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Aliases for HIST1H1D Gene

Aliases for HIST1H1D Gene

  • Histone Cluster 1 H1 Family Member D 2 3 5
  • H1 Histone Family, Member 3 2 3
  • Histone Cluster 1, H1d 2 3
  • Histone 1, H1d 2 3
  • Histone H1s-2 3 4
  • Histone H1c 3 4
  • H1F3 3 4
  • Histone H1.3 3
  • H1s-2 3
  • H1.3 3
  • H1D 3

External Ids for HIST1H1D Gene

Previous HGNC Symbols for HIST1H1D Gene

  • H1F3

Previous GeneCards Identifiers for HIST1H1D Gene

  • GC06M026291
  • GC06M026118
  • GC06M026342
  • GC06M026177

Summaries for HIST1H1D Gene

Entrez Gene Summary for HIST1H1D Gene

  • Histones are basic nuclear proteins responsible for 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 H1 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 HIST1H1D Gene

HIST1H1D (Histone Cluster 1 H1 Family Member D) is a Protein Coding gene. Among its related pathways are Apoptosis induced DNA fragmentation and Regulation of activated PAK-2p34 by proteasome mediated degradation. GO annotations related to this gene include poly(A) RNA binding and chromatin DNA binding. An important paralog of this gene is HIST1H1E.

UniProtKB/Swiss-Prot for HIST1H1D Gene

  • Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).

Gene Wiki entry for HIST1H1D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HIST1H1D Gene

Genomics for HIST1H1D Gene

Regulatory Elements for HIST1H1D Gene

Enhancers for HIST1H1D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F026567 1.5 Ensembl ENCODE 10.9 -335.5 -335514 5.4 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 ABT1 HMGN4 BTN3A2 GUSBP2 LOC102724851 BTN2A1 ZNF391 HCG11 RNU6-502P HIST1H1D
GH06F026575 1.4 Ensembl ENCODE 10.9 -341.8 -341783 2.9 HDGF PKNOX1 CREB3L1 ARNT MLX ARID4B SIN3A FEZF1 ZNF2 SLC30A9 ABT1 HMGN4 BTN3A2 BTN2A1 HIST1H1D GUSBP2 BTN3A1 PIR37715 TRY-GTA3-1
GH06F026363 1.1 ENCODE 11 -130.7 -130685 3.9 PKNOX1 CREB3L1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF766 BTN3A2 HMGN4 ABT1 HIST1H2APS4 ENSG00000271071 HIST1H2APS5 VN1R11P HIST1H2BPS1 HIST1H2BA LOC442172
GH06F026341 1.4 Ensembl ENCODE 5.9 -107.2 -107213 1.6 HDGF PKNOX1 ARNT MLX ARID4B SIN3A YBX1 ZNF2 ZNF766 CBX5 ZNF322 HMGN4 ABT1 BTN3A2 HIST1H2APS4 HIST1H2APS5 ENSG00000271071 HIST1H2BPS1 HIST1H2BA VN1R13P
GH06F026303 1.4 Ensembl ENCODE 4.9 -69.9 -69882 3.1 HDGF PKNOX1 ARNT MLX CREB3L1 ARID4B SIN3A ZNF766 ZNF143 FOS ABT1 ZNF322 HIST1H3E HMGN4 HIST1H3G HIST1H2APS4 TRIM38 HIST1H2APS3 HIST1H4G HIST1H2BE
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HIST1H1D on UCSC Golden Path with GeneCards custom track

Promoters for HIST1H1D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001214027 888 3001 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 SIN3A ZNF2 YY1 ZNF766 ZNF143

Genomic Location for HIST1H1D Gene

Chromosome:
6
Start:
26,234,212 bp from pter
End:
26,234,988 bp from pter
Size:
777 bases
Orientation:
Minus strand

Genomic View for HIST1H1D Gene

Genes around HIST1H1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HIST1H1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HIST1H1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HIST1H1D Gene

Proteins for HIST1H1D Gene

  • Protein details for HIST1H1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P16402-H13_HUMAN
    Recommended name:
    Histone H1.3
    Protein Accession:
    P16402
    Secondary Accessions:
    • B2R751
    • Q2M2I2

    Protein attributes for HIST1H1D Gene

    Size:
    221 amino acids
    Molecular mass:
    22350 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HIST1H1D Gene

Post-translational modifications for HIST1H1D Gene

  • Citrullination at Arg-55 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance.
  • H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HIST1H1D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H1D Gene

Domains & Families for HIST1H1D Gene

Gene Families for HIST1H1D Gene

Protein Domains for HIST1H1D Gene

Suggested Antigen Peptide Sequences for HIST1H1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P16402

UniProtKB/Swiss-Prot:

H13_HUMAN :
  • The C-terminal domain is required for high-affinity binding to chromatin.
  • Belongs to the histone H1/H5 family.
Domain:
  • The C-terminal domain is required for high-affinity binding to chromatin.
  • Contains 1 H15 (linker histone H1/H5 globular) domain.
Family:
  • Belongs to the histone H1/H5 family.
genes like me logo Genes that share domains with HIST1H1D: view

Function for HIST1H1D Gene

Molecular function for HIST1H1D Gene

UniProtKB/Swiss-Prot Function:
Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity).

Gene Ontology (GO) - Molecular Function for HIST1H1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0031490 chromatin DNA binding IDA 15911621
GO:0044822 poly(A) RNA binding IDA 22681889
genes like me logo Genes that share ontologies with HIST1H1D: view
genes like me logo Genes that share phenotypes with HIST1H1D: view

Animal Models for HIST1H1D Gene

MGI Knock Outs for HIST1H1D:

Animal Model Products

miRNA for HIST1H1D Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HIST1H1D Gene

Localization for HIST1H1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for HIST1H1D Gene

Nucleus. Chromosome. Note=According to PubMed:15911621 more commonly found in euchromatin. According to PubMed:10997781 is associated with inactive chromatin.

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 HIST1H1D gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for HIST1H1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0000790 nuclear chromatin IDA 19882353
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005719 nuclear euchromatin IDA 15911621
genes like me logo Genes that share ontologies with HIST1H1D: view

Pathways & Interactions for HIST1H1D Gene

genes like me logo Genes that share pathways with HIST1H1D: view

Gene Ontology (GO) - Biological Process for HIST1H1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0006334 nucleosome assembly IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0016584 nucleosome positioning IEA --
GO:0080182 histone H3-K4 trimethylation IEA --
genes like me logo Genes that share ontologies with HIST1H1D: view

No data available for SIGNOR curated interactions for HIST1H1D Gene

Transcripts for HIST1H1D Gene

mRNA/cDNA for HIST1H1D Gene

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

Unigene Clusters for HIST1H1D Gene

Histone cluster 1, H1d:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HIST1H1D Gene

No ASD Table

Relevant External Links for HIST1H1D Gene

GeneLoc Exon Structure for
HIST1H1D
ECgene alternative splicing isoforms for
HIST1H1D

Expression for HIST1H1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HIST1H1D Gene

mRNA differential expression in normal tissues according to GTEx for HIST1H1D Gene

This gene is overexpressed in Whole Blood (x12.2) and Vagina (x4.2).

Protein differential expression in normal tissues from HIPED for HIST1H1D Gene

This gene is overexpressed in Tlymphocyte (34.1) and Cervix (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HIST1H1D Gene



Protein tissue co-expression partners for HIST1H1D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HIST1H1D Gene:

HIST1H1D

SOURCE GeneReport for Unigene cluster for HIST1H1D Gene:

Hs.136857
genes like me logo Genes that share expression patterns with HIST1H1D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for HIST1H1D Gene

Orthologs for HIST1H1D Gene

This gene was present in the common ancestor of chordates.

Orthologs for HIST1H1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HIST1H1D 35
  • 99 (a)
OneToOne
LOC472227 34
  • 98.49 (n)
cow
(Bos Taurus)
Mammalia HIST1H1E 35
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LOC611113 34
  • 81.86 (n)
-- 35
  • 73 (a)
OneToMany
-- 35
  • 67 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Hist1h1d 34 16 35
  • 80.84 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 80 (a)
ManyToMany
-- 35
  • 73 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 33 (a)
OneToMany
chicken
(Gallus gallus)
Aves HIST1H111L 35
  • 71 (a)
ManyToMany
HIST1H111R 35
  • 70 (a)
ManyToMany
-- 35
  • 64 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii CABZ01086354.1 35
  • 67 (a)
ManyToMany
CU457819.3 35
  • 67 (a)
ManyToMany
FP325123.1 35
  • 66 (a)
ManyToMany
si:ch211-113a14.12 35
  • 66 (a)
ManyToMany
zgc:110425 35
  • 66 (a)
ManyToMany
zgc:153405 35
  • 66 (a)
ManyToMany
histh1l 35
  • 65 (a)
ManyToMany
si:ch211-113a14.18 35
  • 65 (a)
ManyToMany
si:ch211-113a14.24 35
  • 65 (a)
ManyToMany
si:dkey-261m9.12 35
  • 65 (a)
ManyToMany
zgc:163061 35 35
  • 65 (a)
ManyToMany
si:dkey-108k21.10 35
  • 64 (a)
ManyToMany
si:dkey-108k21.14 35
  • 63 (a)
ManyToMany
si:dkey-108k21.21 35
  • 59 (a)
ManyToMany
Species where no ortholog for HIST1H1D 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)

Evolution for HIST1H1D Gene

ENSEMBL:
Gene Tree for HIST1H1D (if available)
TreeFam:
Gene Tree for HIST1H1D (if available)

Paralogs for HIST1H1D Gene

Paralogs for HIST1H1D Gene

(7) SIMAP similar genes for HIST1H1D Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HIST1H1D: view

Variants for HIST1H1D Gene

Sequence variations from dbSNP and Humsavar for HIST1H1D Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs10484436 -- 26,236,927(+) TTATA(C/T)ACCAC upstream-variant-2KB
rs111312434 -- 26,234,945(+) GTCTT(A/C/G/T)CCAGA utr-variant-5-prime
rs111884694 -- 26,236,692(+) TAGGC(A/G)GGCAT upstream-variant-2KB
rs112515836 -- 26,234,545(+) CTTCC(-/TAG)TAGGC cds-indel
rs113563075 -- 26,236,835(+) AAAAA(-/AA)TTACT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HIST1H1D Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
nsv1021294 CNV loss 25217958
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for HIST1H1D Gene

Residual Variation Intolerance Score: 51.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.50; 71.80% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HIST1H1D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HIST1H1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HIST1H1D Gene

Disorders for HIST1H1D Gene

Relevant External Links for HIST1H1D

Genetic Association Database (GAD)
HIST1H1D
Human Genome Epidemiology (HuGE) Navigator
HIST1H1D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HIST1H1D

No disorders were found for HIST1H1D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HIST1H1D Gene

Publications for HIST1H1D Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4 64
  2. Isolation and characterization of two human H1 histone genes within clusters of core histone genes. (PMID: 1916825) Albig W. … Doenecke D. (Genomics 1991) 2 3 4 64
  3. Identification of 15 loci influencing height in a Korean population. (PMID: 19893584) Kim J.J. … Lee J.K. (J. Hum. Genet. 2010) 3 46 64
  4. Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study. (PMID: 20846217) Lee J.J. … Hirschhorn J. (Ann. Hum. Genet. 2010) 3 46 64
  5. Genetic determinants of height growth assessed longitudinally from infancy to adulthood in the northern Finland birth cohort 1966. (PMID: 19266077) Sovio U. … Jarvelin M.R. (PLoS Genet. 2009) 3 46 64

Products for HIST1H1D Gene

Sources for HIST1H1D Gene

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