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Protein

Histone H2A.V

Gene

H2AFV

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Complete GO annotation...

Keywords - Ligandi

DNA-binding

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
ProteomesiUP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:20664. H2AFV.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • nucleosome Source: UniProtKB-KW
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134895050.

Polymorphism and mutation databases

BioMutaiH2AFV.
DMDMi74749787.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 128128Histone H2A.VPRO_0000239068Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei5 – 51N6-acetyllysineBy similarity
Modified residuei8 – 81N6-acetyllysineBy similarity
Modified residuei12 – 121N6-acetyllysineBy similarity
Cross-linki122 – 122Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

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, Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiQ71UI9.
PaxDbiQ71UI9.
PRIDEiQ71UI9.

PTM databases

PhosphoSiteiQ71UI9.

Expressioni

Gene expression databases

BgeeiQ71UI9.
CleanExiHS_H2AFV.
ExpressionAtlasiQ71UI9. baseline and differential.
GenevestigatoriQ71UI9.

Organism-specific databases

HPAiHPA045242.

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

Protein-protein interaction databases

BioGridi125150. 32 interactions.
IntActiQ71UI9. 5 interactions.
MINTiMINT-4828370.
STRINGi9606.ENSP00000308405.

Structurei

Secondary structure

1
128
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi20 – 234Combined sources
Helixi30 – 389Combined sources
Helixi49 – 7527Combined sources
Turni76 – 783Combined sources
Beta strandi80 – 823Combined sources
Helixi84 – 9310Combined sources
Helixi95 – 1006Combined sources
Beta strandi103 – 1053Combined sources
Helixi116 – 1183Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3WAAX-ray3.20C/G1-128[»]
ProteinModelPortaliQ71UI9.
SMRiQ71UI9. Positions 15-121.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2A family.Curated

Phylogenomic databases

eggNOGiCOG5262.
GeneTreeiENSGT00710000106735.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiQ71UI9.
KOiK11251.
OMAiVASIMEY.
PhylomeDBiQ71UI9.
TreeFamiTF354232.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

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

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

Sequence cautioni

The sequence BAD92238.1 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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti125 – 1251Q → R.
Corresponds to variant rs1802437 [ dbSNP | Ensembl ].
VAR_059312

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2727MAGGK…RAGLQ → M in isoform 4. 1 PublicationVSP_045232Add
BLAST
Alternative sequencei28 – 6538Missing in isoform 3. 1 PublicationVSP_044633Add
BLAST
Alternative sequencei67 – 12862Missing in isoform 5. CuratedVSP_046783Add
BLAST
Alternative sequencei109 – 12820GVIPH…QQKTA → EKRRCS in isoform 2. 1 PublicationVSP_042855Add
BLAST

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.2. human. [Q71UI9-2]
uc003tma.2. human. [Q71UI9-1]
uc003tmb.2. human.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3WAAX-ray3.20C/G1-128[»]
ProteinModelPortaliQ71UI9.
SMRiQ71UI9. Positions 15-121.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125150. 32 interactions.
IntActiQ71UI9. 5 interactions.
MINTiMINT-4828370.
STRINGi9606.ENSP00000308405.

PTM databases

PhosphoSiteiQ71UI9.

Polymorphism and mutation databases

BioMutaiH2AFV.
DMDMi74749787.

Proteomic databases

MaxQBiQ71UI9.
PaxDbiQ71UI9.
PRIDEiQ71UI9.

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.2. human. [Q71UI9-2]
uc003tma.2. human. [Q71UI9-1]
uc003tmb.2. human.

Organism-specific databases

CTDi94239.
GeneCardsiGC07M044833.
HGNCiHGNC:20664. H2AFV.
HPAiHPA045242.
neXtProtiNX_Q71UI9.
PharmGKBiPA134895050.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5262.
GeneTreeiENSGT00710000106735.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiQ71UI9.
KOiK11251.
OMAiVASIMEY.
PhylomeDBiQ71UI9.
TreeFamiTF354232.

Miscellaneous databases

ChiTaRSiH2AFV. human.
GeneWikiiH2AFV.
GenomeRNAii94239.
NextBioi78481.
PROiQ71UI9.

Gene expression databases

BgeeiQ71UI9.
CleanExiHS_H2AFV.
ExpressionAtlasiQ71UI9. baseline and differential.
GenevestigatoriQ71UI9.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR007125. Histone_core_D.
IPR002119. Histone_H2A.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Novel human member of the variant histone family."
    Groitl P., Wolf H., Niller H.H.
    Submitted (JUL-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  3. Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  4. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] (ISOFORMS 1; 3 AND 4).
    Tissue: Kidney, Ovarian adenocarcinoma, Prostatic carcinoma, Skin and Uterus.
  7. "Precise characterization of human histones in the H2A gene family by top down mass spectrometry."
    Boyne M.T. II, Pesavento J.J., Mizzen C.A., Kelleher N.L.
    J. Proteome Res. 5:248-253(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY.

Entry informationi

Entry nameiH2AV_HUMAN
AccessioniPrimary (citable) accession number: Q71UI9
Secondary accession number(s): A6NFA8
, A6NKY0, A6NN01, A8MQC5, Q59GV8, Q6PK98
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: January 23, 2007
Last modified: May 27, 2015
This is version 113 of the entry and version 3 of the sequence. [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. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  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. 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.