Human Gene H2AB2 (ENST00000354514.6_4) from GENCODE V47lift37
  Description: H2A.B variant histone 2 (from RefSeq NM_001017991.3)
Gencode Transcript: ENST00000354514.6_4
Gencode Gene: ENSG00000277858.2_7
Transcript (Including UTRs)
   Position: hg19 chrX:154,610,358-154,610,948 Size: 591 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chrX:154,610,436-154,610,783 Size: 348 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:154,610,358-154,610,948)mRNA (may differ from genome)Protein (115 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H2AB2_HUMAN
DESCRIPTION: RecName: Full=Histone H2A-Bbd type 2/3; AltName: Full=H2A Barr body-deficient; Short=H2A.Bbd;
FUNCTION: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with active transcription and mRNA processing. 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. Nucleosomes containing this histone are less rigid and organize less DNA than canonical nucleosomes in vivo. They are enriched in actively transcribed genes and associate with the elongating form of RNA polymerase. They associate with spliceosome components and are required for mRNA splicing. May participate in spermatogenesis.
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. May be incorporated into a proportion of nucleosomes, replacing one or more H2A molecules.
SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Associated with the active X chromosome and with autosomes, while it is absent from the inactive X chromosome and excluded from Barr bodies.
TISSUE SPECIFICITY: Present in mature sperm.
DOMAIN: The docking domain is responsible for the weaker heterodimerization with H2B.
MISCELLANEOUS: In contrast to other H2A histones, it does not contain the conserved residues that are the target of post- translational modifications.
SIMILARITY: Belongs to the histone H2A family.
WEB RESOURCE: Name=Wikipedia; Note=Histone H2A entry; URL="http://en.wikipedia.org/wiki/Histone_H2A";

-  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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.1078-0.271 Picture PostScript Text
3' UTR -37.30165-0.226 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

SCOP Domains:
47113 - Histone-fold

ModBase Predicted Comparative 3D Structure on P0C5Z0
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006334 nucleosome assembly
GO:0006342 chromatin silencing
GO:0006397 mRNA processing

Cellular Component:
GO:0000786 nucleosome
GO:0000788 nuclear nucleosome
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005694 chromosome
GO:0035327 transcriptionally active chromatin


-  Descriptions from all associated GenBank mRNAs
  BC130510 - Homo sapiens H2A histone family, member B3, mRNA (cDNA clone MGC:163382 IMAGE:40146541), complete cds.
BC130512 - Homo sapiens H2A histone family, member B3, mRNA (cDNA clone MGC:163384 IMAGE:40146543), complete cds.
AF254576 - Homo sapiens histone H2A variant Barr-body deficient mRNA, complete cds.
HQ258044 - Synthetic construct Homo sapiens clone IMAGE:100072353 H2A histone family, member B3 (H2AFB3) gene, encodes complete protein.
KJ894901 - Synthetic construct Homo sapiens clone ccsbBroadEn_04295 H2AFB3 gene, encodes complete protein.
KJ900780 - Synthetic construct Homo sapiens clone ccsbBroadEn_10174 H2AFB2 gene, encodes complete protein.
BC134365 - Homo sapiens H2A histone family, member B2, mRNA (cDNA clone MGC:158903 IMAGE:40021542), complete cds.
CR542230 - Homo sapiens full open reading frame cDNA clone RZPDo834G0325D for gene H2AFB, H2A histone family, member B; complete cds, without stopcodon.
BC101409 - Homo sapiens H2A histone family, member B2, mRNA (cDNA clone MGC:125404 IMAGE:40021547), complete cds.
BC101415 - Homo sapiens H2A histone family, member B2, mRNA (cDNA clone MGC:125401 IMAGE:40021541), complete cds.
BC101417 - Homo sapiens H2A histone family, member B2, mRNA (cDNA clone MGC:125402 IMAGE:40021543), complete cds.
BC101418 - Homo sapiens H2A histone family, member B2, mRNA (cDNA clone MGC:125403 IMAGE:40021544), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: A1L4E4, ENST00000354514.1, ENST00000354514.2, ENST00000354514.3, ENST00000354514.4, ENST00000354514.5, H2AB2 , H2AB2_HUMAN, H2AB3 , H2ABBD, H2AFB, H2AFB2 , H2AFB3 , NM_001017991, P0C5Z0, P98176, Q5TZB2, Q6FG78, Q96PR7, uc317yqz.1, uc317yqz.2
UCSC ID: ENST00000354514.6_4
RefSeq Accession: NM_001017991.3
Protein: P0C5Z0 (aka H2AB2_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.