Human Gene H2AZ2 (ENST00000222690.10_5) from GENCODE V47lift37
  Description: H2A.Z variant histone 2, transcript variant 2 (from RefSeq NM_138635.3)
Gencode Transcript: ENST00000222690.10_5
Gencode Gene: ENSG00000105968.19_9
Transcript (Including UTRs)
   Position: hg19 chr7:44,866,390-44,887,676 Size: 21,287 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr7:44,869,743-44,887,570 Size: 17,828 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:44,866,390-44,887,676)mRNA (may differ from genome)Protein (114 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
ReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H2AV_HUMAN
DESCRIPTION: RecName: Full=Histone H2A.V; AltName: Full=H2A.F/Z;
FUNCTION: 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).
SUBUNIT: 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 an heterodimer with H2B (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome (By similarity).
PTM: Monoubiquitination of Lys-122 gives a specific tag for epigenetic transcriptional repression (By similarity).
PTM: Acetylated on Lys-5, Lys-8 and Lys-12 during interphase. Acetylation disappears at mitosis (By similarity).
MASS SPECTROMETRY: Mass=13369.4; Method=Electrospray; Range=2-128; Note=Monoisotopic, not modified; Source=PubMed:16457589;
SIMILARITY: Belongs to the histone H2A family.
SEQUENCE CAUTION: Sequence=BAD92238.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 59.19 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1276.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -62.30106-0.588 Picture PostScript Text
3' UTR -934.703353-0.279 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009072 - Histone-fold
IPR007125 - Histone_core_D
IPR002119 - Histone_H2A

Pfam Domains:
PF00125 - Core histone H2A/H2B/H3/H4

SCOP Domains:
47113 - Histone-fold

ModBase Predicted Comparative 3D Structure on Q71UI9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0003677 DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006342 chromatin silencing
GO:0008150 biological_process

Cellular Component:
GO:0000786 nucleosome
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005694 chromosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ895226 - Synthetic construct Homo sapiens clone ccsbBroadEn_04620 H2AFV gene, encodes complete protein.
AL049324 - Homo sapiens mRNA; cDNA DKFZp564D246 (from clone DKFZp564D246).
AK023973 - Homo sapiens cDNA FLJ13911 fis, clone Y79AA1000214, highly similar to Histone H2AV.
JD556980 - Sequence 538004 from Patent EP1572962.
JD369518 - Sequence 350542 from Patent EP1572962.
JD563533 - Sequence 544557 from Patent EP1572962.
JD337096 - Sequence 318120 from Patent EP1572962.
JD415399 - Sequence 396423 from Patent EP1572962.
JD187945 - Sequence 168969 from Patent EP1572962.
JD497145 - Sequence 478169 from Patent EP1572962.
JD393560 - Sequence 374584 from Patent EP1572962.
JD102936 - Sequence 83960 from Patent EP1572962.
JD195678 - Sequence 176702 from Patent EP1572962.
JD363536 - Sequence 344560 from Patent EP1572962.
JD483494 - Sequence 464518 from Patent EP1572962.
JD436325 - Sequence 417349 from Patent EP1572962.
JD559875 - Sequence 540899 from Patent EP1572962.
JD348260 - Sequence 329284 from Patent EP1572962.
JD312323 - Sequence 293347 from Patent EP1572962.
JD304150 - Sequence 285174 from Patent EP1572962.
JD424554 - Sequence 405578 from Patent EP1572962.
JD283176 - Sequence 264200 from Patent EP1572962.
JD292216 - Sequence 273240 from Patent EP1572962.
JD134465 - Sequence 115489 from Patent EP1572962.
JD452175 - Sequence 433199 from Patent EP1572962.
JD385165 - Sequence 366189 from Patent EP1572962.
JD077286 - Sequence 58310 from Patent EP1572962.
JD430605 - Sequence 411629 from Patent EP1572962.
JD530190 - Sequence 511214 from Patent EP1572962.
JD551475 - Sequence 532499 from Patent EP1572962.
JD270579 - Sequence 251603 from Patent EP1572962.
JD054128 - Sequence 35152 from Patent EP1572962.
JD387290 - Sequence 368314 from Patent EP1572962.
JD319886 - Sequence 300910 from Patent EP1572962.
JD115579 - Sequence 96603 from Patent EP1572962.
JD241239 - Sequence 222263 from Patent EP1572962.
JD312192 - Sequence 293216 from Patent EP1572962.
JD163224 - Sequence 144248 from Patent EP1572962.
JD402171 - Sequence 383195 from Patent EP1572962.
JD071349 - Sequence 52373 from Patent EP1572962.
JD237118 - Sequence 218142 from Patent EP1572962.
JD254675 - Sequence 235699 from Patent EP1572962.
JD368090 - Sequence 349114 from Patent EP1572962.
JD174727 - Sequence 155751 from Patent EP1572962.
JD242597 - Sequence 223621 from Patent EP1572962.
JD505563 - Sequence 486587 from Patent EP1572962.
JD207612 - Sequence 188636 from Patent EP1572962.
JD505562 - Sequence 486586 from Patent EP1572962.
JD345642 - Sequence 326666 from Patent EP1572962.
JD212936 - Sequence 193960 from Patent EP1572962.
JD542876 - Sequence 523900 from Patent EP1572962.
JD560922 - Sequence 541946 from Patent EP1572962.
JD432417 - Sequence 413441 from Patent EP1572962.
JD059566 - Sequence 40590 from Patent EP1572962.
JD262048 - Sequence 243072 from Patent EP1572962.
JD087046 - Sequence 68070 from Patent EP1572962.
JD212935 - Sequence 193959 from Patent EP1572962.
JD295676 - Sequence 276700 from Patent EP1572962.
JD262344 - Sequence 243368 from Patent EP1572962.
JD556841 - Sequence 537865 from Patent EP1572962.
JD091607 - Sequence 72631 from Patent EP1572962.
JD320811 - Sequence 301835 from Patent EP1572962.
JD525014 - Sequence 506038 from Patent EP1572962.
JD374713 - Sequence 355737 from Patent EP1572962.
JD409368 - Sequence 390392 from Patent EP1572962.
JD424662 - Sequence 405686 from Patent EP1572962.
JD536257 - Sequence 517281 from Patent EP1572962.
JD064819 - Sequence 45843 from Patent EP1572962.
JD315530 - Sequence 296554 from Patent EP1572962.
JD282368 - Sequence 263392 from Patent EP1572962.
DQ578790 - Homo sapiens piRNA piR-46902, complete sequence.
JD289608 - Sequence 270632 from Patent EP1572962.
AB209001 - Homo sapiens mRNA for H2A histone family, member V isoform 1 variant protein.
BC000098 - Homo sapiens H2A histone family, member V, mRNA (cDNA clone MGC:1947 IMAGE:3505930), complete cds.
BC070169 - Homo sapiens H2A histone family, member V, mRNA (cDNA clone MGC:88149 IMAGE:6458566), complete cds.
BC004274 - Homo sapiens H2A histone family, member V, mRNA (cDNA clone MGC:10831 IMAGE:3615320), complete cds.
AK129989 - Homo sapiens cDNA FLJ26479 fis, clone KDN05022, highly similar to Histone H2A.
BC014885 - Homo sapiens H2A histone family, member V, mRNA (cDNA clone MGC:10170 IMAGE:3907411), complete cds.
AF081192 - Homo sapiens histone H2A.F/Z variant (H2AV) mRNA, complete cds.
DQ892406 - Synthetic construct clone IMAGE:100005036; FLH186054.01X; RZPDo839A0671D H2A histone family, member V (H2AFV) gene, encodes complete protein.
DQ895618 - Synthetic construct Homo sapiens clone IMAGE:100010078; FLH186050.01L; RZPDo839A0661D H2A histone family, member V (H2AFV) gene, encodes complete protein.
JD127827 - Sequence 108851 from Patent EP1572962.
JD211131 - Sequence 192155 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q71UI9 (Reactome details) participates in the following event(s):

R-HSA-9011983 Overexpressed HIST1H2AC and ESR1:ESTG bind MYC and BCL2 genes
R-HSA-176700 Incorporation Of Extended And Processed Telomere End Into Higher Order T-Loop And Associated Protein Structure
R-HSA-181450 Incorporation Of Extended And Processed Telomere End Into Associated Protein Structure
R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9
R-HSA-1214188 PRDM9 trimethylates histone H3
R-HSA-8935730 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the ITGA2B promoter
R-HSA-8935740 RUNX1 and GATA1 bind the promoter of the ITGA2B gene
R-HSA-8936599 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the GP1BA promoter
R-HSA-8936616 RUNX1 and GATA1 bind the promoter of the GP1BA gene
R-HSA-8936979 RUNX1 and GATA1 bind the promoter of the THBS1 gene
R-HSA-8936989 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the THBS1 gene promoter
R-HSA-8937037 RUNX1 and GATA1 bind the promoter of the MIR27A gene
R-HSA-8937118 RUNX1:CBFB, SIN3A(SIN3B), PRMT6 and HDAC1 bind the MIR27A gene promoter
R-HSA-2288097 Condensin II complex binds H4K20me1-containing nucleosomes
R-HSA-2245218 CDK1 phosphorylates PHF8
R-HSA-3451147 KAT5 HAT complex acetylates TCF4 gene at histone H4
R-HSA-427383 CBX3 (HP1gamma) binds histone H3 dimethylated at lysine-9
R-HSA-427528 Formation of energy-dependent Nucleolar Silencing Complex (eNoSC)
R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes
R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9.
R-HSA-427527 eNoSC dimethylates histone H3 at lysine-9
R-HSA-3788748 EHMT1:EHMT2 methylates IL6 promoter
R-HSA-3788745 EHMT1:EHMT2 methylates IL8 promoter
R-HSA-427337 MBD2 binds methylcytosine in chromatin
R-HSA-5334164 DNMT3B:DNMT3L binds chromatin
R-HSA-5334179 DNMT3A:DNMT3L binds chromatin
R-HSA-5578742 AGO1,2:small RNA complexes interact with chromatin
R-HSA-427514 eNoSC deacetylates histone H3
R-HSA-3240295 PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter
R-HSA-3222593 KDM6B demethylates H3K27me3 on p16-INK4A promoter
R-HSA-5334151 DNMT1 methylates cytosine in hemimethylated DNA
R-HSA-5334160 UHRF1:Chromatin binds DNMT1
R-HSA-5334099 UHRF1 binds chromatin with hemimethylated cytosine
R-HSA-8865491 RUNX1:CBFB:KMT2A binds SPI1 (PU.1) gene
R-HSA-9011949 KDM4B demethylates H3K9me3 on estrogen-responsive target enhancers
R-HSA-3229089 PRC1.4 complex binds H3K27Me3 nucleosomes on CDKN2A promoter
R-HSA-3229102 p-MAPKAPK3 phosphorylates BMI1
R-HSA-8936481 Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936621 Core MLL complex methylates H3K4Me2-Nucleosome at the GP1BA gene promoter
R-HSA-8937016 Core MLL complex methylates H3K4Me2-Nucleosome at the THBS1 gene promoter
R-HSA-8937050 Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A gene promoter
R-HSA-8936584 PRMT6 arginine methylates H3K4me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936608 PRMT6 arginine methylates H3K4me2-Nucleosome at the GP1BA gene promoter
R-HSA-8937022 PRMT6 arginine methylates H3K4me2-Nucleosome at the THBS1 gene promoter
R-HSA-8937113 PRMT6 arginine methylates H3K4me2-Nucleosome at the MIR27A gene promoter
R-HSA-9009371 Binding of AP1 transcriptional activator complexes to CCND1 promoter
R-HSA-9009065 FOXA1 and GATA3 bind to CCND1 promoter
R-HSA-2172678 PHF8 demethylates histone H4K20me1
R-HSA-2301205 SETD8 monomethylates histone H4
R-HSA-2294600 CDK1 phosphorylates condensin II subunit NCAPD3
R-HSA-2294580 PLK1 hyperphosphorylates Condensin II complex
R-HSA-2294590 PLK1 binds phosphorylated condensin II complex
R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene
R-HSA-5625774 PKN1:AR complex binds promoters of KLK2 and KLK3 genes
R-HSA-9011952 ESR1:ESTG and KDM4B bind H3K9me3 target gene enhancers
R-HSA-5625849 Demethylase KDM1A binds KLK2 and KLK3 promoters
R-HSA-5625797 KDM4C demethylates Me3K-10-H3 associated with KLK2 and KLK3 promoters
R-HSA-5625870 KDM1A demethylates monomethylated H3K9 (MeK-10-H3) at KLK2 and KLK3 promoters
R-HSA-212263 PRC2 trimethylates histone H3 at lysine-27
R-HSA-212222 PRC2 recruits DNA methyltransferases
R-HSA-5334097 DNMT3B:DNMT3L methylates cytosine in DNA
R-HSA-5334152 DNMT3A:DNMT3L methylates cytosine in DNA
R-HSA-8865498 KMT2A trimethylates nucleosomes at the SPI1 gene locus producing H3K4Me3 mark
R-HSA-5625784 PKN1 phosphorylates histone 3 of nucleosomes associate with KLK2 and KLK3 promoters
R-HSA-5625796 Demethylase KDM4C binds KLK2 and KLK3 promoters
R-HSA-5625848 KDM1A demethylates dimethylated H3K9 (Me2K-10-H3) at KLK2 and KLK3 promoters
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-171306 Packaging Of Telomere Ends
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-912446 Meiotic recombination
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-774815 Nucleosome assembly
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8939211 ESR-mediated signaling
R-HSA-1221632 Meiotic synapsis
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-157579 Telomere Maintenance
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-5334118 DNA methylation
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-1500620 Meiosis
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-68875 Mitotic Prophase
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-73886 Chromosome Maintenance
R-HSA-4839726 Chromatin organization
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-2559583 Cellular Senescence
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-211000 Gene Silencing by RNA
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-1474165 Reproduction
R-HSA-1640170 Cell Cycle
R-HSA-212436 Generic Transcription Pathway
R-HSA-68886 M Phase
R-HSA-5625740 RHO GTPases activate PKNs
R-HSA-162582 Signal Transduction
R-HSA-2262752 Cellular responses to stress
R-HSA-195721 Signaling by WNT
R-HSA-74160 Gene expression (Transcription)
R-HSA-1266738 Developmental Biology
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-195258 RHO GTPase Effectors
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-194315 Signaling by Rho GTPases

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFA8, A6NKY0, A6NN01, A8MQC5, ENST00000222690.1, ENST00000222690.2, ENST00000222690.3, ENST00000222690.4, ENST00000222690.5, ENST00000222690.6, ENST00000222690.7, ENST00000222690.8, ENST00000222690.9, H2AFV , H2AV, H2AV_HUMAN, H2AZ2 , NM_138635, Q59GV8, Q6PK98, Q71UI9, uc317dfm.1
UCSC ID: ENST00000222690.10_5
RefSeq Accession: NM_138635.3
Protein: Q71UI9 (aka H2AV_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.