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Aliases for H1FX Gene

Aliases for H1FX Gene

  • H1 Histone Family Member X 2 3 5
  • H1 Histone Family, Member X 2
  • Histone H1x 3
  • H1.10 3
  • H1X 3

External Ids for H1FX Gene

Previous GeneCards Identifiers for H1FX Gene

  • GC00U990454
  • GC03U900028
  • GC03M130315
  • GC03M130354
  • GC03M130516
  • GC03M129033
  • GC03M126418

Summaries for H1FX Gene

Entrez Gene Summary for H1FX Gene

  • Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H1 family. [provided by RefSeq, Oct 2015]

GeneCards Summary for H1FX Gene

H1FX (H1 Histone Family Member X) is a Protein Coding gene. Among its related pathways are Cell cycle_Chromosome condensation in prometaphase and E2F mediated regulation of DNA replication.

UniProtKB/Swiss-Prot for H1FX Gene

  • Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures.

Gene Wiki entry for H1FX Gene

Additional gene information for H1FX Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H1FX Gene

Genomics for H1FX Gene

GeneHancer (GH) Regulatory Elements for H1FX Gene

Promoters and enhancers for H1FX Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J128877 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 20.5 +436.7 436725 3.6 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ACAD9 PIR50406 ENSG00000244932 RPL32P3 ISY1 H1FX LOC653712 H1FX-AS1 MBD4 RPS15AP16
GH03J129447 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 20.5 -132.9 -132946 4 HDAC1 PKNOX1 SMAD1 ATF1 TAF9B NFRKB ZBTB40 TCF12 POLR2B ZNF766 RPL32P3 ISY1 ENSG00000244932 H1FX RHO PLXND1 IFT122 ACAD9 MBD4 GC03P129876
GH03J129178 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.5 +133.7 133733 8.4 PKNOX1 SMAD1 FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 CNBP LOC105374101 RPL32P3 ENSG00000244932 ISY1 H1FX-AS1 MBD4 RPS15AP16 H1FX COPG1
GH03J129428 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 13.5 -112.8 -112761 1.8 CLOCK ATF1 ARID4B SIN3A DMAP1 POLR2B FOS SP3 SP5 NFYC EFCAB12 ENSG00000244932 RPL32P3 ISY1 H1FX MBD4 COPG1 RPS15AP16 IFT122
GH03J129888 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 11.3 -575.2 -575196 6.3 PKNOX1 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 FOS SP3 TMCC1 ENSG00000244932 PIK3R4 RPL32P3 ISY1 H1FX RNY3P13 COPG1 TMCC1-AS1 ENSG00000203644
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around H1FX on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the H1FX gene promoter:
  • Nkx2-5
  • NRSF form 2
  • NRSF form 1
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1a
  • c-Myb
  • LyF-1
  • HSF1 (long)

Genomic Locations for H1FX Gene

Genomic Locations for H1FX Gene
1,507 bases
Minus strand
1,507 bases
Minus strand

Genomic View for H1FX Gene

Genes around H1FX on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H1FX Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H1FX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H1FX Gene

Proteins for H1FX Gene

  • Protein details for H1FX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histone H1x
    Protein Accession:

    Protein attributes for H1FX Gene

    213 amino acids
    Molecular mass:
    22487 Da
    Quaternary structure:
    • Interacts with RRP1B.

    Three dimensional structures from OCA and Proteopedia for H1FX Gene

neXtProt entry for H1FX Gene

Post-translational modifications for H1FX Gene

  • Citrullination at Arg-62 (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.
  • Ubiquitination at Lys106 and Lys47
  • Modification sites at PhosphoSitePlus

Other Protein References for H1FX Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for H1FX Gene

Domains & Families for H1FX Gene

Gene Families for H1FX Gene

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

Protein Domains for H1FX Gene

Suggested Antigen Peptide Sequences for H1FX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the histone H1/H5 family.
  • Belongs to the histone H1/H5 family.
genes like me logo Genes that share domains with H1FX: view

Function for H1FX Gene

Molecular function for H1FX Gene

UniProtKB/Swiss-Prot Function:
Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures.

Phenotypes From GWAS Catalog for H1FX Gene

Gene Ontology (GO) - Molecular Function for H1FX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding HDA 22681889
GO:0045296 cadherin binding IDA 25468996
genes like me logo Genes that share ontologies with H1FX: view
genes like me logo Genes that share phenotypes with H1FX: view

Animal Models for H1FX Gene

MGI Knock Outs for H1FX:
  • H1fx H1fx<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for H1FX Gene

miRTarBase miRNAs that target H1FX

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H1FX

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for H1FX Gene

Localization for H1FX Gene

Subcellular locations from UniProtKB/Swiss-Prot for H1FX Gene

Nucleus. Chromosome.

Subcellular locations from

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 H1FX gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (4)
  • Nucleus (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for H1FX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000786 nucleosome IEA --
GO:0005634 nucleus IDA --
GO:0005694 chromosome IEA --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with H1FX: view

Pathways & Interactions for H1FX Gene

genes like me logo Genes that share pathways with H1FX: view

Pathways by source for H1FX Gene

Gene Ontology (GO) - Biological Process for H1FX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006334 nucleosome assembly IEA --
genes like me logo Genes that share ontologies with H1FX: view

No data available for SIGNOR curated interactions for H1FX Gene

Drugs & Compounds for H1FX Gene

No Compound Related Data Available

Transcripts for H1FX Gene

mRNA/cDNA for H1FX Gene

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

Unigene Clusters for H1FX Gene

H1 histone family, member X:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for H1FX

Alternative Splicing Database (ASD) splice patterns (SP) for H1FX Gene

No ASD Table

Relevant External Links for H1FX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for H1FX Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for H1FX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for H1FX Gene

This gene is overexpressed in Tlymphocyte (24.6) and Peripheral blood mononuclear cells (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for H1FX Gene

Protein tissue co-expression partners for H1FX Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of H1FX Gene:


SOURCE GeneReport for Unigene cluster for H1FX Gene:


mRNA Expression by UniProt/SwissProt for H1FX Gene:

Tissue specificity: Expressed ubiquitously.

Evidence on tissue expression from TISSUES for H1FX Gene

  • Lung(5)
  • Nervous system(4.3)
  • Liver(4.2)
  • Intestine(3.6)
  • Kidney(3.6)
  • Eye(3.4)
  • Pancreas(3)
  • Bone marrow(2.4)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with H1FX: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for H1FX Gene

Orthologs for H1FX Gene

This gene was present in the common ancestor of chordates.

Orthologs for H1FX Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia H1FX 34 33
  • 99.22 (n)
(Canis familiaris)
Mammalia H1FX 33
  • 91.55 (n)
(Bos Taurus)
Mammalia H1FX 34 33
  • 88.89 (n)
(Mus musculus)
Mammalia H1fx 16 34 33
  • 79.96 (n)
(Rattus norvegicus)
Mammalia H1fx 33
  • 77.95 (n)
(Ornithorhynchus anatinus)
Mammalia H1FX 34
  • 75 (a)
(Monodelphis domestica)
Mammalia H1FX 34
  • 67 (a)
(Danio rerio)
Actinopterygii h1fx 34
  • 51 (a)
Species where no ortholog for H1FX 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)
  • 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)
  • 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)
  • 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 H1FX Gene

Gene Tree for H1FX (if available)
Gene Tree for H1FX (if available)
Evolutionary constrained regions (ECRs) for H1FX: view image

Paralogs for H1FX Gene

(5) SIMAP similar genes for H1FX Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with H1FX: view

No data available for Paralogs for H1FX Gene

Variants for H1FX Gene

Sequence variations from dbSNP and Humsavar for H1FX Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000300176 -- 129,314,955(-) C/G 3_prime_UTR_variant
rs1000650884 -- 129,314,784(-) C/A 3_prime_UTR_variant
rs1001035078 -- 129,316,140(-) A/G 5_prime_UTR_variant
rs1001267679 -- 129,315,042(-) G/A 3_prime_UTR_variant
rs1001404877 -- 129,314,905(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for H1FX Gene

Variant ID Type Subtype PubMed ID
nsv520607 CNV gain+loss 19592680
nsv591651 CNV loss 21841781
nsv822244 CNV gain 20364138
nsv829722 CNV gain 17160897

Variation tolerance for H1FX Gene

Gene Damage Index Score: 0.53; 11.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H1FX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H1FX Gene

Disorders for H1FX Gene

Additional Disease Information for H1FX

No disorders were found for H1FX Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for H1FX Gene

Publications for H1FX Gene

  1. Cloning of the cDNA encoding a novel subtype of histone H1. (PMID: 8964515) Yamamoto T … Horikoshi M (Gene 1996) 2 3 4 58
  2. The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor. (PMID: 19710015) Crawford NP … Hunter KW (The Journal of biological chemistry 2009) 3 4 58
  3. Histone H1x is highly expressed in human neuroendocrine cells and tumours. (PMID: 19108733) Warneboldt J … Happel N (BMC cancer 2008) 3 22 58
  4. G1 phase-dependent nucleolar accumulation of human histone H1x. (PMID: 17868027) Stoldt S … Happel N (Biology of the cell 2007) 3 22 58
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58

Products for H1FX Gene

Sources for H1FX Gene

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