Human Gene H1-4 (ENST00000304218.6_4) from GENCODE V47lift37
  Description: H1.4 linker histone, cluster member (from RefSeq NM_005321.3)
Gencode Transcript: ENST00000304218.6_4
Gencode Gene: ENSG00000168298.7_7
Transcript (Including UTRs)
   Position: hg19 chr6:26,156,557-26,157,343 Size: 787 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr6:26,156,619-26,157,278 Size: 660 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:26,156,557-26,157,343)mRNA (may differ from genome)Protein (219 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H14_HUMAN
DESCRIPTION: RecName: Full=Histone H1.4; AltName: Full=Histone H1b; AltName: Full=Histone H1s-4;
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).
INTERACTION: Q9Y468:L3MBTL1; NbExp=7; IntAct=EBI-358163, EBI-1265089; P16333:NCK1; NbExp=2; IntAct=EBI-358163, EBI-389883;
SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Mainly localizes in heterochromatin. Dysplays a punctuate staining pattern in the nucleus.
DOMAIN: The C-terminal domain is required for high-affinity binding to chromatin (By similarity).
PTM: H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter (By similarity).
PTM: Acetylated at Lys-26. Deacetylated at Lys-26 by SIRT1.
MISCELLANEOUS: This variant accounts for 60% of histone H1.
SIMILARITY: Belongs to the histone H1/H5 family.
SIMILARITY: Contains 1 H15 (linker histone H1/H5 globular) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.62 RPKM in Pituitary
Total median expression: 26.35 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.1062-0.211 Picture PostScript Text
3' UTR -12.4065-0.191 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005818 - Histone_H1/H5
IPR005819 - Histone_H5
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00538 - linker histone H1 and H5 family

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3TZD - X-ray


ModBase Predicted Comparative 3D Structure on P10412
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003723 RNA binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016208 AMP binding
GO:0031490 chromatin DNA binding
GO:0032564 dATP binding
GO:0043531 ADP binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006334 nucleosome assembly
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0016584 nucleosome positioning
GO:0080182 histone H3-K4 trimethylation
GO:0098532 histone H3-K27 trimethylation

Cellular Component:
GO:0000786 nucleosome
GO:0000788 nuclear nucleosome
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005720 nuclear heterochromatin


-  Descriptions from all associated GenBank mRNAs
  BC055095 - Homo sapiens cDNA clone IMAGE:6498952, containing frame-shift errors.
AK313681 - Homo sapiens cDNA, FLJ94268, highly similar to Homo sapiens histone 1, H1e (HIST1H1E), mRNA.
JD125295 - Sequence 106319 from Patent EP1572962.
BC096168 - Homo sapiens histone cluster 1, H1e, mRNA (cDNA clone MGC:116818 IMAGE:40003408), complete cds.
BC096169 - Homo sapiens histone cluster 1, H1e, mRNA (cDNA clone MGC:116820 IMAGE:40003411), complete cds.
BC096170 - Homo sapiens histone cluster 1, H1e, mRNA (cDNA clone MGC:116821 IMAGE:40003413), complete cds.
BC099632 - Homo sapiens histone cluster 1, H1e, mRNA (cDNA clone MGC:116819 IMAGE:40003410), complete cds.
EF065554 - Homo sapiens liver histone H1e mRNA, complete cds.
EF065555 - Homo sapiens histone H1e mRNA, complete cds.
DQ585138 - Homo sapiens piRNA piR-52250, complete sequence.
DQ585139 - Homo sapiens piRNA piR-52251, complete sequence.
KJ891321 - Synthetic construct Homo sapiens clone ccsbBroadEn_00715 HIST1H1E gene, encodes complete protein.
DQ591095 - Homo sapiens piRNA piR-58207, complete sequence.
DQ572216 - Homo sapiens piRNA piR-40328, complete sequence.
DQ590173 - Homo sapiens piRNA piR-57285, complete sequence.
JD335081 - Sequence 316105 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P10412 (Reactome details) participates in the following event(s):

R-HSA-4647594 SAHF formation
R-HSA-211239 Association of DFF40 with chromatin
R-HSA-211247 Cleavage of DNA by DFF40
R-HSA-2559584 Formation of Senescence-Associated Heterochromatin Foci (SAHF)
R-HSA-211227 Activation of DNA fragmentation factor
R-HSA-2559586 DNA Damage/Telomere Stress Induced Senescence
R-HSA-140342 Apoptosis induced DNA fragmentation
R-HSA-2559583 Cellular Senescence
R-HSA-75153 Apoptotic execution phase
R-HSA-2262752 Cellular responses to stress
R-HSA-109581 Apoptosis
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-5357801 Programmed Cell Death

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000304218.1, ENST00000304218.2, ENST00000304218.3, ENST00000304218.4, ENST00000304218.5, H1-4 , H14_HUMAN, H1F4 , HIST1H1E , NM_005321, P10412, Q4VB25, uc317njo.1, uc317njo.2
UCSC ID: ENST00000304218.6_4
RefSeq Accession: NM_005321.3
Protein: P10412 (aka H14_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene H1-4:
h1-4 (HIST1H1E Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.