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Aliases for HIST1H1D Gene

Aliases for HIST1H1D Gene

  • Histone Cluster 1, H1d 2 3
  • H1F3 3 4 6
  • H1 Histone Family, Member 3 2 3
  • Histone 1, H1d 2 3
  • Histone H1s-2 3 4
  • Histone H1c 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 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, Jul 2008]

GeneCards Summary for HIST1H1D Gene

HIST1H1D (Histone Cluster 1, H1d) is a Protein Coding gene. Diseases associated with HIST1H1D include paratyphoid fever. Among its related pathways are Cellular Senescence and Cellular Senescence. An important paralog of this gene is HIST1H1A.

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

Genomic Location for HIST1H1D Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for HIST1H1D Gene at MOPED

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.
  • Ubiquitination at Lys35, Lys47, Lys64, Lys65, Lys76, Lys86, Lys91, Lys98, and Lys107
  • Modification sites at PhosphoSitePlus

Other Protein References for HIST1H1D Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for HIST1H1D Gene

Domains for HIST1H1D Gene

Gene Families for HIST1H1D Gene

HGNC:
  • HIST :Histones / Replication-dependent

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 :
  • P16402
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 --
GO:0005515 protein binding --
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:

miRNA for HIST1H1D Gene

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H1D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting 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
Jensen Localization Image for HIST1H1D Gene COMPARTMENTS Subcellular localization image for HIST1H1D gene
Compartment Confidence
nucleus 5
cytosol 2

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 --
GO:0005719 nuclear euchromatin IDA 15911621
genes like me logo Genes that share ontologies with HIST1H1D: view

Pathways for HIST1H1D Gene

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

Pathways by source for HIST1H1D Gene

Gene Ontology (GO) - Biological Process for HIST1H1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IEA --
GO:0016584 nucleosome positioning IEA --
genes like me logo Genes that share ontologies with HIST1H1D: view

Transcripts for HIST1H1D Gene

mRNA/cDNA for HIST1H1D Gene

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

Unigene Clusters for HIST1H1D Gene

Histone cluster 1, H1d:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HIST1H1D

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for HIST1H1D
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

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 for HIST1H1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (12.2) and Vagina (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HIST1H1D Gene

SOURCE GeneReport for Unigene cluster for HIST1H1D Gene Hs.136857

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

In Situ Assay Products

No data available for 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 36
  • 99 (a)
OneToOne
LOC472227 35
  • 98.49 (n)
  • 98.64 (a)
cow
(Bos Taurus)
Mammalia HIST1H1E 36
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 67 (a)
OneToMany
-- 36
  • 73 (a)
OneToMany
LOC611113 35
  • 81.86 (n)
  • 89.12 (a)
mouse
(Mus musculus)
Mammalia Hist1h1d 35
  • 80.84 (n)
  • 91.02 (a)
Hist1h1d 16
Hist1h1d 36
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 80 (a)
ManyToMany
-- 36
  • 73 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 33 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 36
  • 64 (a)
ManyToMany
HIST1H111L 36
  • 71 (a)
ManyToMany
HIST1H111R 36
  • 70 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii CABZ01086354.1 36
  • 67 (a)
ManyToMany
CU457819.3 36
  • 67 (a)
ManyToMany
FP325123.1 36
  • 66 (a)
ManyToMany
histh1l 36
  • 65 (a)
ManyToMany
si:ch211-113a14.12 36
  • 66 (a)
ManyToMany
si:ch211-113a14.18 36
  • 65 (a)
ManyToMany
si:ch211-113a14.24 36
  • 65 (a)
ManyToMany
si:dkey-108k21.10 36
  • 64 (a)
ManyToMany
si:dkey-108k21.14 36
  • 63 (a)
ManyToMany
si:dkey-108k21.21 36
  • 59 (a)
ManyToMany
si:dkey-261m9.12 36
  • 65 (a)
ManyToMany
zgc:110425 36
  • 66 (a)
ManyToMany
zgc:153405 36
  • 66 (a)
ManyToMany
zgc:163061 36
  • 65 (a)
ManyToMany
zgc:163061 36
  • 66 (a)
ManyToMany
Species with no ortholog for HIST1H1D:
  • 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

Selected 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 MAF
rs2050948 -- 26,234,724(-) GCTGC(C/T)GGCTA synonymous-codon, reference
rs2050949 - 26,234,711(-) ATGTA(A/G)AAAAA missense, reference
rs2050950 -- 26,234,655(-) GGTAC(C/T)CTGGT synonymous-codon, reference
rs10484436 -- 26,236,927(+) TTATA(C/T)ACCAC upstream-variant-2KB
rs16891456 -- 26,233,899(+) CTGTG(C/T)CAGAA downstream-variant-500B

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

Variant ID Type Subtype PubMed ID
nsv428137 CNV Loss 18775914

Relevant External Links for HIST1H1D Gene

HapMap Linkage Disequilibrium report
HIST1H1D

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

Disorders for HIST1H1D Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for HIST1H1D Gene including...

Search for HIST1H1D Gene in MalaCards »

(2) University of Copenhagen DISEASES for HIST1H1D Gene

Relevant External Links for HIST1H1D

Genetic Association Database (GAD)
HIST1H1D
Human Genome Epidemiology (HuGE) Navigator
HIST1H1D
genes like me logo Genes that share disorders with HIST1H1D: view

No data available for UniProtKB/Swiss-Prot for HIST1H1D Gene

Publications for HIST1H1D Gene

  1. 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
  2. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff W.F. … Maltais L.J. (Genomics 2002) 2 3 4
  3. The distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin: distribution in human fetal fibroblasts. (PMID: 10997781) Parseghian M.H. … Hamkalo B.A. (Chromosome Res. 2000) 3 4
  4. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall A.J. … Beck S. (Nature 2003) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for HIST1H1D Gene

Sources for HIST1H1D Gene

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