Human Gene HIST1H2BD (uc003ngr.3) Description and Page Index
  Description: Homo sapiens histone cluster 1, H2bd (HIST1H2BD), transcript variant 1, mRNA.
RefSeq Summary (NM_021063): Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Two transcripts that encode the same protein have been identified for this gene, which is found in the large histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015].
Transcript (Including UTRs)
   Position: hg19 chr6:26,158,349-26,158,835 Size: 487 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr6:26,158,398-26,158,778 Size: 381 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:26,158,349-26,158,835)mRNA (may differ from genome)Protein (126 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Histone H2B type 1-D; AltName: Full=HIRA-interacting protein 2; AltName: Full=Histone H2B.1 B; AltName: Full=Histone H2B.b; Short=H2B/b;
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.
MISCELLANEOUS: The mouse orthologous protein seems not to exist.
SIMILARITY: Belongs to the histone H2B family.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 55.54 RPKM in Prostate
Total median expression: 400.23 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.3049-0.108 Picture PostScript Text
3' UTR -13.1057-0.230 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 P58876
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
GO:0016567 protein ubiquitination

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
  AK292712 - Homo sapiens cDNA FLJ78520 complete cds, highly similar to Homo sapiens histone 1, H2bn (HIST1H2BN), mRNA.
BC002842 - Homo sapiens histone cluster 1, H2bd, mRNA (cDNA clone MGC:3802 IMAGE:3659807), complete cds.
AJ223353 - Homo sapiens mRNA for histone H2B, clone pJG4-5-15.
AB463734 - Synthetic construct DNA, clone: pF1KB7083, Homo sapiens HIST1H2BD gene for histone cluster 1, H2bd, without stop codon, in Flexi system.
KJ896954 - Synthetic construct Homo sapiens clone ccsbBroadEn_06348 HIST1H2BD gene, encodes complete protein.
BC096122 - Homo sapiens histone cluster 1, H2bd, mRNA (cDNA clone MGC:116768 IMAGE:40002354), complete cds.
MF125239 - Homo sapiens bio-material MLL_11932 case HIST1H2BD/PVT1 fusion mRNA, partial sequence.
JD224836 - Sequence 205860 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05322 - Systemic lupus erythematosus

Reactome (by CSHL, EBI, and GO)

Protein P58876 (Reactome details) participates in the following event(s):

R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B
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-5683930 WICH phosphorylates H2AFX on Y142
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-5684071 RNF4 ubiquitinates MDC1
R-HSA-5693599 Association of Ku heterodimer with ends of DNA double-strand break
R-HSA-5693602 ATM recognizes H2AFX-Nucleosomes
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-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-9011983 Overexpressed HIST1H2AC and ESR1:ESTG bind MYC and BCL2 genes
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-912467 BRCA1 is recruited to unsynapsed regions
R-HSA-912470 ATR phosphorylates Histone H2A.X at unsynapsed regions
R-HSA-5693583 MDC1 associates with gamma-H2AFX at nuclear foci
R-HSA-5683967 EYA1-4 dephosphorylates tyrosine Y142 of H2AFX
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-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-5693549 ATM phosphorylates histone H2AFX on S139 at DNA DSBs
R-HSA-5683986 APBB1 and MAPK8 bind diphosphorylated H2AFX
R-HSA-9011984 KDM1A is recruited to MYC and BCL2 genes
R-HSA-9011981 EP300 is recruited to MYC and BCL2 genes
R-HSA-9011985 KDM1A demethylates H3 on MYC and BCL genes in response to estrogen
R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene
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-912450 ATR Kinase is recruited to unsynapsed regions
R-HSA-5682967 WHSC1 binds DNA DSBs
R-HSA-5693536 ATM phosphorylates MDC1
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-5683964 ATM phosphorylates EYA1-4
R-HSA-977224 Serum amyloid P binds DNA and chromatin
R-HSA-5682983 ATM phosphorylates WHSC1
R-HSA-5682965 WHSC1 dimethylates histone H4 on lysine K21 at DSBs
R-HSA-5682992 KDM4A,B bind H4K20Me2
R-HSA-5682588 RNF8 binds phosphorylated MDC1 at DNA DSBs
R-HSA-5693566 TP53BP1 associates with H4K20Me2 at DNA DSBs
R-HSA-5683077 RNF8 and RNF168 ubiquitinate KDM4A,B
R-HSA-5682586 HERC2 and PIAS4 are recruited to DNA DSBs
R-HSA-5682629 HERC2 facilitates UBE2N:UBE2V2 binding to RNF8
R-HSA-5682607 PIAS4 SUMOylates HERC2 with SUMO1 at DNA DSBs
R-HSA-5682863 RNF168 binds DNA DSBs
R-HSA-5682858 RNF8 and RNF168 ubiquitinate H2AFX
R-HSA-5683384 UIMC1 and FAM175A bind DNA DSBs
R-HSA-5683405 PPP5C dephosphorylates TP53BP1
R-HSA-5683425 ATM phosphorylates TP53BP1 at DNA DSBs
R-HSA-5682598 ATM phosphorylates HERC2
R-HSA-5693551 Phosphorylation of BRCA1-A complex at multiple sites by ATM
R-HSA-5683385 Formation of BRCA1-A complex at DNA DSBs
R-HSA-5683735 CHEK2 is recruited to DNA DSBs
R-HSA-5683801 CHEK2 phosphorylates BRCA1
R-HSA-69891 Phosphorylation and activation of CHEK2 by ATM
R-HSA-5684052 PIAS4 SUMOylates MDC1
R-HSA-5686685 RIF1 and PAX1IP bind TP53BP1 at DNA DSBs
R-HSA-5686900 TP53BP1 recruits DCLRE1C to ATM
R-HSA-5686704 Activated ATM phosphorylates DCLRE1C
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-8852135 Protein ubiquitination
R-HSA-171306 Packaging Of Telomere Ends
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-912446 Meiotic recombination
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-5693571 Nonhomologous End-Joining (NHEJ)
R-HSA-774815 Nucleosome assembly
R-HSA-3214847 HATs acetylate histones
R-HSA-5689880 Ub-specific processing proteases
R-HSA-597592 Post-translational protein modification
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-9018519 Estrogen-dependent gene expression
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-1500620 Meiosis
R-HSA-5693606 DNA Double Strand Break Response
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
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-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-73886 Chromosome Maintenance
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-3214815 HDACs deacetylate histones
R-HSA-5688426 Deubiquitination
R-HSA-392499 Metabolism of proteins
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-8939211 ESR-mediated signaling
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-211000 Gene Silencing by RNA
R-HSA-1474165 Reproduction
R-HSA-1640170 Cell Cycle
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-212436 Generic Transcription Pathway
R-HSA-68886 M Phase
R-HSA-5625740 RHO GTPases activate PKNs
R-HSA-5693538 Homology Directed Repair
R-HSA-73894 DNA Repair
R-HSA-977225 Amyloid fiber formation
R-HSA-4839726 Chromatin organization
R-HSA-2262752 Cellular responses to stress
R-HSA-195721 Signaling by WNT
R-HSA-9006931 Signaling by Nuclear Receptors
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-162582 Signal Transduction
R-HSA-194315 Signaling by Rho GTPases
R-HSA-69473 G2/M DNA damage checkpoint
R-HSA-69481 G2/M Checkpoints
R-HSA-69620 Cell Cycle Checkpoints

-  Other Names for This Gene
  Alternate Gene Symbols: H2B1D_HUMAN, H2BFB, HIRIP2, NM_021063, NP_619790, P58876
UCSC ID: uc003ngr.3
RefSeq Accession: NM_021063
Protein: P58876 (aka H2B1D_HUMAN)
CCDS: CCDS4587.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_021063.3
exon count: 1CDS single in 3' UTR: no RNA size: 487
ORF size: 381CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 962.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.