3]
Q71UI9-4 [Q71UI9-4]

Protocols and materials databases

DNASUi94239
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000222690; ENSP00000222690; ENSG00000105968 [Q71UI9-2]
ENST00000308153; ENSP00000308405; ENSG00000105968 [Q71UI9-1]
ENST00000349299; ENSP00000342714; ENSG00000105968 [Q71UI9-3]
ENST00000350771; ENSP00000340708; ENSG00000105968 [Q71UI9-4]
ENST00000381124; ENSP00000370516; ENSG00000105968 [Q71UI9-5]
GeneIDi94239
KEGGihsa:94239
UCSCiuc003tlz.3 human [Q71UI9-1]

Organism-specific databases

CTDi94239
EuPathDBiHostDB:ENSG00000105968.18
GeneCardsiH2AFV
HGNCiHGNC:20664 H2AFV
HPAiHPA057236
neXtProtiNX_Q71UI9
OpenTargetsiENSG00000105968
PharmGKBiPA134895050
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1757 Eukaryota
COG5262 LUCA
GeneTreeiENSGT00900000140979
HOGENOMiHOG000234652
HOVERGENiHBG009342
InParanoidiQ71UI9
KOiK11251
OMAiIHRYLMN
OrthoDBiEOG091G0XGD
PhylomeDBiQ71UI9
TreeFamiTF354232

Enzyme and pathway databases

ReactomeiR-HSA-1221632 Meiotic synapsis
R-HSA-171306 Packaging Of Telomere Ends
R-HSA-1912408 Pre-NOTCH Transcription and Translation
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-5334118 DNA methylation
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-73728 RNA Polymerase I Promoter Opening
R-HSA-73777 RNA Polymerase I Chain Elongation
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-912446 Meiotic recombination

Miscellaneous databases

ChiTaRSiH2AFV human
GeneWikiiH2AFV
GenomeRNAii94239
PROiPR:Q71UI9

Gene expression databases

BgeeiENSG00000105968 Expressed in 231 organ(s), highest expression level in substantia nigra
CleanExiHS_H2AFV
ExpressionAtlasiQ71UI9 baseline and differential
GenevisibleiQ71UI9 HS

Family and domain databases

CDDicd00074 H2A, 1 hit
Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072 Histone-fold
IPR002119 Histone_H2A
IPR007125 Histone_H2A/H2B/H3
IPR032454 Histone_H2A_C
IPR032458 Histone_H2A_CS
PfamiView protein in Pfam
PF00125 Histone, 1 hit
PF16211 Histone_H2A_C, 1 hit
PRINTSiPR00620 HISTONEH2A
SMARTiView protein in SMART
SM00414 H2A, 1 hit
SUPFAMiSSF47113 SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00046 HISTONE_H2A, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiH2AV_HUMAN
AccessioniPrimary (citable) accession number: Q71UI9
Secondary accession number(s): A6NFA8
, A6NKY0, A6NN01, A8MQC5, Q59GV8, Q6PK98
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 143 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
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