FlyBase Gene Report: Dmel\His3.3B

General Information

Symbol

Dmel\His3.3B

Species

D. melanogaster

Name

Histone H3.3B

Annotation Symbol

CG8989

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004828

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Summary

Histone H3.3B (His3.3B) encodes one of two single copy histone H3 variants. His3.3A and His3.3B transcription is not under control of the cell cycle. His3.3B has a long 3'-UTR (> 1500 nucleotides) and can be processed at different polyadenylation sites which are tissue-specific. [Date last reviewed: 2019-03-21] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

H3.3, H3.3B, His3.3, histone H3.3, PH3

Key Links

Genomic Location

Cytogenetic map

8C14-8C14

Sequence location

X:9,152,523..9,156,669 [-]

Recombination map

1-26

RefSeq locus

NC_004354 REGION:9152523..9156669

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 (7 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables structural constituent of chromatin

inferred from genetic interaction with FLYBASE:His3.3A; FB:FBgn0014857

(Sakai et al., 2009)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables DNA binding

non-traceable author statement

(Fretzin et al., 1991)

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

(InterPro Project Members, 2004-)

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-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in nucleosome assembly

non-traceable author statement

(Fretzin et al., 1991)

Cellular Component (3 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 (2 terms)

CV Term

Evidence

References

part_of nucleosome

non-traceable author statement

(Fretzin et al., 1991)

inferred from electronic annotation with InterPro:IPR000164

(InterPro Project Members, 2004-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN008517671

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the histone H3 family. (C0HL67)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Protein Function (UniProtKB)

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, C0HL67)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\His3.3B 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 C0HL67)

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.50

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

His3.3B-RA

FBtr0071345

NM_078540

1399

136

His3.3B-RB

FBtr0071346

NM_167180

1537

136

His3.3B-RC

FBtr0071347

NM_176719

1519

136

His3.3B-RE

FBtr0340343

NM_001272445

2114

136

Additional Transcript Data and Comments

Reported size (kB)

2.4, 1.7, 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

His3.3B-PA

FBpp0071280

15.3

136

11.83

FBpp0071281

15.3

136

11.83

FBpp0071282

15.3

136

11.83

FBpp0309302

15.3

136

11.83

P84249

NP_001259374

AGB95217

Polypeptides with Identical Sequences

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

136 aa isoforms: His3.3B-PA, His3.3B-PB, His3.3B-PC, His3.3B-PE

Additional Polypeptide Data and Comments

Reported size (kDa)

136 (aa)

(Akhmanova et al., 1995, Fretzin et al., 1991)

Comments

His3.3A protein and His3.3B protein are identical in amino acid sequence. The genes differ substantially in their untranslated regions.

(Akhmanova et al., 1995)

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, C0HL67)

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, C0HL67)

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

C0HL67

Mapped Features

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

-0.88

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Akhmanova et al., 1995)

adult stage | female

(Akhmanova et al., 1995)

adult stage | male

(Akhmanova et al., 1995)

oogenesis & adult stage | female

ovary

(Akhmanova et al., 1995)

spermatogenesis & adult stage

testis

(Akhmanova et al., 1995)

Additional Descriptive Data

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)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

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\His3.3B in JBrowse

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

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

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

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

31848/tissue=All

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

FBgn0004828

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004828

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

FBgn0004828

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

CG8989

Flygut - An atlas of the Drosophila adult midgut

FBgn0004828

Images

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 ( 22 )

For All Alleles Carried on Transgenic Constructs Show

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

Transgenic constructs containing regulatory region of His3.3B

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 15 )

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

viable

His3.3B^K9R

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

His3.3B^GD4749

viable, with Scer\GAL4^Mef2.PR

His3.3B^GD4749

viable, with Scer\GAL4^pnr-MD237

His3.3B^GD4749

viable, with Scer\GAL4^tin.CΔ4

His3.3B^GD4749

Sterility

Allele

fertile

His3.3B^K9R

sterile, with His3.3B^K9R.tg

His3.3B^K9R

sterile, with His3.3B^K9R

His3.3B^K9R.tg

Phenotype manifest in

Allele

chromatin

His3.3B^K9R

chromosome, telomeric region

His3.3B^K9R

polytene chromosome

His3.3B^K9R

polytene chromosome chromocenter

His3.3B^K9R

wing disc

His3.3B^K9R

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) (21)

Hsap\H3-3A

12 of 14

Yes

6 of 14

6 of 14

5 of 14

5 of 14

5 of 14

4 of 14

Yes

Hsap\H3Y2

3 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (18)

Rnor\H3f3b

11 of 14

Yes

7 of 14

6 of 14

6 of 14

5 of 14

Yes

Rnor\RGD1564447

3 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Rnor\Hist1h3b

1 of 14

Rnor\LOC690126

1 of 14

Yes

Rnor\LOC100910095

1 of 14

Yes

Rnor\LOC102548682

1 of 14

Rnor\LOC102549173

1 of 14

Rnor\LOC103691547

1 of 14

Yes

Rnor\LOC108348882

1 of 14

Yes

Rnor\LOC108349691

1 of 14

Yes

Mus musculus (laboratory mouse) (18)

Mmus\H3f3a

10 of 14

Yes

Mmus\H3c8

6 of 14

Mmus\H3c14

6 of 14

Mmus\H3f3c

6 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

Yes

Mmus\Gm12657

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (7)

Xtro\h3f3b

9 of 13

Yes

Xtro\h3c14

4 of 13

Xtro\cenpa

3 of 13

Yes

2 of 13

2 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (6)

Drer\h3f3c

9 of 14

Yes

Drer\hist2h3c

5 of 14

Drer\zgc:173552

5 of 14

Yes

Drer\hist2h3ca1

4 of 14

Drer\cenpa

3 of 14

Yes

Drer\h3f3a

2 of 14

Caenorhabditis elegans (Nematode, roundworm) (23)

Cele\his-71

11 of 14

Yes

Cele\his-72

8 of 14

Yes

Cele\his-74

8 of 14

Yes

6 of 14

5 of 14

3 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (6)

Agam\AgaP_AGAP001813

10 of 12

Yes

4 of 12

4 of 12

4 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (8)

Atha\AT3G27360

7 of 13

Yes

6 of 13

6 of 13

5 of 13

4 of 13

3 of 13

2 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\HHT1

9 of 13

Yes

Scer\CSE4

1 of 13

Scer\HHT2

1 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\hht3

9 of 12

Yes

Spom\cnp1

2 of 12

Spom\hht1

2 of 12

Spom\hht2

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:His3.3B. 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)

His3:CG31613

11 of 13

His3.3A

4 of 13

cid

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

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

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 ( 1 )

Human Ortholog

Disease

Evidence

References

H3-3A; H3.3 histone A

model of Bryant-Li-Bhoj neurodevelopmental syndrome 1

IEA

(FlyBase, 2019-)

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?

H3-3A; H3.3 histone A

12 of 14

H3 HISTONE, FAMILY 3A; H3F3A

BRYANT-LI-BHOJ NEURODEVELOPMENTAL SYNDROME 1; BRYLIB1

Bryant-Li-Bhoj neurodevelopmental syndrome 1

H3-5; H3.5 histone

6 of 14

616134

H3C14; H3 clustered histone 14

6 of 14

142780

H3-7; H3.7 histone (putative)

5 of 14

H3-4; H3.4 histone, cluster member

5 of 14

602820

H3C1; H3 clustered histone 1

5 of 14

602810

H3Y1; H3.Y histone 1

4 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

RNA-protein

Physical Interaction

Assay

References

His3.3B - Ubx

anti tag coimmunoprecipitation, quantitative reverse transcription pcr

(Carnesecchi et al., 2022)

protein-protein

Physical Interaction

Assay

References

His3.3B - Caf1-105

tandem affinity purification, western blot, Identification by mass spectrometry

(Fromental-Ramain et al., 2017)

His3.3B - Daxx

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

(Fromental-Ramain et al., 2017)

His3.3B - Dek

anti tag coimmunoprecipitation, western blot, pull down

(Sawatsubashi et al., 2010)

His3.3B - Hira

tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3B - Nap1

tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3B - Pex14

experimental knowledge based

(Guruharsha et al., 2011)

His3.3B - Pex5

experimental knowledge based

(Guruharsha et al., 2011)

His3.3B - RpS15Ab

experimental knowledge based

(Guruharsha et al., 2011)

His3.3B - asf1

tandem affinity purification, Identification by mass spectrometry, western blot

(Fromental-Ramain et al., 2017)

His3.3B - βTub85D

experimental knowledge based

(Guruharsha et al., 2011)

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

BRWD3

suppressible

His3.3B

(Chen et al., 2015)

suppressible

His3.3B

(Schneiderman et al., 2010)

External Data

Subunit Structure (UniProtKB)

(UniProt, C0HL67 )

Linkouts

BioGRID - A database of protein and genetic interactions.

58303

DroID - A comprehensive database of gene and protein interactions.

FBgn0004828

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

31848

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

1-26

Cytogenetic map

8C14-8C14

Sequence location

X:9,152,523..9,156,669 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

8C14-8C14

Limits computationally determined from genome sequence between P{EP}EP1450&P{EP}EP1356 and P{EP}EP912^EP912

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

8C-8D

(determined by in situ hybridisation)

(Zhang, 1996.10.14)

Position at variance with that in FBrf0082998.

(Zhang, 1996.10.14)

Experimentally Determined Recombination Data

Location

1-26

(FlyBase, 2016)

1-28.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

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

Bloomington

11274

w¹¹¹⁸ P{EP}His3.3B^EP1598

34940

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00148}attP2

68240

y¹ w^* His3.3B⁰; His3.3A^2X1/CyO, S²

98089

P{hsp70-FLP}1, w^* P+PBac{XP3.RB5}His3.3B^KO; His3.3A^KO/SM6b

Korea

11415

P{EP}His3.3B^G11006

Kyoto

104563

y^* w^* P{GawB}His3.3B^NP4000 / FM7c

NIG-Fly

8989R-2

P{NIG.8989R}2

VDRC

v12771

w¹¹¹⁸; P{GD4749}v12771

v16176

w¹¹¹⁸; P{GD7175}v16176

Genomic Clones (17)

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

cDNA Clones (349)

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

LD17717

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.

FBgn0004828

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004828

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)

His3.3B 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)

Isolated from a D.melanogaster embryo cDNA library using a chicken H3.3B clone as a probe.

(Fretzin et al., 1991)

A His3.3B cDNA has been cloned and sequenced.

(Fretzin et al., 1991)

Encodes a Histone-H3 variant.

Relationship to Other Genes

Source for database merge of

Source for merge of: His3.3B anon- EST:fe1B6

(FlyBase, 1996-)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: His3.3B CG8989

(Beasley, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (19)

Reported As

Symbol Synonym

CG8989

(Rosa-Ferreira et al., 2015, Cammarato et al., 2011, Ni et al., 2011.7.19, Schneiderman et al., 2010, Quinones-Coello, 2007, Wagner et al., 2007)

H3.3

(Tirgar et al., 2023, Shindo et al., 2022, Chaouch et al., 2021, Llorens-Giralt et al., 2021, Fromental-Ramain et al., 2017, Shih et al., 2016, Horard and Loppin, 2015, Vlijm et al., 2015, Li and Zhou, 2013, Ito 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, Braunschweig et al., 2009, Landmann et al., 2009, Schneiderman and Ahmad, 2008, Bell et al., 2007, de Wit et al., 2007, Konev et al., 2007, Li et al., 2007, Pinnola et al., 2007, Ellis, 2006, Graves and Tamkun, 2006, Moorman et al., 2006, Orian, 2006, Spradling et al., 2006, Jin, 2005, Mito et al., 2005, Zhou, 2005, Heinkoff et al., 2004, McKittrick et al., 2004, McKittrick et al., 2004, Schwartz and Ahmad, 2004, Hennig, 2003, Ahmad and Henikoff, 2002, Goll and Bestor, 2002, Akhmanova et al., 1997, Fretzin et al., 1991)

H3.3B

(Brown et al., 2024, Zhang et al., 2024, McPherson et al., 2023, Salzler et al., 2023, Lindehell et al., 2021, Matsuo, 2021, Leatham-Jensen et al., 2019, Armstrong et al., 2018, Penke et al., 2018, Chen et al., 2015, Rathke et al., 2014, Somma et al., 2008, Wagner et al., 2007, Feng et al., 2005, Page et al., 2000, Akhmanova et al., 1995)

His 3.3 B

(Konev et al., 2016)

His 3.3B

(Taliaferro et al., 2013)

His3.3

(Valon et al., 2021, Cavalli, 2006, Kamakaka and Biggins, 2005, Lippman and Martienssen, 2004, Ahmad and Henikoff, 2002)

His3.3B

(Yu and Lesch, 2024, Bilder et al., 2021, Michki et al., 2021, Dorafshan et al., 2019, Fear et al., 2016, Kwon et al., 2013, Thomae et al., 2013, Hödl and Basler, 2012, Japanese National Institute of Genetics, 2012.5.21, Schneiderman et al., 2012, Kallappagoudar et al., 2010, Mourikis et al., 2010, Schneiderman et al., 2010, Hödl and Basler, 2009, Sakai et al., 2009, Maines et al., 2007, Quinones-Coello, 2007, Cardoso et al., 2006, Dorus et al., 2006)

His3.3b

(Vesala et al., 2024)

HisH3-3Q

PH3

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

anon-EST:fe1B6

dH3.3B

(Wagner et al., 2007)

Name Synonyms

Histone H3-3Q

Histone H3.3B

(Cammarato et al., 2011)

HistoneH3

(Bossuyt et al., 2009)

anon-fast-evolving-1B6

histone H3.3

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

histone variant 3.3

(Ellis, 2006)

histone variant H3.3

(Zhou, 2005)

Secondary FlyBase IDs

FBgn0025266

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 68 )

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.

31848

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.

C0HL67

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

C0HL67

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.

C0HL67

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

31848/tissue=All

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

FBgn0004828

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

FBgn0004828

FlyMine - An integrated database for Drosophila genomics

FBgn0004828

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

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

dme:Dmel_CG8989

MARRVEL_MODEL - MARRVEL (model organism gene)

31848

Linkouts

BioGRID - A database of protein and genetic interactions.

58303

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

FBgn0004828

DroID - A comprehensive database of gene and protein interactions.

FBgn0004828

DRSC - Results frm RNAi screens

FBgn0004828

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004828

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004828

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

CG8989

Flygut - An atlas of the Drosophila adult midgut

FBgn0004828

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

FBgn0004828

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

TC005398

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

31848

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

References (136)

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

-0.88

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