Human Gene H1-6 (ENST00000338379.6_6) from GENCODE V47lift37
  Description: H1.6 linker histone, cluster member (from RefSeq NM_005323.4)
Gencode Transcript: ENST00000338379.6_6
Gencode Gene: ENSG00000187475.6_8
Transcript (Including UTRs)
   Position: hg19 chr6:26,107,640-26,108,363 Size: 724 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr6:26,107,698-26,108,321 Size: 624 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:26,107,640-26,108,363)mRNA (may differ from genome)Protein (207 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: H1T_HUMAN
DESCRIPTION: RecName: Full=Histone H1t; AltName: Full=Testicular H1 histone;
FUNCTION: Histones H1 are necessary for the condensation of nucleosome chains into higher-order structures.
SUBCELLULAR LOCATION: Nucleus. Chromosome.
DEVELOPMENTAL STAGE: This histone is a testis-specific H1 variant that appears during meiosis in spermatogenesis.
PTM: Phosphorylated in early spermatids (By similarity).
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: 0.98 RPKM in Testis
Total median expression: 1.18 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.7042-0.064 Picture PostScript Text
3' UTR -16.5058-0.284 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 P22492
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 DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding

Biological Process:
GO:0006334 nucleosome assembly
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  LF209727 - JP 2014500723-A/17230: Polycomb-Associated Non-Coding RNAs.
BC069517 - Homo sapiens histone cluster 1, H1t, mRNA (cDNA clone MGC:96974 IMAGE:7262183), complete cds.
JD481293 - Sequence 462317 from Patent EP1572962.
BC130350 - Homo sapiens histone cluster 1, H1t, mRNA (cDNA clone MGC:163222 IMAGE:40146381), complete cds.
LF331323 - JP 2014500723-A/138826: Polycomb-Associated Non-Coding RNAs.
CU686878 - Synthetic construct Homo sapiens gateway clone IMAGE:100022610 5' read HIST1H1T mRNA.
KJ891322 - Synthetic construct Homo sapiens clone ccsbBroadEn_00716 HIST1H1T gene, encodes complete protein.
EU446962 - Synthetic construct Homo sapiens clone IMAGE:100069945; IMAGE:100012171; FLH257134.01L histone cluster 1, H1t (HIST1H1T) gene, encodes complete protein.
HQ258096 - Synthetic construct Homo sapiens clone IMAGE:100072405 histone cluster 1, H1t (HIST1H1T) gene, encodes complete protein.
KJ896953 - Synthetic construct Homo sapiens clone ccsbBroadEn_06347 HIST1H1T gene, encodes complete protein.
LF331322 - JP 2014500723-A/138825: Polycomb-Associated Non-Coding RNAs.
DQ584149 - Homo sapiens piRNA piR-51261, complete sequence.
LF331321 - JP 2014500723-A/138824: Polycomb-Associated Non-Coding RNAs.
DQ595565 - Homo sapiens piRNA piR-61677, complete sequence.
DQ591265 - Homo sapiens piRNA piR-58377, complete sequence.
DQ598398 - Homo sapiens piRNA piR-36464, complete sequence.
DQ596961 - Homo sapiens piRNA piR-35027, complete sequence.
DQ583275 - Homo sapiens piRNA piR-50387, complete sequence.
DQ599488 - Homo sapiens piRNA piR-37554, complete sequence.
DQ581365 - Homo sapiens piRNA piR-49477, complete sequence.
DQ598305 - Homo sapiens piRNA piR-36371, complete sequence.
DQ578564 - Homo sapiens piRNA piR-46676, complete sequence.
MA566900 - JP 2018138019-A/138826: Polycomb-Associated Non-Coding RNAs.
MA566899 - JP 2018138019-A/138825: Polycomb-Associated Non-Coding RNAs.
MA566898 - JP 2018138019-A/138824: Polycomb-Associated Non-Coding RNAs.
MA445304 - JP 2018138019-A/17230: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000338379.1, ENST00000338379.2, ENST00000338379.3, ENST00000338379.4, ENST00000338379.5, H1-6 , H1FT, H1T, H1T_HUMAN, HIST1H1T , NM_005323, P22492, Q6ISI1, Q8IUE8, uc317vaa.1, uc317vaa.2
UCSC ID: ENST00000338379.6_6
RefSeq Accession: NM_005323.4
Protein: P22492 (aka H1T_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.