H1-6 Gene (Protein Coding)

H1.6 Linker Histone, Cluster Member

GC06M044866
GIFtS:
30
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 ... See more...

Aliases for H1-6 Gene

Aliases for H1-6 Gene

  • H1.6 Linker Histone, Cluster Member 2 3 5
  • H1 Histone Family, Member T (Testis-Specific) 2 3
  • Histone Cluster 1 H1 Family Member T 2 3
  • Histone Cluster 1, H1t 2 3
  • Testicular H1 Histone 3 4
  • Histone 1, H1t 2 3
  • Histone H1t 3 4
  • HIST1H1T 3 4
  • H1FT 3 4
  • H1t 2 3
  • DJ221C16.2 3
  • H1.6 3
  • H1-6 5
  • H1T 4

External Ids for H1-6 Gene

Previous HGNC Symbols for H1-6 Gene

  • H1FT
  • HIST1H1T

Previous GeneCards Identifiers for H1-6 Gene

  • GC06M026828
  • GC06M027052
  • GC06M027312
  • GC06M027819

Summaries for H1-6 Gene

Entrez Gene Summary for H1-6 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 H1-6 Gene

H1-6 (H1.6 Linker Histone, Cluster Member) is a Protein Coding gene. Diseases associated with H1-6 include Timothy Grass Allergy. Among its related pathways are Activation of cAMP-Dependent PKA and Granzyme-A Pathway. An important paralog of this gene is H1-4.

UniProtKB/Swiss-Prot Summary for H1-6 Gene

  • Testis-specific histone H1 that forms less compacted chromatin compared to other H1 histone subtypes (PubMed:26757249). Formation of more relaxed chromatin may be required to promote chromatin architecture required for proper chromosome regulation during meiosis, such as homologous recombination (PubMed:26757249). Histones H1 act as linkers that bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration (Probable).

Gene Wiki entry for H1-6 Gene

Additional gene information for H1-6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for H1-6 Gene

Genomics for H1-6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for H1-6 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
GH06J026110 Enhancer 0.4 Ensembl 250.7 -1.6 -1566 0.2 ZBTB33 CEBPB ZNF335 CEBPG H1-6 piR-35027 piR-36371 piR-36464 piR-37554 piR-58377 piR-46676 piR-51261 H2BC4 piR-31751
GH06J026108 Promoter 0.3 EPDnew 250.7 0.0 -21 0.1 H1-6 piR-35027 piR-36371 piR-36464 piR-37554 piR-58377 piR-46676 piR-51261 ENSG00000272462 H2BC4
GH06J026086 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 11.8 +20.1 20059 2.8 IKZF1 ZNF592 POLR2A ZBTB10 YY1 NONO KLF11 BHLHE40 MBD2 ZNF341 HFE HSALNG0048729 NONHSAG043229.2 ENSG00000272462 H1-2 H1-6 LARP1P1 BTN3A2 HFE-AS1 HSALNG0048728
GH06J026060 Enhancer 0.5 Ensembl ENCODE 11.3 +47.8 47834 2.2 ZBTB33 CEBPB H4C3 ENSG00000272462 HFE H1-6 H1-4 H2BC5 LARP1P1 HMGN4 H1-2 piR-46501-084
GH06J026136 Enhancer 0.4 Ensembl 12.2 -28.5 -28546 1.4 PKNOX1 GATAD2A PRDM1 PML H1-6 H4C3 LARP1P1 H2AC10P ENSG00000272462 HSALNG0048733 H2AC6 piR-40096 H1-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H1-6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for H1-6

Genomic Locations for H1-6 Gene

Latest Assembly
chr6:26,107,412-26,108,135
(GRCh38/hg38)
Size:
724 bases
Orientation:
Minus strand

Previous Assembly
chr6:26,107,640-26,108,363
(GRCh37/hg19 by Entrez Gene)
Size:
724 bases
Orientation:
Minus strand

chr6:26,107,640-26,108,364
(GRCh37/hg19 by Ensembl)
Size:
725 bases
Orientation:
Minus strand

Genomic View for H1-6 Gene

Genes around H1-6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H1-6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H1-6 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for H1-6 Gene

Proteins for H1-6 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for H1-6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P22492-H1T_HUMAN
    Recommended name:
    Histone H1t
    Protein Accession:
    P22492
    Secondary Accessions:
    • Q6ISI1
    • Q8IUE8

    Protein attributes for H1-6 Gene

    Size:
    207 amino acids
    Molecular mass:
    22019 Da
    Quaternary structure:
    No Data Available

neXtProt entry for H1-6 Gene

Post-translational modifications for H1-6 Gene

  • Phosphorylated in early spermatids.
  • Citrullination at Arg-58 (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.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for H1-6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H1-6 Gene

Domains & Families for H1-6 Gene

Gene Families for H1-6 Gene

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

Protein Domains for H1-6 Gene

InterPro:
Blocks:
  • Histone H1/H5

Suggested Antigen Peptide Sequences for H1-6 Gene

GenScript: Design optimal peptide antigens:
  • Histone cluster 1, H1t (A1L407_HUMAN)
  • Testicular H1 histone (H1T_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P22492

UniProtKB/Swiss-Prot:

H1T_HUMAN :
  • Belongs to the histone H1/H5 family.
Family:
  • Belongs to the histone H1/H5 family.
genes like me logo Genes that share domains with H1-6: view

Function for H1-6 Gene

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  3. miRNA products for research
  4. Inhibitory RNAs for research
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  6. Cell Lines for research

Molecular function for H1-6 Gene

UniProtKB/Swiss-Prot Function:
Testis-specific histone H1 that forms less compacted chromatin compared to other H1 histone subtypes (PubMed:26757249). Formation of more relaxed chromatin may be required to promote chromatin architecture required for proper chromosome regulation during meiosis, such as homologous recombination (PubMed:26757249). Histones H1 act as linkers that bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration (Probable).

Phenotypes From GWAS Catalog for H1-6 Gene

Gene Ontology (GO) - Molecular Function for H1-6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IBA 21873635
GO:0031492 nucleosomal DNA binding IBA 21873635
genes like me logo Genes that share ontologies with H1-6: view
genes like me logo Genes that share phenotypes with H1-6: view

Animal Models for H1-6 Gene

MGI Knock Outs for H1-6:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H1-6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for H1-6 Gene

Localization for H1-6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for H1-6 Gene

Nucleus. Chromosome.

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 H1-6 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for H1-6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0000791 euchromatin IBA --
GO:0005634 nucleus IBA 21873635
GO:0005694 chromosome IEA --
GO:0042025 host cell nucleus IEA --
genes like me logo Genes that share ontologies with H1-6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for H1-6 Gene

Pathways & Interactions for H1-6 Gene

PathCards logo

SuperPathways for H1-6 Gene

SuperPathway Contained pathways
1 Granzyme-A Pathway
Granzyme-A Pathway
-
2 Activation of cAMP-Dependent PKA
PKA Signaling
.56
3 E2F mediated regulation of DNA replication
Cell cycle Start of DNA replication in early S phase
.53
4 Cell cycle_Chromosome condensation in prometaphase
Cell cycle_Chromosome condensation in prometaphase
-
genes like me logo Genes that share pathways with H1-6: view

Pathways by source for H1-6 Gene

2 GeneGo (Thomson Reuters) pathways for H1-6 Gene
  • Cell cycle Start of DNA replication in early S phase
  • Cell cycle_Chromosome condensation in prometaphase
2 Qiagen pathways for H1-6 Gene
  • Granzyme-A Pathway
  • PKA Signaling

Gene Ontology (GO) - Biological Process for H1-6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IEA --
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis TAS,IBA 21873635
GO:0016584 nucleosome positioning IBA 21873635
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with H1-6: view

No data available for SIGNOR curated interactions for H1-6 Gene

Drugs & Compounds for H1-6 Gene

Products:

  1. Drug products for research

(1) Drugs for H1-6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with H1-6: view

Transcripts for H1-6 Gene

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mRNA/cDNA for H1-6 Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H1-6

Alternative Splicing Database (ASD) splice patterns (SP) for H1-6 Gene

No ASD Table

Relevant External Links for H1-6 Gene

GeneLoc Exon Structure for
H1-6

Expression for H1-6 Gene

Products:

  1. Primer products for research

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for H1-6

SOURCE GeneReport for Unigene cluster for H1-6 Gene:

Hs.533293

mRNA Expression by UniProt/SwissProt for H1-6 Gene:

P22492-H1T_HUMAN
Tissue specificity: Testis-specific.
genes like me logo Genes that share expression patterns with H1-6: view

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for H1-6 Gene

Orthologs for H1-6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for H1-6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia LOC471879 29
  • 98.23 (n)
HIST1H1T 30
  • 96 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia HIST1H1T 29 30
  • 70.55 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Hist1h1t 29
  • 68.8 (n)
Mouse
(Mus musculus)
 Mammalia Hist1h1t 29 30
  • 67.32 (n)
 OneToOne
H1f6 16
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 28 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves HIST1H111R 29
  • 58.54 (n)
Lizard
(Anolis carolinensis)
 Reptilia -- 30
  • 74 (a)
 ManyToMany
-- 30
  • 44 (a)
 ManyToMany
-- 30
  • 43 (a)
 ManyToMany
-- 30
  • 40 (a)
 ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC101732947 29
  • 58.94 (n)
Zebrafish
(Danio rerio)
 Actinopterygii zgc:163061 29 30 30
  • 66.2 (n)
 ManyToMany
CABZ01086354.1 30
  • 52 (a)
 ManyToMany
CU457819.3 30
  • 50 (a)
 ManyToMany
FP325123.1 30
  • 50 (a)
 ManyToMany
zgc:110425 30
  • 47 (a)
 ManyToMany
histh1l 30
  • 47 (a)
 ManyToMany
si:dkey-261m9.12 30
  • 45 (a)
 ManyToMany
si:ch211-113a14.24 30
  • 45 (a)
 ManyToMany
si:dkey-108k21.14 30
  • 45 (a)
 ManyToMany
zgc:153405 30
  • 45 (a)
 ManyToMany
si:ch211-113a14.18 30
  • 45 (a)
 ManyToMany
si:dkey-108k21.10 30
  • 45 (a)
 ManyToMany
si:ch211-113a14.12 30
  • 44 (a)
 ManyToMany
si:dkey-108k21.21 30
  • 41 (a)
 ManyToMany
Species where no ortholog for H1-6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Cow (Bos Taurus)
  • 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)
  • 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 Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for H1-6 Gene

ENSEMBL:
Gene Tree for H1-6 (if available)
TreeFam:
Gene Tree for H1-6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for H1-6: view image
Alliance of Genome Resources:
Additional Orthologs for H1-6

Paralogs for H1-6 Gene

Paralogs for H1-6 Gene

genes like me logo Genes that share paralogs with H1-6: view

Variants for H1-6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for H1-6 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs198844 -- p.Val14Leu
rs198845 -- p.Gln178Lys
rs2051542 -- p.Leu52Phe

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for H1-6 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for H1-6 Gene

Variant ID Type Subtype PubMed ID
dgv5926n100 CNV gain 25217958
esv3608393 CNV gain 21293372
nsv1023453 CNV gain 25217958
nsv428137 CNV loss 18775914

Variation tolerance for H1-6 Gene

Residual Variation Intolerance Score: 90% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.94; 79.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H1-6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
H1-6
Leiden Open Variation Database (LOVD)
H1-6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H1-6 Gene

Disorders for H1-6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for H1-6 Gene - From: COP

Disorder Aliases PubMed IDs
timothy grass allergy
- elite association - COSMIC cancer census association via MalaCards
Search H1-6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for H1-6

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with H1-6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for H1-6 Gene

Publications for H1-6 Gene

  1. The human and mouse replication-dependent histone genes. (PMID: 12408966) Marzluff WF … Maltais LJ (Genomics 2002) 2 3 4
  2. Primate testicular histone H1t genes are highly conserved and the human H1t gene is located on chromosome 6. (PMID: 8175896) Koppel DA … Grimes SR (Journal of cellular biochemistry 1994) 2 3 4
  3. Structure and expression of the human gene encoding testicular H1 histone (H1t). (PMID: 1889752) Drabent B … Doenecke D (Gene 1991) 3 4 22
  4. Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T. (PMID: 26757249) Machida S … Kurumizaka H (Biochemistry 2016) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

ExternalLinks

View latest publications for H1-6 gene in Mastermind

Products for H1-6 Gene

Sources for H1-6 Gene