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Aliases for HIST1H3D Gene

Aliases for HIST1H3D Gene

  • Histone Cluster 1 H3 Family Member D 2 3 5
  • H3 Histone Family, Member B 2 3
  • Histone Cluster 1, H3d 2 3
  • Histone 1, H3d 2 3
  • Histone H3/B 3 4
  • H3FB 3 4
  • Histone H3.1 3
  • Histone H3/A 4
  • Histone H3/C 4
  • Histone H3/D 4
  • Histone H3/F 4
  • Histone H3/H 4
  • Histone H3/I 4
  • Histone H3/J 4
  • Histone H3/K 4
  • Histone H3/L 4
  • H3/B 3
  • H3FA 4
  • H3FC 4
  • H3FD 4
  • H3FF 4
  • H3FH 4
  • H3FI 4
  • H3FJ 4
  • H3FK 4
  • H3FL 4

External Ids for HIST1H3D Gene

Previous HGNC Symbols for HIST1H3D Gene

  • H3FB

Previous GeneCards Identifiers for HIST1H3D Gene

  • GC06M026254
  • GC06M026306
  • GC06M026310
  • GC06M026312
  • GC06M026314
  • GC06M026197
  • GC06M026140
  • GC06M026211
  • GC06M026582

Summaries for HIST1H3D Gene

Entrez Gene Summary for HIST1H3D 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 H3 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015]

GeneCards Summary for HIST1H3D Gene

HIST1H3D (Histone Cluster 1 H3 Family Member D) is a Protein Coding gene. Diseases associated with HIST1H3D include Corneal Dystrophy, Posterior Polymorphous, 1 and Diffuse Intrinsic Pontine Glioma. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Cell Cycle, Mitotic. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and histone binding. An important paralog of this gene is HIST1H3C.

UniProtKB/Swiss-Prot for HIST1H3D 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 HIST1H3D Gene

Additional gene information for HIST1H3D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H3D Gene

Genomics for HIST1H3D Gene

GeneHancer (GH) Regulatory Elements for HIST1H3D Gene

Promoters and enhancers for HIST1H3D 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
GH06J026193 Promoter/Enhancer 1.9 Ensembl ENCODE dbSUPER 650.7 -1.5 -1499 14.6 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ENSG00000282988 HIST1H2AD HIST1H2BF HIST1H3D RPS10P1 ABT1 HMGN4 BTN2A3P BTN2A1 BTN2A2
GH06J026309 Enhancer 1.5 Ensembl ENCODE dbSUPER 10.5 -112.5 -112548 4.9 MLX YBX1 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 NFYC MEF2D GC06M026697 TRQ-TTG3-1 TRQ-TTG3-2 TRS-TGA3-1 TRX-CAT1-3 ABT1 BTN2A2 ZNF322 BTN2A3P BTN2A1
GH06J026162 Enhancer 0.6 Ensembl 11.2 +37.8 37792 0.2 BCOR ARNT MNT DPF2 FOSL1 POLR2B PRDM6 POLR2A IKZF1 ZSCAN5C HIST1H4D HIST1H1PS1 HIST1H2AD HIST1H3D HIST1H3E HIST1H2APS3 HIST1H2BF RPS10P1 HIST1H4C HIST1H4F
GH06J025339 Enhancer 0.6 ENCODE 4 +857.9 857945 3.8 ZNF362 RFX1 BATF SP1 JUND GATA3 POLR2A ZSCAN5C BCL6B CARMIL1 RPL21P68 TDP2 ENSG00000272810 HIST1H3D GC06M025334 GC06P025384 CMAHP
GH06J025247 Enhancer 0.4 ENCODE 4.1 +950.8 950830 1.4 JUND CEBPB KATNBL1P5 CARMIL1 LOC100533655 CMAHP HIST1H3D RPL21P68 LOC101928663
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HIST1H3D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HIST1H3D gene promoter:
  • Olf-1
  • GCNF-2
  • GCNF-1
  • GCNF
  • XBP-1
  • GATA-1
  • Arnt
  • AhR
  • AML1a

Genomic Locations for HIST1H3D Gene

Genomic Locations for HIST1H3D Gene
chr6:26,196,784-26,199,293
(GRCh38/hg38)
Size:
2,510 bases
Orientation:
Minus strand
chr6:26,197,012-26,199,521
(GRCh37/hg19)
Size:
2,510 bases
Orientation:
Minus strand

Genomic View for HIST1H3D Gene

Genes around HIST1H3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H3D Gene

Proteins for HIST1H3D Gene

  • Protein details for HIST1H3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P68431-H31_HUMAN
    Recommended name:
    Histone H3.1
    Protein Accession:
    P68431
    Secondary Accessions:
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081
    • A0PJT7
    • A5PLR1
    • P02295
    • P02296
    • P16106
    • Q6ISV8
    • Q6NWP8
    • Q6NWP9
    • Q6NXU4
    • Q71DJ3
    • Q93081

    Protein attributes for HIST1H3D Gene

    Size:
    136 amino acids
    Molecular mass:
    15404 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    Miscellaneous:
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).
    • This histone is only present in mammals and is enriched in acetylation of Lys-15 and dimethylation of Lys-10 (H3K9me2).

    Three dimensional structures from OCA and Proteopedia for HIST1H3D Gene

neXtProt entry for HIST1H3D Gene

Post-translational modifications for HIST1H3D Gene

  • 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). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • 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.
  • Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. 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) 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) 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.
  • Phosphorylated at Thr-4 (H3T3ph) by 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 MAP3K20 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 Thr-12 (H3T11ph) by chromatin-associated CHEK1 regulates the transcription of cell cycle regulatory genes by modulating acetylation of Lys-10 (H3K9ac). Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
  • Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins.
  • 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.
  • 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.
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Succinylation at Lys-80 (H3K79succ) by KAT2A takes place with a maximum frequency around the transcription start sites of genes (PubMed:29211711). It gives a specific tag for epigenetic transcription activation (PubMed:29211711).
  • Ubiquitination at isoforms=116
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H3D Gene

Domains & Families for HIST1H3D Gene

Gene Families for HIST1H3D Gene

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

Protein Domains for HIST1H3D Gene

Graphical View of Domain Structure for InterPro Entry

P68431

UniProtKB/Swiss-Prot:

H31_HUMAN :
  • Belongs to the histone H3 family.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with HIST1H3D: view

No data available for Suggested Antigen Peptide Sequences for HIST1H3D Gene

Function for HIST1H3D Gene

Molecular function for HIST1H3D 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 HIST1H3D Gene

Gene Ontology (GO) - Molecular Function for HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 10949293
GO:0031492 nucleosomal DNA binding IBA --
GO:0045296 cadherin binding IDA 25468996
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with HIST1H3D: view
genes like me logo Genes that share phenotypes with HIST1H3D: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HIST1H3D Gene

Localization for HIST1H3D Gene

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 HIST1H3D gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000786 nucleosome IBA,IDA 21636898
GO:0000788 nuclear nucleosome IDA 20498094
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IBA,IDA 21636898
genes like me logo Genes that share ontologies with HIST1H3D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HIST1H3D Gene

Pathways & Interactions for HIST1H3D Gene

SuperPathways for HIST1H3D Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence (REACTOME)
3 Cell Cycle, Mitotic
.60
4 Chromatin organization
5 Mitotic Prophase
genes like me logo Genes that share pathways with HIST1H3D: view

Gene Ontology (GO) - Biological Process for HIST1H3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006325 chromatin organization TAS --
GO:0006334 nucleosome assembly IMP,IBA 25615412
GO:0006335 DNA replication-dependent nucleosome assembly IDA 14718166
GO:0007596 blood coagulation TAS --
genes like me logo Genes that share ontologies with HIST1H3D: view

No data available for SIGNOR curated interactions for HIST1H3D Gene

Drugs & Compounds for HIST1H3D Gene

No Compound Related Data Available

Transcripts for HIST1H3D Gene

mRNA/cDNA for HIST1H3D Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(30) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HIST1H3D Gene

Histone cluster 1, H3d:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H3D Gene

No ASD Table

Relevant External Links for HIST1H3D Gene

GeneLoc Exon Structure for
HIST1H3D
ECgene alternative splicing isoforms for
HIST1H3D

Expression for HIST1H3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HIST1H3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HIST1H3D Gene

This gene is overexpressed in Whole Blood (x20.1).

Protein differential expression in normal tissues from HIPED for HIST1H3D Gene

This gene is overexpressed in Heart (41.5), Urine (13.4), and Cervix (9.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HIST1H3D Gene



Protein tissue co-expression partners for HIST1H3D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HIST1H3D Gene:

HIST1H3D

SOURCE GeneReport for Unigene cluster for HIST1H3D Gene:

Hs.532144

Evidence on tissue expression from TISSUES for HIST1H3D Gene

  • Nervous system(4.4)
  • Blood(4.1)
  • Spleen(4)
  • Stomach(4)
genes like me logo Genes that share expression patterns with HIST1H3D: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HIST1H3D Gene

Orthologs for HIST1H3D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HIST1H3D Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
OneToMany
LOC100684574 33
  • 88.48 (n)
cow
(Bos Taurus)
Mammalia -- 34
  • 100 (a)
ManyToMany
LOC525511 33
  • 89.46 (n)
mouse
(Mus musculus)
Mammalia Hist1h3i 34
  • 100 (a)
ManyToMany
Hist1h3a 16 33
  • 87.75 (n)
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 100 (a)
ManyToMany
LOC462506 33
  • 87.75 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia LOC691496 33
  • 83.09 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 96 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487139 33
  • 85.29 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100329422 33
  • 84.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3:CG33848 33
  • 81.37 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CSE4 36
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.10591 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 93 (a)
ManyToMany
-- 34
  • 93 (a)
ManyToMany
Cin.15445 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15445 33
Species where no ortholog for HIST1H3D 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)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HIST1H3D Gene

ENSEMBL:
Gene Tree for HIST1H3D (if available)
TreeFam:
Gene Tree for HIST1H3D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HIST1H3D: view image

Paralogs for HIST1H3D Gene

(9) SIMAP similar genes for HIST1H3D Gene using alignment to 1 proteins:

  • H31_HUMAN
genes like me logo Genes that share paralogs with HIST1H3D: view

Variants for HIST1H3D Gene

Sequence variations from dbSNP and Humsavar for HIST1H3D Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000210523 -- 26,197,464(-) C/T intron_variant
rs1000309773 -- 26,196,951(-) G/A coding_sequence_variant, synonymous_variant
rs1001285373 -- 26,200,351(-) A/C upstream_transcript_variant
rs1001612008 -- 26,200,208(-) T/A upstream_transcript_variant
rs1002049037 -- 26,197,865(-) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HIST1H3D Gene

Variant ID Type Subtype PubMed ID
dgv375n21 CNV loss 19592680
dgv5926n100 CNV gain 25217958
esv3608397 CNV loss 21293372
esv3608398 CNV loss 21293372
esv3608399 CNV gain 21293372
nsv1021294 CNV loss 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for HIST1H3D Gene

Residual Variation Intolerance Score: 27.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.20; 4.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HIST1H3D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H3D Gene

Disorders for HIST1H3D Gene

MalaCards: The human disease database

(3) MalaCards diseases for HIST1H3D Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
corneal dystrophy, posterior polymorphous, 1
  • ppcd1
diffuse intrinsic pontine glioma
  • dipg
brain stem glioma
  • brainstem neuroglial tumor
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

H31_HUMAN
  • Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269 PubMed:22286216}. Note=The gene represented in this entry is involved in disease pathogenesis. HIST1H3B mutations affecting residue Lys-28 involved in post-translational modifications of histone H3.1 are recurrent in malignant, aggressive gliomas including pediatric non-brain stem glioblastoma and diffuse intrinsic pontine glioma (DIPG) (PubMed:22286216). The mechanism through which mutations lead to tumorigenesis involves altered histone methylation, impaired regulation of Polycomb repressive complex 2 (PRC2) activity, and aberrant epigenetic regulation of gene expression (PubMed:23603901). {ECO:0000269 PubMed:22286216, ECO:0000269 PubMed:23603901}.
  • Note=HIST1H3B or HIST1H3C mutations affecting residue Lys-37 of histone H3.1 are involved in the pathogenesis of pediatric undifferentiated soft tissue sarcomas. The mechanism through which mutations lead to tumorigenesis involves altered histones methylation with gain of global H3K27 methylation, altered Polycomb repressive complex 1 (PRC1) activity, aberrant epigenetic regulation of gene expression and impaired differentiation of mesenchimal progenitor cells. {ECO:0000269 PubMed:27174990}.

Additional Disease Information for HIST1H3D

genes like me logo Genes that share disorders with HIST1H3D: view

No data available for Genatlas for HIST1H3D Gene

Publications for HIST1H3D Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4 58
  2. Human histone gene organization: nonregular arrangement within a large cluster. (PMID: 9119399) Albig W … Doenecke D (Genomics 1997) 2 3 4 58
  3. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. (PMID: 16267050) Hake SB … Hunt DF (The Journal of biological chemistry 2006) 3 4 58
  4. Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. (PMID: 16246723) Macdonald N … Mahadevan LC (Molecular cell 2005) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for HIST1H3D Gene

Sources for HIST1H3D Gene

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