Human Gene H2AC20 (ENST00000331380.4_4) from GENCODE V47lift37
  Description: H2A clustered histone 20 (from RefSeq NM_003517.3)
Gencode Transcript: ENST00000331380.4_4
Gencode Gene: ENSG00000184260.6_7
Transcript (Including UTRs)
   Position: hg19 chr1:149,858,468-149,858,961 Size: 494 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr1:149,858,525-149,858,914 Size: 390 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:149,858,468-149,858,961)mRNA (may differ from genome)Protein (129 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H2A2C_HUMAN
DESCRIPTION: RecName: Full=Histone H2A type 2-C; AltName: Full=Histone H2A-GL101; AltName: Full=Histone H2A/q;
FUNCTION: Core component of nucleosome. 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.
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.
SUBCELLULAR LOCATION: Nucleus. Chromosome.
PTM: The chromatin-associated form is phosphorylated on Thr-121 during mitosis (Probable).
PTM: Deiminated on Arg-4 in granulocytes upon calcium entry.
PTM: Monoubiquitination of Lys-120 (H2AK119Ub) by RING1 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys- 16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced 'Lys- 63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events.
PTM: Phosphorylation on Ser-2 is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1.
PTM: Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage (By similarity).
PTM: Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
MASS SPECTROMETRY: Mass=13890.8; Method=Electrospray; Range=2-129; Note=Monoisotopic with N-acetylserine; Source=PubMed:16457589;
SIMILARITY: Belongs to the histone H2A family.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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+  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: 3.35 RPKM in Whole Blood
Total median expression: 48.55 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -8.9057-0.156 Picture PostScript Text
3' UTR -10.1047-0.215 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
PF00808 - Histone-like transcription factor (CBF/NF-Y) and archaeal histone
PF16211 - C-terminus of histone H2A

SCOP Domains:
47113 - Histone-fold

ModBase Predicted Comparative 3D Structure on Q16777
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-  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    
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-  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
  DL491335 - Novel nucleic acids.
DL489967 - Novel nucleic acids.
BC060324 - Homo sapiens histone cluster 2, H2ac, mRNA (cDNA clone MGC:74460 IMAGE:3892650), complete cds.
EU446979 - Synthetic construct Homo sapiens clone IMAGE:100070114; IMAGE:100012188; FLH258140.01L histone cluster 2, H2ac (HIST2H2AC) gene, encodes complete protein.
KJ892502 - Synthetic construct Homo sapiens clone ccsbBroadEn_01896 HIST2H2AC gene, encodes complete protein.

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

Protein Q16777 (Reactome details) participates in the following event(s):

R-HSA-9011983 Overexpressed HIST1H2AC and ESR1:ESTG bind MYC and BCL2 genes
R-HSA-5690790 Histone H2A is dubiquitinated by the PR-DUB complex
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-5690157 USP16,USP21 deubiquitinate Histone H2A
R-HSA-5691381 MYSM1 deubiquitinates Histone H2A
R-HSA-5691411 BRCA1-A complex deubiquitinates K63polyUb-histone H2A
R-HSA-3321975 NuA4 complex acetylates histone H2A, HIST1H4
R-HSA-3662335 EP300 acetylates histone H2A, H2B, H3, H4
R-HSA-5205867 PRMT1 methylates arginine-12 of histone H2A (H2AR11)
R-HSA-5229203 PRMT6 methylates histone H2A arginine-30 (H2AR29)
R-HSA-5205820 PRMT6 methylates arginine-4 of histone H2A (H2AR3)
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-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-3777129 HDAC3 containing complexes deacetylate histone
R-HSA-3782637 HDAC8 deacetylates histones
R-HSA-3782655 HDAC10 deacetylates histone
R-HSA-5690080 USP3,SAGA deubiquitinate Histone H2A,H2B
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-977224 Serum amyloid P binds DNA and chromatin
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-5689603 UCH proteinases
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-5689880 Ub-specific processing proteases
R-HSA-5689901 Metalloprotease DUBs
R-HSA-3214847 HATs acetylate histones
R-HSA-5688426 Deubiquitination
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-3214815 HDACs deacetylate histones
R-HSA-597592 Post-translational protein modification
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-977225 Amyloid fiber formation
R-HSA-392499 Metabolism of proteins
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: ENST00000331380.1, ENST00000331380.2, ENST00000331380.3, H2A2C_HUMAN, H2AC20 , H2AFQ, HIST2H2AC , NM_003517, Q16777, Q6DRA7, Q8IUE5, uc317tet.1, uc317tet.2
UCSC ID: ENST00000331380.4_4
RefSeq Accession: NM_003517.3
Protein: Q16777 (aka H2A2C_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.