Human Gene H1-2 (ENST00000343677.4_7) from GENCODE V47lift37
  Description: H1.2 linker histone, cluster member (from RefSeq NM_005319.4)
Gencode Transcript: ENST00000343677.4_7
Gencode Gene: ENSG00000187837.5_9
Transcript (Including UTRs)
   Position: hg19 chr6:26,055,968-26,056,698 Size: 731 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr6:26,056,015-26,056,656 Size: 642 Coding Exon Count: 1 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:26,055,968-26,056,698)mRNA (may differ from genome)Protein (213 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H12_HUMAN
DESCRIPTION: RecName: Full=Histone H1.2; AltName: Full=Histone H1c; AltName: Full=Histone H1d; AltName: Full=Histone H1s-1;
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).
SUBCELLULAR LOCATION: Nucleus. Chromosome. Note=Mainly localizes in euchromatin. Distribution goes in parallel with DNA concentration.
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: Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
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: 98.82 RPKM in Prostate
Total median expression: 1415.08 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 -6.5042-0.155 Picture PostScript Text
3' UTR -9.4047-0.200 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

ModBase Predicted Comparative 3D Structure on P16403
FrontTopSide
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031490 chromatin DNA 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:0005634 nucleus
GO:0005694 chromosome
GO:0005719 nuclear euchromatin
GO:0035327 transcriptionally active chromatin


-  Descriptions from all associated GenBank mRNAs
  AK290947 - Homo sapiens cDNA FLJ76039 complete cds, highly similar to Homo sapiens histone 1, H1c (HIST1H1C), mRNA.
BC052623 - Homo sapiens cDNA clone IMAGE:6574644, **** WARNING: chimeric clone ****.
BC002649 - Homo sapiens histone cluster 1, H1c, mRNA (cDNA clone IMAGE:3608862).
AB451259 - Homo sapiens HIST1H1C mRNA for histone H1.2, complete cds, clone: FLJ08073AAAN.
CU678090 - Synthetic construct Homo sapiens gateway clone IMAGE:100018027 5' read HIST1H1C mRNA.
KJ891320 - Synthetic construct Homo sapiens clone ccsbBroadEn_00714 HIST1H1C gene, encodes complete protein.
EU446960 - Synthetic construct Homo sapiens clone IMAGE:100069870; IMAGE:100012169; FLH258590.01L histone cluster 1, H1c (HIST1H1C) gene, encodes complete protein.
EU832089 - Synthetic construct Homo sapiens clone HAIB:100067118; DKFZo008A0125 histone cluster 1, H1c protein (HIST1H1C) gene, encodes complete protein.
EU832181 - Synthetic construct Homo sapiens clone HAIB:100067210; DKFZo004A0126 histone cluster 1, H1c protein (HIST1H1C) gene, encodes complete protein.
AB590706 - Synthetic construct DNA, clone: pFN21AE1218, Homo sapiens HIST1H1C gene for histone cluster 1, H1c, without stop codon, in Flexi system.
AB451385 - Homo sapiens HIST1H1C mRNA for histone H1.2, partial cds, clone: FLJ08073AAAF.
D28457 - Homo sapiens mRNA for histone H1D, 5'UTR region.

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

Protein P16403 (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: A8K4I2, ENST00000343677.1, ENST00000343677.2, ENST00000343677.3, H1-2 , H12_HUMAN, H1F2 , HIST1H1C , NM_005319, P16403, uc317wsd.1, uc317wsd.2
UCSC ID: ENST00000343677.4_7
RefSeq Accession: NM_005319.4
Protein: P16403 (aka H12_HUMAN)

-  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.