FlyBase Gene Report: Dmel\His3.3A

General Information

Symbol

Dmel\His3.3A

Species

D. melanogaster

Name

Histone H3.3A

Annotation Symbol

CG5825

Feature Type

protein_coding_gene

FlyBase ID

FBgn0014857

Gene Model Status

Current

Stock Availability

16 publicly available

Gene Summary

Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes and is specifically enriched in modifications associated with active chromatin. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. (UniProt, C0HL66)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

H3.3, H3.3A, histone H3.3, His3.3, PH3

Key Links

Genomic Location

Cytogenetic map

25C3-25C3

Sequence location

2L:5,055,058..5,056,149 [+]

Recombination map

2-15

RefSeq locus

NT_033779 REGION:5055058..5056149

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (12 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables structural constituent of chromatin

inferred from genetic interaction with FLYBASE:His3.3B; FB:FBgn0004828

(Sakai et al., 2009)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables DNA binding

non-traceable author statement

(Akhmanova et al., 1995)

inferred from electronic annotation with InterPro:IPR000164, InterPro:IPR007125

(InterPro Project Members, 2004-)

enables nucleosomal DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

enables protein heterodimerization activity

inferred from electronic annotation with InterPro:IPR009072

(InterPro Project Members, 2004-)

enables structural constituent of chromatin

inferred from electronic annotation with InterPro:IPR000164

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in heterochromatin formation

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

involved_in kinetochore assembly

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

involved_in mitotic metaphase chromosome alignment

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

involved_in nucleosome assembly

non-traceable author statement

(Akhmanova et al., 1995)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

part_of nucleosome

inferred from direct assay

(Sakai et al., 2009)

located_in polytene chromosome

inferred from direct assay

(Sakai et al., 2009, Akhmanova et al., 1997)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

is_active_in kinetochore

inferred from biological aspect of ancestor with PANTHER:PTN008517672

(GO Reference Genome Project, 2011-)

part_of nucleosome

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

non-traceable author statement

(Akhmanova et al., 1995)

inferred from electronic annotation with InterPro:IPR000164

(InterPro Project Members, 2004-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN008967730

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the histone H3 family. (C0HL66)

Protein Signatures (InterPro)

Summaries

Protein Function (UniProtKB)

(UniProt, C0HL66)

Summary (Interactive Fly)

H3 histone subtype - deposition is coupled to transcription and continues while a gene is active - histone replacement suggests a mechanism to maintain both the structure of chromatin and access to DNA at active genes

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\His3.3A 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 C0HL66)

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

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.46

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

His3.3A-RA

FBtr0079010

NM_078755

848

136

His3.3A-RC

FBtr0333536

NM_001273153

926

136

His3.3A-RD

FBtr0333537

NM_164624

772

136

Additional Transcript Data and Comments

Reported size (kB)

0.9 (northern blot)

(Akhmanova et al., 1995)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

His3.3A-PA

FBpp0078649

15.3

136

11.83

FBpp0305716

15.3

136

11.83

FBpp0305717

15.3

136

11.83

P84249

NP_723056

AAN10526

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

136 aa isoforms: His3.3A-PA, His3.3A-PC, His3.3A-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

136 (aa)

(Akhmanova et al., 1995)

Comments

External Data

Subunit Structure (UniProtKB)

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts with Daxx (via C-terminus) (PubMed:28320872). Interacts with Nasp (PubMed:36930688).

(UniProt, C0HL66)

Post Translational Modification

Phosphorylation at Ser-11 by aurB/ial during mitosis and meiosis is crucial for chromosome condensation and cell-cycle progression. Phosphorylation at Ser-11 by JIL-1 during interphase is linked to gene activation and restricts the formation of heterochromatin at inappropriate sites. Phosphorylation at Ser-11 is enriched on male X chromosome compared to the autosome.

Acetylation is generally linked to gene activation. Acetylated on Lys-15 during prophase I of meiosis. Phosphorylation of H2A 'Thr-119' is a prerequisite for H3 Lys-15 acetylation. Acetylation on Lys-15 is enriched on male X chromosome compared to the autosome.

Methylation at Lys-5 or Lys-80 is generally associated with active chromatin. Methylation at Lys-80 by gpp occurs at low levels in specific developmental stages and tissues undergoing active cell division, and at highest levels in epidermal cells undergoing differentiation.

(UniProt, C0HL66)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\His3.3A using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

His3.3A_1

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).

1.85

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

spermatogenesis & adult stage

testis

(Akhmanova et al., 1995)

Additional Descriptive Data

His3.3A is strongly transcribed in the testes.

(Akhmanova et al., 1995)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

larval stage

embryonic/larval salivary gland

• polytene chromosome

(Akhmanova et al., 1997)

spermatogenesis & adult stage

protein body

(Akhmanova et al., 1997)

Y chromosome loop

(Akhmanova et al., 1997)

spermatid

(Akhmanova et al., 1997)

spermatocyte

(Akhmanova et al., 1997)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Dorus et al., 2006)

Additional Descriptive Data

Antibodies against His3.3 protein stain uniformly over the polytene chromosomes. His3.3 protein staining is seen in meiotic prophase chromatin of primary spermatocytes. One or two strongly staining foci were observed in each nucleus. The distribution of label coincides with the location of some of the Y-chromosomal lampbrush loops. At this stage His3 protein is observed mainly in the autosomal chromatin. In postmeiotic stages, His3.3 protein is observed in the protein body while the His3 protein is found mainly in the chromatin. During spermatid elongation, His3.3 protein is deposited in chromatin. At subsequent stages no major differences were observed in the distribution of His3 protein and His3.3 protein. In post-elongation spermatid cysts, the pattern of staining changes from an even distribution to a dispersed pattern. In mature sperm, no staining is observed.

(Akhmanova et al., 1997)

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of nucleosome

inferred from direct assay

(Sakai et al., 2009)

located_in polytene chromosome

inferred from direct assay

(Sakai et al., 2009, Akhmanova et al., 1997)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\His3.3A in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\His3.3A

View exonic expression by tissue for Dmel\His3.3A

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33736/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0014857

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0014857

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0014857

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG5825

Flygut - An atlas of the Drosophila adult midgut

FBgn0014857

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 10 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 40 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of His3.3A

Transgenic constructs containing regulatory region of His3.3A

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel7022

(Ryder, 2004.4.26)

Inferred from location ( 5 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

His3.3A^GD4748

viable

His3.3A^UAS.hs.GFP

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

His3.3A^GD4748

Other Phenotypes

Allele

some die during pupal stage, with Scer\GAL4^pnr-MD237

His3.3A^GD4748

Phenotype manifest in

Allele

chromatin (with Df(2L)BSC110)

His3.3A^2X1

chromosome, telomeric region (with Df(2L)BSC110)

His3.3A^2X1

polytene chromosome (with Df(2L)BSC110)

His3.3A^2X1

polytene chromosome chromocenter (with Df(2L)BSC110)

His3.3A^2X1

wing disc (with Df(2L)BSC110)

His3.3A^2X1

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (22)

Hsap\H3-3B

12 of 14

Yes

Hsap\H3-5

7 of 14

Yes

Hsap\H3-2

6 of 14

Yes

Hsap\H3C2

6 of 14

Yes

Hsap\H3C3

6 of 14

Yes

Hsap\H3C4

6 of 14

Hsap\H3C6

6 of 14

Hsap\H3C7

6 of 14

Yes

Hsap\H3C8

6 of 14

Yes

Hsap\H3C10

6 of 14

Yes

Hsap\H3C11

6 of 14

Yes

Hsap\H3C12

6 of 14

Yes

6 of 14

6 of 14

5 of 14

3 of 14

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (14)

Rnor\H3f3a

11 of 14

Yes

Rnor\H3f3c

8 of 14

Yes

Rnor\H3c1

6 of 14

Rnor\H3c13

5 of 14

Rnor\Hist1h3b

5 of 14

Yes

Rnor\LOC102548682

5 of 14

Rnor\LOC102549173

5 of 14

Rnor\RGD1564548

5 of 14

Yes

Rnor\H3f3b

4 of 14

Rnor\RGD1564447

3 of 14

Yes

Rnor\Cenpa

2 of 14

Rnor\Hist1h2ail1

2 of 14

Rnor\Hfe

1 of 14

Yes

Rnor\Hist2h3c2

1 of 14

Mus musculus (laboratory mouse) (18)

Mmus\H3f3b

12 of 14

Yes

Mmus\H3c1

6 of 14

Yes

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

Yes

Mmus\H3c13

6 of 14

Mmus\H3c15

6 of 14

Mmus\Gm7426

5 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (36)

Xtro\h3-3a

10 of 13

Yes

Xtro\h3-3b

9 of 13

Yes

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

4 of 13

3 of 13

Yes

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

Danio rerio (Zebrafish) (19)

Drer\h3f3a

13 of 14

Yes

Drer\si:ch1073-429i10.3

11 of 14

Yes

Drer\h3f3b.1

10 of 14

Yes

Drer\h3f3d

10 of 14

Yes

Drer\si:ch211-113a14.27

6 of 14

Yes

Drer\zgc:113983

6 of 14

Drer\LOC108190746

5 of 14

Yes

Drer\LOC108190747

5 of 14

Yes

Drer\si:ch73-36p18.2

5 of 14

Drer\si:ch1073-153i20.2

5 of 14

Yes

Drer\si:dkey-108k21.25

5 of 14

5 of 14

5 of 14

4 of 14

3 of 14

Yes

3 of 14

2 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (24)

Cele\his-71

11 of 14

Yes

Cele\his-72

8 of 14

Yes

Cele\his-74

8 of 14

Yes

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

6 of 14

5 of 14

4 of 14

2 of 14

2 of 14

Yes

Cele\hcp-3

2 of 14

Cele\his-9

2 of 14

Cele\his-73

2 of 14

Yes

Anopheles gambiae (African malaria mosquito) (11)

Agam\AgaP_AGAP001813

10 of 12

Yes

Agam\AgaP_AGAP012196

6 of 12

Yes

5 of 12

5 of 12

5 of 12

5 of 12

5 of 12

5 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (14)

Atha\AT1G09200

8 of 13

Yes

Atha\AT5G10390

8 of 13

Yes

Atha\AT5G10400

8 of 13

Yes

Atha\AT5G65360

8 of 13

Yes

Atha\AT1G75600

7 of 13

Atha\AT4G40040

7 of 13

Atha\AT5G10980

7 of 13

Yes

Atha\HTR11

6 of 13

Yes

5 of 13

4 of 13

3 of 13

3 of 13

2 of 13

2 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\HHT2

10 of 13

Yes

Scer\HHT1

3 of 13

Scer\CSE4

2 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\hht1

10 of 12

Yes

Spom\hht2

10 of 12

Yes

Spom\cnp1

3 of 12

Yes

Spom\hht3

3 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:His3.3A. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (25)

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

11 of 13

4 of 13

4 of 13

cid

3 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

cancer, malignant glioma, H3-3A-related

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

His3.3A^K27M.UASp

model of diffuse midline glioma, H3 K27M-mutant

CEA

(Ahmad and Henikoff, 2021)

CEA with vg^UAS.cKa

(Ahmad and Henikoff, 2021)

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

H3-3B; H3.3 histone B

model of Bryant-Li-Bhoj neurodevelopmental syndrome 2

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 8 )

Allele

Disease

Interaction

References

His3.3A^K27M.UASp

model of diffuse midline glioma, H3 K27M-mutant

is exacerbated by vg^UAS.cKa

(Ahmad and Henikoff, 2021)

His3.3A^{K27R.UAS.Tag:FLAG}

exacerbates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K9Q.UAS.Tag:FLAG}

exacerbates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K9R.UAS.Tag:FLAG}

exacerbates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K9M.UAS.Tag:FLAG}

ameliorates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K14Q.UAS.Tag:FLAG}

ameliorates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K14R.UAS.Tag:FLAG}

exacerbates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

His3.3A^{K27Q.UAS.Tag:FLAG}

exacerbates Huntington's disease

modeled by Hsap\HTT^90.Q120.UAS

(Faragó et al., 2022)

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?

H3-3B; H3.3 histone B

12 of 14

601058

BRYANT-LI-BHOJ NEURODEVELOPMENTAL SYNDROME 2; BRYLIB2

Bryant-Li-Bhoj neurodevelopmental syndrome 2

H3-5; H3.5 histone

7 of 14

616134

H3-7; H3.7 histone (putative)

6 of 14

H3C2; H3 clustered histone 2

6 of 14

602819

H3C3; H3 clustered histone 3

6 of 14

602812

H3C4; H3 clustered histone 4

6 of 14

602811

H3C6; H3 clustered histone 6

6 of 14

602813

H3C7; H3 clustered histone 7

6 of 14

602816

H3C8; H3 clustered histone 8

6 of 14

602815

H3C10; H3 clustered histone 10

6 of 14

602818

H3C11; H3 clustered histone 11

6 of 14

602814

H3C12; H3 clustered histone 12

6 of 14

602817

H3C13; H3 clustered histone 13

6 of 14

H3C15; H3 clustered histone 15

6 of 14

H3-4; H3.4 histone, cluster member

5 of 14

602820

H3Y1; H3.Y histone 1

3 of 14

H3Y2; H3.Y histone 2

3 of 14

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

His3.3A - Caf1-105

tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3A - Daxx

anti tag coimmunoprecipitation, anti tag western blot, tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3A - Dek

anti tag coimmunoprecipitation, western blot, pull down

(Sawatsubashi et al., 2010)

His3.3A - Hira

tandem affinity purification, western blot, Identification by mass spectrometry

(Fromental-Ramain et al., 2017)

His3.3A - Nap1

tandem affinity purification, western blot, Identification by mass spectrometry

(Fromental-Ramain et al., 2017)

His3.3A - asf1

tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3A - l(3)mbt

anti bait coimmunoprecipitation, Identification by mass spectrometry

(Yamamoto-Matsuda et al., 2022)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

His3.3A|His3.3B

suppressible

His3

(Hödl and Basler, 2012)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Subunit Structure (UniProtKB)

(UniProt, C0HL66 )

Linkouts

BioGRID - A database of protein and genetic interactions.

59912

DroID - A comprehensive database of gene and protein interactions.

FBgn0014857

MIST (protein-protein) - An integrated Molecular Interaction Database

33736

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-15

Cytogenetic map

25C3-25C3

Sequence location

2L:5,055,058..5,056,149 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

25C3-25C3

Limits computationally determined from genome sequence between P{lacW}vkg^k16721&P{lacW}Cg25C^k00405 and P{lacW}l(2)k11206^k11206

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-15

(FlyBase, 2016)

2-16.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (16)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

606947

w^*; P{His3.3A.Halo}attP2

606948

w^*; P{His3.3A.mEos3.2}attP2

68241

w¹¹¹⁸; P{UAS-hs-His3.3A.GFP}B6/CyO

95104

w^*; P{nanos-His3.3A.mIFP}attP40/CyO

95105

w^*; PBac{nanos-His3.3A.mIFP}VK00005/TM3, Sb¹

13315

y¹ w^67c23; P{SUPor-P}His3.3A^KG02455/CyO

42620

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02455}attP2

Kyoto

125787

w¹¹¹⁸; P{RS5}His3.3A^5-HA-3051

5825R-2

5825R-3

v106516

v12769

w¹¹¹⁸ P{GD4748}v12769

More stocks available...

Genomic Clones (12)

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

cDNA Clones (202)

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.

FBgn0014857

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0014857

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Akhmanova et al., 1997)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

The canonical "H3.2" histone (His3, present in multiple copies in the genome as part of the repeating histone gene unit) and variant "His3.3" histone (encoded by His3.3A and His3.3B) forms can functionally replace each other. Cells are able to divide and differentiate when H3.2 is entirely absent but is replaced by S phase-expressed His3.3.

(Hödl and Basler, 2012)

Cells that contain a non-methylatable residue instead of K4 in all canonical and variant H3 genes are competent to respond to major developmental signaling pathways by activating target gene expression, although their proliferative capacity is slowed down relative to wild type.

(Hödl and Basler, 2012)

Nucleosomes containing His3.3A protein but not His3 protein are specifically assembled in paternal chromatin before the first round of DNA replication in the fertilised egg.

(Loppin et al., 2005)

RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R⁺ cells.

(Boutros et al., 2004)

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

RNAi screen using dsRNA made from templates generated with primers directed against this gene causes a phenotype when assayed in Kc167 and S2R⁺ cells: cells become round and detached.

(Kiger et al., 2003)

Replication independent deposition of His3.3A occurs at particular loci, including active rDNA arrays.

(Ahmad and Henikoff, 2002)

His3.3A has been cloned and sequenced.

(Akhmanova et al., 1995)

The histone H3.3 replacement variant is encoded by two genes, His3.3A and His3.3B, in D.melanogaster. These genes encode exactly the same protein but are widely divergent in their untranslated regions.

(Akhmanova et al., 1995)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (16)

Reported As

Symbol Synonym

CG5825

(National Institute of Genetics Fly Stocks, 2022-, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Wagner et al., 2007)

H3.3

(Brown et al., 2024, Jayakrishnan et al., 2024, Corcoran and Jacob, 2023, Melnikova and Golovnin, 2023, Tirgar et al., 2023, Shindo et al., 2022, Chaouch et al., 2021, Llorens-Giralt et al., 2021, Schoberleitner et al., 2021, Armstrong et al., 2018, Fromental-Ramain et al., 2017, Zenk et al., 2017, Shih et al., 2016, Horard and Loppin, 2015, Vlijm et al., 2015, Li and Zhou, 2013, Orsi et al., 2013, Ito et al., 2012, Nakayama et al., 2012, Tran et al., 2012, Szenker et al., 2011, Deal et al., 2010, Guertin and Lis, 2010, Macalpine et al., 2010, modENCODE Consortium et al., 2010, Sawatsubashi et al., 2010, van Steensel et al., 2010, Braunschweig et al., 2009, Henikoff et al., 2009, Landmann et al., 2009, Schneiderman et al., 2009, Doheny et al., 2008, Schneiderman and Ahmad, 2008, Bell et al., 2007, Bonnefoy et al., 2007, de Wit et al., 2007, Konev et al., 2007, Konev et al., 2007, Li et al., 2007, Mito et al., 2007, Nakayama et al., 2007, Pinnola et al., 2007, Rathke et al., 2007, Ellis, 2006, Graves and Tamkun, 2006, Moorman et al., 2006, Orian, 2006, Polo and Almouzni, 2006, Spradling et al., 2006, Jin, 2005, Loppin et al., 2005, Mito et al., 2005, Schwartz and Ahmad, 2005, Zhou, 2005, Heinkoff et al., 2004, McKittrick et al., 2004, McKittrick et al., 2004, Schwartz and Ahmad, 2004, Fahrner and Baylin, 2003, Hennig, 2003, Ahmad and Henikoff, 2002, Ahmad and Henikoff, 2002, Goll and Bestor, 2002, Akhmanova et al., 1997, Akhmanova et al., 1995)

H3.3 A

(Zhang et al., 2023)

H3.3A

(Zhang et al., 2024, McPherson et al., 2023, Weaver et al., 2023, Ábrahám et al., 2022, Yamamoto-Matsuda et al., 2022, Kamiyama et al., 2021, Lindehell et al., 2021, Matsuo, 2021, Leatham-Jensen et al., 2019, Shindo and Amodeo, 2019, Penke et al., 2018, Chen et al., 2015, Rathke et al., 2014, Shevelyov et al., 2009, Doheny et al., 2008, Wagner et al., 2007, Feng et al., 2005)

His-3.3A

(Shevelyov et al., 2009)

His3.3

(Valon et al., 2021, Cavalli, 2006, Kamakaka and Biggins, 2005, Lippman and Martienssen, 2004)

PH3

(Whittaker et al., 2000, Su et al., 1999)

dH3.3A

(Wagner et al., 2007)

Name Synonyms

H3L-like histone

(Mancini, 2003.9.9)

Histone H3.3A

(Doheny et al., 2008)

histone H3.3

(Rathke et al., 2007, Ringrose and Paro, 2007, Mito et al., 2005, Wirbelauer et al., 2005)

histone H3.3 variant

(Bonnefoy et al., 2007)

histone H3.3A

(Thimmegowda et al., 2020, Bindels, 1994.10.20)

histone variant 3.3

(Ellis, 2006)

histone variant H3.3

(Zhou, 2005)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 66 )

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.

33736

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.

C0HL66

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

C0HL66

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q6TXQ1

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.

C0HL66

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33736/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0014857

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0014857

FlyMine - An integrated database for Drosophila genomics

FBgn0014857

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG5825

MARRVEL_MODEL - MARRVEL (model organism gene)

33736

Linkouts

BioGRID - A database of protein and genetic interactions.

59912

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0014857

DroID - A comprehensive database of gene and protein interactions.

FBgn0014857

DRSC - Results frm RNAi screens

FBgn0014857

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

His3.3A_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0014857

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0014857

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG5825

Flygut - An atlas of the Drosophila adult midgut

FBgn0014857

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0014857

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

MIST (protein-protein) - An integrated Molecular Interaction Database

33736

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (160)

The following external sites may use different assemblies or annotations than FlyBase.

1.85

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