Human Gene H2BC18 (ENST00000369167.3_5) from GENCODE V47lift37
  Description: H2B clustered histone 18, transcript variant 1 (from RefSeq NM_001024599.5)
Gencode Transcript: ENST00000369167.3_5
Gencode Gene: ENSG00000203814.7_10
Transcript (Including UTRs)
   Position: hg19 chr1:149,783,434-149,783,925 Size: 492 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr1:149,783,498-149,783,878 Size: 381 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 (chr1:149,783,434-149,783,925)mRNA (may differ from genome)Protein (126 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
ReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H2B2F_HUMAN
DESCRIPTION: RecName: Full=Histone H2B type 2-F;
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: Monoubiquitination of Lys-121 by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II.
PTM: Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription (By similarity). Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination.
PTM: GlcNAcylation at Ser-113 promotes monoubiquitination of Lys- 121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (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 H2B 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: 4.66 RPKM in Ovary
Total median expression: 49.59 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 -1.6047-0.034 Picture PostScript Text
3' UTR -12.9064-0.202 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
IPR000558 - Histone_H2B

Pfam Domains:
PF00125 - Core histone H2A/H2B/H3/H4
PF00808 - Histone-like transcription factor (CBF/NF-Y) and archaeal histone

SCOP Domains:
47113 - Histone-fold

ModBase Predicted Comparative 3D Structure on Q5QNW6
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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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0003677 DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006334 nucleosome assembly

Cellular Component:
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK296916 - Homo sapiens cDNA FLJ56780 complete cds, highly similar to Histone H2B type 2-F.
AK299108 - Homo sapiens cDNA FLJ56787 complete cds, highly similar to Histone H2B type 2-F.
BC110793 - Homo sapiens histone cluster 2, H2bf, mRNA (cDNA clone MGC:131639 IMAGE:5224812), complete cds.
AK289664 - Homo sapiens cDNA FLJ77920 complete cds, highly similar to Homo sapiens histone 1, H2bh (HIST1H2BH), mRNA.
JD250829 - Sequence 231853 from Patent EP1572962.
JD120481 - Sequence 101505 from Patent EP1572962.
KJ896277 - Synthetic construct Homo sapiens clone ccsbBroadEn_05671 HIST2H2BF gene, encodes complete protein.

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

Protein Q5QNW6 (Reactome details) participates in the following event(s):

R-HSA-3318415 ATF2 acetylates histone H2B, H4
R-HSA-5696960 USP49 deubiquitinates H2B
R-HSA-3697008 CREBBP acetylates histone H2B, H3, H4
R-HSA-3662335 EP300 acetylates histone H2A, H2B, H3, H4
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-3214847 HATs acetylate histones
R-HSA-5689880 Ub-specific processing proteases
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-3214815 HDACs deacetylate histones
R-HSA-5688426 Deubiquitination
R-HSA-4839726 Chromatin organization
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0U9, B4DLA9, ENST00000369167.1, ENST00000369167.2, H2B2F_HUMAN, H2BC18 , HIST2H2BF , NM_001024599, Q5QNW6, uc318hjt.1, uc318hjt.2
UCSC ID: ENST00000369167.3_5
RefSeq Accession: NM_001024599.5
Protein: Q5QNW6 (aka H2B2F_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.