Human Gene H3-3B (ENST00000254810.8_8) from GENCODE V47lift37
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Sequence and Links to Tools and Databases
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Comments and Description Text from UniProtKB
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ID: H33_HUMAN
DESCRIPTION: RecName: Full=Histone H3.3;
FUNCTION: Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. 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. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes. SUBCELLULAR LOCATION: Nucleus. Chromosome. DEVELOPMENTAL STAGE: Expressed throughout the cell cycle independently of DNA synthesis. PTM: Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). PTM: Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription. PTM: Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters. PTM: Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me), Lys-37 and Lys- 80. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me), which are linked to gene repression, are underrepresented. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication. PTM: Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes. PTM: Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). PTM: Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression (PubMed:22483618). 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 H3 family. SEQUENCE CAUTION: Sequence=CAH73371.1; Type=Erroneous gene model prediction; WEB RESOURCE: Name=Wikipedia; Note=Histone H3 entry; URL="http://en.wikipedia.org/wiki/Histone_H3";
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Primer design for this transcript
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Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
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Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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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.
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Protein Domain and Structure Information
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InterPro Domains: Graphical view of domain structure IPR009072 - Histone-fold
IPR007125 - Histone_core_D
IPR000164 - Histone_H3
Pfam Domains: PF00125 - Core histone H2A/H2B/H3/H4
SCOP Domains: 47113 - Histone-fold
Protein Data Bank (PDB) 3-D Structure
ModBase Predicted Comparative 3D Structure on P84243
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.
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Orthologous Genes in Other Species
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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.
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Gene Ontology (GO) Annotations with Structured Vocabulary
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Descriptions from all associated GenBank mRNAs
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AK054591 - Homo sapiens cDNA FLJ30029 fis, clone 3NB692001334. BX537379 - Homo sapiens mRNA; cDNA DKFZp686C2282 (from clone DKFZp686C2282); complete cds. AF218029 - Homo sapiens clone PP781 unknown mRNA. AK130772 - Homo sapiens cDNA FLJ27262 fis, clone TMS00164, highly similar to Histone H3.3. BX647280 - Homo sapiens mRNA; cDNA DKFZp686O0399 (from clone DKFZp686O0399). AK304607 - Homo sapiens cDNA FLJ52843 complete cds, highly similar to Histone H3.3. JD498771 - Sequence 479795 from Patent EP1572962. JD327318 - Sequence 308342 from Patent EP1572962. JD082119 - Sequence 63143 from Patent EP1572962. JD082611 - Sequence 63635 from Patent EP1572962. JD109997 - Sequence 91021 from Patent EP1572962. JD081172 - Sequence 62196 from Patent EP1572962. JD508830 - Sequence 489854 from Patent EP1572962. JD435254 - Sequence 416278 from Patent EP1572962. JD364767 - Sequence 345791 from Patent EP1572962. BC006497 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone MGC:2160 IMAGE:2959756), complete cds. BC012813 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone MGC:4123 IMAGE:2959756), complete cds. BC108701 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone MGC:131844 IMAGE:6144255), complete cds. BC017558 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone MGC:9614 IMAGE:3910031), complete cds. L05088 - Homo sapiens histone H3.3 mRNA, 3' untranslated region. JD322805 - Sequence 303829 from Patent EP1572962. JD096586 - Sequence 77610 from Patent EP1572962. BC020466 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone IMAGE:3870030). BC001124 - Homo sapiens H3 histone, family 3B (H3.3B), mRNA (cDNA clone MGC:2161 IMAGE:2988279), complete cds. JD079296 - Sequence 60320 from Patent EP1572962. JD181990 - Sequence 163014 from Patent EP1572962. AK312762 - Homo sapiens cDNA, FLJ93172, highly similar to Homo sapiens H3 histone, family 3B (H3.3B) (H3F3B), mRNA. KJ891325 - Synthetic construct Homo sapiens clone ccsbBroadEn_00719 H3F3B gene, encodes complete protein. EU446957 - Synthetic construct Homo sapiens clone IMAGE:100069932; IMAGE:100012166; FLH257123.01L H3 histone, family 3B (H3.3B) (H3F3B) gene, encodes complete protein. AB463740 - Synthetic construct DNA, clone: pF1KB8141, Homo sapiens H33 gene for Histone H3.3, without stop codon, in Flexi system. AM393192 - Synthetic construct Homo sapiens clone IMAGE:100002304 for hypothetical protein (H3F3B gene).
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Biochemical and Signaling Pathways
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Reactome (by CSHL, EBI, and GO)
Protein P84243 (Reactome details) participates in the following event(s):
R-HSA-994106 HP1 alpha binds Histone H3K9(me)3
R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9
R-HSA-997263 JMJD1C demethylates H3K9 mono- and di-methylation
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-3222593 KDM6B demethylates H3K27me3 on p16-INK4A promoter
R-HSA-3229089 PRC1.4 complex binds H3K27Me3 nucleosomes on CDKN2A promoter
R-HSA-3229102 p-MAPKAPK3 phosphorylates BMI1
R-HSA-3240295 PRC2-EZH2 trimethylates nucleosomes associated with CDKN2A promoter
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-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-3788748 EHMT1:EHMT2 methylates IL6 promoter
R-HSA-3788745 EHMT1:EHMT2 methylates IL8 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-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-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-427337 MBD2 binds methylcytosine in chromatin
R-HSA-9011983 Overexpressed HIST1H2AC and ESR1:ESTG bind MYC and BCL2 genes
R-HSA-9011984 KDM1A is recruited to MYC and BCL2 genes
R-HSA-8936584 PRMT6 arginine methylates H3K4me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936481 Core MLL complex methylates H3K4Me2-Nucleosome at the ITGA2B gene promoter
R-HSA-8936608 PRMT6 arginine methylates H3K4me2-Nucleosome at the GP1BA 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-8937022 PRMT6 arginine methylates H3K4me2-Nucleosome at the THBS1 gene promoter
R-HSA-8937050 Core MLL complex methylates H3K4Me2-Nucleosome at the MIR27A 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-2288097 Condensin II complex binds H4K20me1-containing nucleosomes
R-HSA-2245218 CDK1 phosphorylates PHF8
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-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-977224 Serum amyloid P binds DNA and chromatin
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-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-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-109582 Hemostasis
R-HSA-912446 Meiotic recombination
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-5334118 DNA methylation
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-1500620 Meiosis
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-2299718 Condensation of Prophase Chromosomes
R-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-2559583 Cellular Senescence
R-HSA-5619507 Activation of HOX genes during differentiation
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-211000 Gene Silencing by RNA
R-HSA-8939211 ESR-mediated signaling
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-977225 Amyloid fiber formation
R-HSA-1474165 Reproduction
R-HSA-1640170 Cell Cycle
R-HSA-212436 Generic Transcription Pathway
R-HSA-68875 Mitotic Prophase
R-HSA-5625740 RHO GTPases activate PKNs
R-HSA-2262752 Cellular responses to stress
R-HSA-1266738 Developmental Biology
R-HSA-74160 Gene expression (Transcription)
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-195721 Signaling by WNT
R-HSA-392499 Metabolism of proteins
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-68886 M Phase
R-HSA-195258 RHO GTPase Effectors
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-162582 Signal Transduction
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-194315 Signaling by Rho GTPases
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Other Names for This Gene
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Alternate Gene Symbols: ENST00000254810.1, ENST00000254810.2, ENST00000254810.3, ENST00000254810.4, ENST00000254810.5, ENST00000254810.6, ENST00000254810.7, H3-3A , H3-3B , H3.3A, H3.3B, H33_HUMAN, H3F3, H3F3A, H3F3B, NM_005324, P06351, P33155, P84243, PP781, Q5VV55, Q5VV56, Q66I33, Q9V3W4, uc317fpr.1, uc317fpr.2 UCSC ID: ENST00000254810.8_8 RefSeq Accession: NM_005324.5
Protein: P84243
(aka H33_HUMAN)
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GeneReviews for This Gene
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GeneReviews article(s) related to gene H3-3B: brylib (Bryant-Li-Bhoj Neurodevelopmental Syndrome)
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Gene Model Information
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Click here
for a detailed description of the fields of the table above.
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Methods, Credits, and Use Restrictions
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Click here
for details on how this gene model was made and data restrictions if any.
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