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Aliases for HIST1H2BN Gene

Aliases for HIST1H2BN Gene

  • Histone Cluster 1 H2B Family Member N 2 3 5
  • H2B Histone Family, Member D 2 3
  • Histone Cluster 1, H2bn 2 3
  • Histone 1, H2bn 2 3
  • Histone H2B.D 3 4
  • H2BFD 3 4
  • H2B/D 3 4
  • Histone H2B Type 1-N 3

External Ids for HIST1H2BN Gene

Previous HGNC Symbols for HIST1H2BN Gene

  • H2BFD

Previous GeneCards Identifiers for HIST1H2BN Gene

  • GC06P027864
  • GC06P027914
  • GC06P027913
  • GC06P027805
  • GC06P027614

Summaries for HIST1H2BN Gene

Entrez Gene Summary for HIST1H2BN Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the small histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST1H2BN Gene

HIST1H2BN (Histone Cluster 1 H2B Family Member N) is a Protein Coding gene. Diseases associated with HIST1H2BN include Systemic Lupus Erythematosus. Among its related pathways are Mitotic Prophase and Meiosis. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is HIST1H2BG.

UniProtKB/Swiss-Prot for HIST1H2BN Gene

  • 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.

Gene Wiki entry for HIST1H2BN Gene

Additional gene information for HIST1H2BN Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H2BN Gene

Genomics for HIST1H2BN Gene

GeneHancer (GH) Regulatory Elements for HIST1H2BN Gene

Promoters and enhancers for HIST1H2BN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I027834 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 564.2 -0.5 -467 6.4 CLOCK FEZF1 DMAP1 IRF4 YY1 SLC30A9 E2F8 SP3 NFYC MEF2D HIST1H2BN HIST1H2AK GC06M027849 ZKSCAN3 ZKSCAN8 ZKSCAN4 ZSCAN9 ZSCAN12 HIST1H3J GUSBP2
GH06I027887 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15 +55.7 55721 11.9 ZFP64 DMAP1 IRF4 YY1 E2F8 ZNF143 NFYC SSRP1 ZNF610 RCOR2 HIST1H2AM HIST1H2BO HIST1H3J GC06M028114 PIR50251 PIR45952 PIR61297 PIR62073 ZKSCAN8 ZKSCAN3
GH06I027161 Enhancer 1.2 Ensembl ENCODE 10.1 -675.6 -675627 1.1 HDGF ATF1 ARNT ZNF2 NCOA2 GTF3C2 ZNF766 ZNF213 ARID2 ZNF143 GC06P027188 TRT-AGT6-1 ZNF322 ZKSCAN8 LOC102724851 HIST1H2AK HIST1H2BN HIST1H4K PRSS16 TRH-GTG1-5
GH06I027805 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.1 -25.6 -25645 12.7 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 NFYC HIST1H2AI HIST1H3H HIST1H2BM HIST1H2AJ HIST1H2BL ZKSCAN3 ZKSCAN8 ZNF603P ZSCAN9 ZKSCAN4
GH06I027791 Enhancer 1.6 FANTOM5 Ensembl ENCODE 1.5 -44.8 -44823 3.6 IRF4 SLC30A9 ZNF213 E2F8 ZNF143 SP3 MEF2D SSRP1 RCOR2 NBN GC06M027793 PIR59071 TRQ-CTG6-1 ZKSCAN8 ZKSCAN3 ZSCAN9 ZSCAN12 ZNF204P ENSG00000271755 ZSCAN23
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HIST1H2BN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST1H2BN gene promoter:

Genomic Locations for HIST1H2BN Gene

Genomic Locations for HIST1H2BN Gene
chr6:27,837,760-27,865,798
(GRCh38/hg38)
Size:
28,039 bases
Orientation:
Plus strand
chr6:27,806,323-27,823,487
(GRCh37/hg19)

Genomic View for HIST1H2BN Gene

Genes around HIST1H2BN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H2BN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H2BN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H2BN Gene

Proteins for HIST1H2BN Gene

  • Protein details for HIST1H2BN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99877-H2B1N_HUMAN
    Recommended name:
    Histone H2B type 1-N
    Protein Accession:
    Q99877
    Secondary Accessions:
    • B2R5L4
    • Q494S8
    • Q96FB7

    Protein attributes for HIST1H2BN Gene

    Size:
    126 amino acids
    Molecular mass:
    13922 Da
    Quaternary structure:
    • 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.

neXtProt entry for HIST1H2BN Gene

Post-translational modifications for HIST1H2BN Gene

  • 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.
  • GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes (By similarity).
  • Monoubiquitination at Lys-35 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 Lys-4 (H3K4me) and Lys-79 (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-121 (H2BK120Ub) 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. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons.
  • 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.
  • Ubiquitination at posLast=121121
  • Glycosylation at posLast=113113

Other Protein References for HIST1H2BN Gene

No data available for DME Specific Peptides for HIST1H2BN Gene

Domains & Families for HIST1H2BN Gene

Gene Families for HIST1H2BN Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HIST1H2BN Gene

Suggested Antigen Peptide Sequences for HIST1H2BN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q99877

UniProtKB/Swiss-Prot:

H2B1N_HUMAN :
  • Belongs to the histone H2B family.
Family:
  • Belongs to the histone H2B family.
genes like me logo Genes that share domains with HIST1H2BN: view

Function for HIST1H2BN Gene

Molecular function for HIST1H2BN Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for HIST1H2BN Gene

Gene Ontology (GO) - Molecular Function for HIST1H2BN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA,NAS 9439656
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H2BN: view
genes like me logo Genes that share phenotypes with HIST1H2BN: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H2BN Gene

Localization for HIST1H2BN Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H2BN Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HIST1H2BN gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HIST1H2BN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome NAS 9439656
GO:0005634 nucleus IDA 16319397
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with HIST1H2BN: view

Pathways & Interactions for HIST1H2BN Gene

SuperPathways for HIST1H2BN Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 DNA Double-Strand Break Repair
3 Cellular Senescence (REACTOME)
4 Chromosome Maintenance
5 Cell Cycle, Mitotic
.60
genes like me logo Genes that share pathways with HIST1H2BN: view

Gene Ontology (GO) - Biological Process for HIST1H2BN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IBA,NAS 9439656
GO:0016567 protein ubiquitination TAS --
genes like me logo Genes that share ontologies with HIST1H2BN: view

No data available for SIGNOR curated interactions for HIST1H2BN Gene

Drugs & Compounds for HIST1H2BN Gene

No Compound Related Data Available

Transcripts for HIST1H2BN Gene

mRNA/cDNA for HIST1H2BN Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H2BN Gene

No ASD Table

Relevant External Links for HIST1H2BN Gene

GeneLoc Exon Structure for
HIST1H2BN
ECgene alternative splicing isoforms for
HIST1H2BN

Expression for HIST1H2BN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST1H2BN Gene

Protein differential expression in normal tissues from HIPED for HIST1H2BN Gene

This gene is overexpressed in Saliva (57.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HIST1H2BN Gene



Protein tissue co-expression partners for HIST1H2BN Gene

NURSA nuclear receptor signaling pathways regulating expression of HIST1H2BN Gene:

HIST1H2BN

SOURCE GeneReport for Unigene cluster for HIST1H2BN Gene:

Hs.673851

Evidence on tissue expression from TISSUES for HIST1H2BN Gene

  • Eye(4.2)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with HIST1H2BN: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H2BN Gene

Orthologs for HIST1H2BN Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H2BN Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia H2B 34
  • 100 (a)
OneToOne
LOC787269 33
  • 91.53 (n)
chimpanzee
(Pan troglodytes)
Mammalia HIST1H2BN 34
  • 100 (a)
OneToOne
LOC462508 33
  • 99.47 (n)
dog
(Canis familiaris)
Mammalia LOC478743 33
  • 93.65 (n)
-- 34
  • 92 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Hist1h2bm 33 16
  • 93.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 92 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Hist1h2bd 33
  • 90.48 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.12831 33
Species where no ortholog for HIST1H2BN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for HIST1H2BN Gene

ENSEMBL:
Gene Tree for HIST1H2BN (if available)
TreeFam:
Gene Tree for HIST1H2BN (if available)

Paralogs for HIST1H2BN Gene

Variants for HIST1H2BN Gene

Sequence variations from dbSNP and Humsavar for HIST1H2BN Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000325118 -- 27,838,750(+) G/A coding_sequence_variant, missense_variant
rs1000705005 -- 27,837,000(+) G/T upstream_transcript_variant
rs1003496755 -- 27,837,167(+) G/T upstream_transcript_variant
rs1003529689 -- 27,837,384(+) C/G upstream_transcript_variant
rs1004472846 -- 27,837,222(+) TATGT/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H2BN Gene

Variant ID Type Subtype PubMed ID
esv3608441 CNV gain 21293372
nsv969367 CNV duplication 23825009

Variation tolerance for HIST1H2BN Gene

Residual Variation Intolerance Score: 30.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.43; 9.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIST1H2BN Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H2BN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H2BN Gene

Disorders for HIST1H2BN Gene

MalaCards: The human disease database

(1) MalaCards diseases for HIST1H2BN Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
systemic lupus erythematosus
  • sle
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HIST1H2BN

genes like me logo Genes that share disorders with HIST1H2BN: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HIST1H2BN Gene

Publications for HIST1H2BN Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 58
  2. The human histone gene cluster at the D6S105 locus. (PMID: 9439656) Albig W … Doenecke D (Human genetics 1997) 2 3 4 58
  3. Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry. (PMID: 16319397) Bonenfant D … van Oostrum J (Molecular & cellular proteomics : MCP 2006) 3 4 58
  4. Quantitative proteomic analysis of post-translational modifications of human histones. (PMID: 16627869) Beck HC … Jensen ON (Molecular & cellular proteomics : MCP 2006) 3 4 58
  5. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. (PMID: 16713563) Pavri R … Reinberg D (Cell 2006) 3 4 58

Products for HIST1H2BN Gene

Sources for HIST1H2BN Gene

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