Human Gene H3-5 (ENST00000340398.5_6) from GENCODE V47lift37
  Description: H3.5 histone (from RefSeq NM_001013699.3)
Gencode Transcript: ENST00000340398.5_6
Gencode Gene: ENSG00000188375.5_10
Transcript (Including UTRs)
   Position: hg19 chr12:31,944,119-31,945,232 Size: 1,114 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr12:31,944,693-31,945,100 Size: 408 Coding Exon Count: 1 

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RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:31,944,119-31,945,232)mRNA (may differ from genome)Protein (135 aa)
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-  Comments and Description Text from UniProtKB
  ID: H3C_HUMAN
DESCRIPTION: RecName: Full=Histone H3.3C; AltName: Full=Histone H3.5;
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. Hominid-specific H3.5/H3F3C preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes.
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.
TISSUE SPECIFICITY: Specifically expressed in the seminiferous tubules of testis.
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) (By similarity).
PTM: Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription (By similarity).
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 (By similarity).
PTM: Methylation at Lys-5 (H3K4me) is linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. 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) requires 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-56 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication (By similarity).
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-41 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin (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 (By similarity).
SIMILARITY: Belongs to the histone H3 family.

-  Primer design for this transcript
 

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+  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: 25.56 RPKM in Testis
Total median expression: 125.60 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 -47.90132-0.363 Picture PostScript Text
3' UTR -138.90574-0.242 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
IPR000164 - Histone_H3

Pfam Domains:
PF00125 - Core histone H2A/H2B/H3/H4

SCOP Domains:
47113 - Histone-fold

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3KV4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q6NXT2
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-  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
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0031492 nucleosomal DNA binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006334 nucleosome assembly
GO:0030307 positive regulation of cell growth

Cellular Component:
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005719 nuclear euchromatin


-  Descriptions from all associated GenBank mRNAs
  KJ900765 - Synthetic construct Homo sapiens clone ccsbBroadEn_10159 H3F3C gene, encodes complete protein.
BC066906 - Homo sapiens histone H3-like, mRNA (cDNA clone MGC:87082 IMAGE:5267388), complete cds.
HQ873957 - Homo sapiens histone variant H3.5 (H3F3C) mRNA, complete cds.
JD096586 - Sequence 77610 from Patent EP1572962.
JD063466 - Sequence 44490 from Patent EP1572962.
JD510993 - Sequence 492017 from Patent EP1572962.
JD147865 - Sequence 128889 from Patent EP1572962.
JD316781 - Sequence 297805 from Patent EP1572962.
JD235244 - Sequence 216268 from Patent EP1572962.
JD079296 - Sequence 60320 from Patent EP1572962.
JD181990 - Sequence 163014 from Patent EP1572962.
JF432417 - Synthetic construct Homo sapiens clone IMAGE:100073623 histone H3-like (LOC440093) gene, encodes complete protein.
JD326649 - Sequence 307673 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: E9P281, ENST00000340398.1, ENST00000340398.2, ENST00000340398.3, ENST00000340398.4, H3-5 , H3C_HUMAN, H3F3C , NM_001013699, Q6NXT2, uc317vqx.1, uc317vqx.2
UCSC ID: ENST00000340398.5_6
RefSeq Accession: NM_001013699.3
Protein: Q6NXT2 (aka H3C_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.