FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\BigH1
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General Information
Symbol
Dmel\BigH1
Species
D. melanogaster
Name
Histone H1 variant BigH1
Annotation Symbol
CG3509
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038252
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
Histone H1 variant BigH1 (BigH1) encodes a germline linker histone H1 variant that is retained in the early embryo until cellularization. It is required for gametogenesis and to maintain silencing of the zygotic genome during early embryogenesis. [Date last reviewed: 2018-11-15] (FlyBase Gene Snapshot)
All Summaries
Also Known As

dBigH1

Key Links
Genomic Location
Cytogenetic map
88C10-88C10
Sequence location
Recombination map
3-55
RefSeq locus
NT_033777 REGION:14663450..14664822
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables nucleosome binding
inferred from direct assay
(Pérez-Montero et al., 2013)
enables structural constituent of chromatin
inferred from direct assay
(Pérez-Montero et al., 2013)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables DNA binding
inferred from electronic annotation with InterPro:IPR005818
(InterPro Project Members, 2004-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in negative regulation of DNA-templated transcription
inferred from mutant phenotype
(Pérez-Montero et al., 2013)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in nucleosome assembly
inferred from electronic annotation with InterPro:IPR005818
(InterPro Project Members, 2004-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Pérez-Montero et al., 2013)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of nucleosome
inferred from electronic annotation with InterPro:IPR005818
(InterPro Project Members, 2004-)
part_of Swr1 complex
inferred from biological aspect of ancestor with PANTHER:PTN000328224
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Histone H1 variant BigH1 (BigH1) encodes a germline linker histone H1 variant that is retained in the early embryo until cellularization. It is required for gametogenesis and to maintain silencing of the zygotic genome during early embryogenesis. [Date last reviewed: 2018-11-15]
Summary (Interactive Fly)

germline linker histone that enhances transcriptional silencing - replaced by somatic dH1 in somatic cells - oogenesis and spermatogenesis - along with the translational regulator Bam forms a repressor loop essential for male germ stem cell differentiation

Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\BigH1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q8MSC4)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.39

Gene model reviewed during 5.53

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
BigH1-RA
FBtr0082969
NM_142126
1279
353
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
BigH1-PA
FBpp0082428
38.7
353
10.18
Q8MSC4
NP_650383
AAF55087
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\BigH1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.71

Transcript Expression
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 12
germline cell
(Pérez-Montero et al., 2013)
adult stage | male
spermatocyte
(Carbonell et al., 2017, Pérez-Montero et al., 2013)
testis
(Carbonell et al., 2017)
spermatogonium
(Carbonell et al., 2017)
male germline stem cell
(Carbonell et al., 2017)
adult stage | female
oocyte
(Pérez-Montero et al., 2013)
nurse cell
(Pérez-Montero et al., 2013)
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 4
organism
(Pérez-Montero et al., 2013)
adult stage | male
testis
(Pérez-Montero et al., 2013)
adult stage | female
ovary
(Pérez-Montero et al., 2013)
Additional Descriptive Data

BigH1 expression is is successively turned on and off during spermatogenesis. It is expressed in the tip region of the testis, becomes undetectable during the transit-amplifying spermatogonial divisions, strongly increases in spermatocytes and then is shut off in spermatids. Expression is germ cell-specific and it strong in the germline stem cells anchored to the hub.

(Carbonell et al., 2017)

BigH1 levels are high in 1-3 hr embryos and then decline. BigH1 protein is observed in primordial germline cells as they migrate during embryonic development. It is observed in spermatocytes in the testis and is found in the oocyte and then later in nurse cells proximal to the oocyte in the ovary.

(Pérez-Montero et al., 2013)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Pérez-Montero et al., 2013)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\BigH1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 12 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 17 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of BigH1
Transgenic constructs containing regulatory region of BigH1
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel8160
(Ryder, 2004.4.26)
Inferred from location ( 7 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (10)
Hsap\H1-0
2 of 14
Yes
No
Hsap\H1-8
2 of 14
Yes
Yes
Hsap\H1-1
1 of 14
No
No
Hsap\H1-2
1 of 14
No
No
Hsap\H1-3
1 of 14
No
No
Hsap\H1-4
1 of 14
No
No
Hsap\H1-5
1 of 14
No
No
Hsap\H1-10
1 of 14
No
No
Hsap\HP1BP3
1 of 14
No
No
Hsap\SHPRH
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
Rnor\H1f0
1 of 14
Yes
No
Rnor\H1f8
1 of 14
Yes
No
Mus musculus (laboratory mouse) (2)
Mmus\H1f0
1 of 14
Yes
No
Mmus\H1f8
1 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (2)
Xtro\h1-0
2 of 13
Yes
No
Xtro\shprh
1 of 13
No
No
Danio rerio (Zebrafish) (2)
Drer\h1-0
1 of 14
Yes
No
Drer\h1m
1 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (7)
Cele\hil-1
2 of 14
Yes
No
Cele\hil-2
2 of 14
Yes
No
Cele\hil-3
2 of 14
Yes
No
Cele\hil-4
2 of 14
Yes
No
Cele\hil-5
2 of 14
Yes
No
Cele\hil-6
2 of 14
Yes
No
Cele\his-24
2 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (5)
Agam\AgaP_AGAP005264
1 of 12
Yes
No
Agam\AgaP_AGAP005265
1 of 12
Yes
No
Agam\AgaP_AGAP005266
1 of 12
Yes
No
Agam\AgaP_AGAP010461
1 of 12
Yes
No
Agam\AgaP_AGAP011193
1 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (9)
Atha\AT1G06760
2 of 13
Yes
No
Atha\AT2G30620
2 of 13
Yes
No
Atha\HIS1-3
2 of 13
Yes
No
Atha\HMGA
2 of 13
Yes
Yes
Atha\HON4
2 of 13
Yes
Yes
Atha\HON5
2 of 13
Yes
Yes
Atha\AT1G54230
1 of 13
No
Yes
Atha\AT1G54240
1 of 13
No
Yes
Atha\AT5G08780
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\HHO1
2 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:BigH1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    Interaction Browsers
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-55
    Cytogenetic map
    88C10-88C10
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    88C10-88C10
    Limits computationally determined from genome sequence between P{PZ}put10460 and P{EP}CG33967EP666
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    3-55

    (FlyBase, 2016)

    3-54.2

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (16)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (55)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
    Drosophila Genomics Resource Center cDNA clones

    For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Pérez-Montero et al., 2013)
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
      Other Comments

      BigH1 encodes an early embryonic and germline-specific variant of Histone H1. BigH1 protein is abundant prior to cellularisation. Upon cellularisation, BigH1 is replaced by somatic His1 in the soma, but not in the primordial germ cells. BigH1 prevents premature zygotic genome activation in both the soma and the germline.

      (Pérez-Montero et al., 2013)
      Relationship to Other Genes
      Source for database merge of
      Additional comments
      Nomenclature History
      Source for database identify of

      Source for identity of: BigH1 CG3509

      (Pérez-Montero et al., 2013)
      Nomenclature comments
      Etymology

      The CG3509 gene, which encodes a Histone H1 variant, is named "BigH1" for its high molecular weight in comparison to His1.

      (Pérez-Montero et al., 2013)
      Synonyms and Secondary IDs (6)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      External Crossreferences and Linkouts ( 32 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
      UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      FlyMine - An integrated database for Drosophila genomics
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      References (51)