Human Gene H2AC1 (ENST00000297012.5_7) from GENCODE V47lift37
  Description: H2A clustered histone 1 (from RefSeq NM_170745.3)
Gencode Transcript: ENST00000297012.5_7
Gencode Gene: ENSG00000164508.6_9
Transcript (Including UTRs)
   Position: hg19 chr6:25,726,291-25,726,790 Size: 500 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr6:25,726,360-25,726,755 Size: 396 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 (chr6:25,726,291-25,726,790)mRNA (may differ from genome)Protein (131 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H2A1A_HUMAN
DESCRIPTION: RecName: Full=Histone H2A type 1-A; AltName: Full=Histone H2A/r;
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.
SIMILARITY: Belongs to the histone H2A family.

-  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: 4.53 RPKM in Testis
Total median expression: 4.55 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 -9.3035-0.266 Picture PostScript Text
3' UTR -15.7069-0.228 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 Q96QV6
FrontTopSide
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 Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006325 chromatin organization
GO:0006342 chromatin silencing

Cellular Component:
GO:0000784 nuclear chromosome, telomeric region
GO:0000786 nucleosome
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005694 chromosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF385397 - JP 2014500723-A/192900: Polycomb-Associated Non-Coding RNAs.
BC062211 - Homo sapiens histone cluster 1, H2aa, mRNA (cDNA clone MGC:71871 IMAGE:6614487), complete cds.
LF331331 - JP 2014500723-A/138834: Polycomb-Associated Non-Coding RNAs.
LF209731 - JP 2014500723-A/17234: Polycomb-Associated Non-Coding RNAs.
CU687518 - Synthetic construct Homo sapiens gateway clone IMAGE:100023077 5' read HIST1H2AA mRNA.
HQ447550 - Synthetic construct Homo sapiens clone IMAGE:100070889; CCSB014828_01 histone cluster 1, H2aa (HIST1H2AA) gene, encodes complete protein.
KJ895868 - Synthetic construct Homo sapiens clone ccsbBroadEn_05262 HIST1H2AA gene, encodes complete protein.
DQ585258 - Homo sapiens piRNA piR-52370, complete sequence.
DQ583342 - Homo sapiens piRNA piR-50454, complete sequence.
DQ585961 - Homo sapiens piRNA piR-53073, complete sequence.
MA620974 - JP 2018138019-A/192900: Polycomb-Associated Non-Coding RNAs.
MA566908 - JP 2018138019-A/138834: Polycomb-Associated Non-Coding RNAs.
MA445308 - JP 2018138019-A/17234: Polycomb-Associated Non-Coding RNAs.

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

Protein Q96QV6 (Reactome details) participates in the following event(s):

R-HSA-5690790 Histone H2A is dubiquitinated by the PR-DUB complex
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-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-3214858 RMTs methylate histone arginines
R-HSA-5689603 UCH proteinases
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5689901 Metalloprotease DUBs
R-HSA-3214847 HATs acetylate histones
R-HSA-5688426 Deubiquitination
R-HSA-4839726 Chromatin organization
R-HSA-3214815 HDACs deacetylate histones
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000297012.1, ENST00000297012.2, ENST00000297012.3, ENST00000297012.4, H2A1A_HUMAN, H2AC1 , H2AFR, HIST1H2AA , NM_170745, Q96QV6, uc317lxy.1, uc317lxy.2
UCSC ID: ENST00000297012.5_7
RefSeq Accession: NM_170745.3
Protein: Q96QV6 (aka H2A1A_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.