FlyBase Gene Report: Dmel\His4r

General Information

Symbol

Dmel\His4r

Species

D. melanogaster

Name

Histone H4 replacement

Annotation Symbol

CG3379

Feature Type

protein_coding_gene

FlyBase ID

FBgn0013981

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Core component of nucleosome. 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. Involved in recruitment of Parp1 to chromatin and regulates its activity; mediates nucleosome-dependent activation of Parp1 (PubMed:17827147). (UniProt, P84040)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

H4r

Key Links

Genomic Location

Cytogenetic map

88C9-88C9

Sequence location

3R:14,625,755..14,626,614 [+]

Recombination map

3-55

RefSeq locus

NT_033777 REGION:14625755..14626614

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 (5 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR001951, InterPro:IPR019809

(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:IPR001951

(InterPro Project Members, 2004-)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in chromatin organization

inferred from mutant phenotype

(Faragó et al., 2021)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of nucleosome

inferred from electronic annotation with InterPro:IPR019809

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

Protein Family (UniProt)

Belongs to the histone H4 family. (P84040)

Protein Signatures (InterPro)

Summaries

Protein Function (UniProtKB)

(UniProt, P84040)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\His4r 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 P84040)

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

PDB - An information portal to biological macromolecular structures

Comments on Gene Model

Gene model reviewed during 5.46

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

Gene model reviewed during 5.55

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

His4r-RA

FBtr0082962

NM_169592

576

103

His4r-RB

FBtr0082963

NM_169593

645

103

His4r-RC

FBtr0082964

NM_079628

753

103

His4r-RD

FBtr0334029

NM_001275647

553

103

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

His4r-PA

FBpp0082421

11.4

103

11.91

FBpp0082422

11.4

103

11.91

FBpp0082423

11.4

103

11.91

FBpp0306146

11.4

103

11.91

P84040

NP_001262576

AGB95957

Polypeptides with Identical Sequences

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

103 aa isoforms: His4r-PA, His4r-PB, His4r-PC, His4r-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

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 Nasp; the interaction is probably indirect, mediated by histone H3 (PubMed:36930688). Interacts with Parp1 (via C-terminus); the interaction is direct and regulates Parp1 enzymatic activity (PubMed:17827147, PubMed:24508391).

(UniProt, P84040)

Post Translational Modification

Acetylated on Lys-6 (H4K5ac) and Lys-13 (H4K12ac) during prophase I of meiosis. Phosphorylation of H2A 'Thr-119' is a prerequisite for H4 Lys-6 acetylation but not for H4 Lys-13 acetylation (PubMed:16230526, PubMed:18327897). Acetylated on Lys-6 and Lys-13 by the Ada2a-containing (ATAC) histone acetyltransferase complex (PubMed:22796493).

(UniProt, P84040)

Domain

The N-terminal tail is essential for nucleosome dependent activation of Parp1.

(UniProt, P84040)

Crossreferences

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

PDB - An information portal to biological macromolecular structures

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\His4r using the Feature Mapper tool.

External Data

Crossreferences

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

His4r_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).

0.11

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

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

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\His4r in JBrowse

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

View exonic expression by developmental stage for Dmel\His4r

View exonic expression by tissue for Dmel\His4r

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

41773/tissue=All

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

FBgn0013981

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0013981

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

FBgn0013981

Flygut - An atlas of the Drosophila adult midgut

FBgn0013981

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 11 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of His4r

Transgenic constructs containing regulatory region of His4r

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 6 )

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

partially lethal

viable

His4r^Δ

Sterility

Allele

fertile

fertile (with His4r^LL05512)

His4r^Δ42

fertile (with His4r^Δ42)

His4r^LL05512

sterile

His4r^LL05512

Other Phenotypes

Allele

abnormal heat stress response | adult stage

His4r^Δ42

some die during P-stage

His4r^Δ42

suppressor of variegation | adult stage | dominant

His4r^Δ42

Phenotype manifest in

Allele

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) (15)

Hsap\H4C9

9 of 14

Yes

Hsap\H4C7

5 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 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) (2)

Rnor\Hist1h4b

8 of 14

Yes

Rnor\Hist2h4

1 of 14

Mus musculus (laboratory mouse) (13)

Mmus\H4c8

10 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

Xenopus tropicalis (Western clawed frog) (7)

Xtro\h4c1

7 of 13

Yes

Xtro\h4c3

2 of 13

Xtro\cenpt

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (9)

Drer\si:ch211-113a14.17

8 of 14

Yes

Drer\zgc:163040

8 of 14

Yes

Drer\si:ch73-368j24.1

4 of 14

Yes

Drer\si:dkey-261m9.17

2 of 14

Yes

Drer\cenpt

1 of 14

Yes

Drer\hist1h4l

1 of 14

Drer\si:ch211-113a14.6

1 of 14

Drer\si:dkey-108k21.12

1 of 14

Drer\zgc:153409

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (16)

Cele\his-14

10 of 14

Yes

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) (8)

Agam\AgaP_AGAP012558

10 of 12

Yes

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (8)

Atha\HIS4

11 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\HHF1

12 of 13

Yes

Scer\HHF2

3 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\hhf3

10 of 12

Yes

Spom\hhf1

3 of 12

Spom\hhf2

2 of 12

Spom\SPBC800.13

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:His4r. 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) (22)

4 of 13

4 of 13

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 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 ( 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?

H4C9; H4 clustered histone 9

9 of 14

602833

TESSADORI-BICKNELL-VAN HAAFTEN NEURODEVELOPMENTAL SYNDROME 4; TEBIVANED4

H4C7; H4 clustered histone 7

5 of 14

602832

H4C13; H4 clustered histone 13

4 of 14

602831

H4C16; H4 histone 16

3 of 14

615069

H4C1; H4 clustered histone 1

3 of 14

602822

H4C2; H4 clustered histone 2

3 of 14

602829

H4C3; H4 clustered histone 3

3 of 14

602827

TESSADORI-BICKNELL-VAN HAAFTEN NEURODEVELOPMENTAL SYNDROME 1; TEBIVANED1

H4C4; H4 clustered histone 4

3 of 14

602823

H4C5; H4 clustered histone 5

3 of 14

602830

TESSADORI-BICKNELL-VAN HAAFTEN NEURODEVELOPMENTAL SYNDROME 3; TEBIVANED3

H4C6; H4 clustered histone 6

3 of 14

602824

H4C8; H4 clustered histone 8

3 of 14

602828

H4C11; H4 clustered histone 11

3 of 14

602826

TESSADORI-BICKNELL-VAN HAAFTEN NEURODEVELOPMENTAL SYNDROME 2; TEBIVANED2

H4C12; H4 clustered histone 12

3 of 14

602825

H4C14; H4 clustered histone 14

3 of 14

142750

H4C15; H4 clustered histone 15

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

His4r - Fas2

experimental knowledge based

(Guruharsha et al., 2011)

His4r - Taf9

experimental knowledge based

(Guruharsha et al., 2011)

His4r - retinin

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

His4

enhanceable

His4r

(Crain et al., 2022)

External Data

Subunit Structure (UniProtKB)

(UniProt, P84040 )

Linkouts

BioGRID - A database of protein and genetic interactions.

66847

DroID - A comprehensive database of gene and protein interactions.

FBgn0013981

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

41773

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-55

Cytogenetic map

88C9-88C9

Sequence location

3R:14,625,755..14,626,614 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88C9-88C9

Limits computationally determined from genome sequence between P{PZ}put¹⁰⁴⁶⁰ and P{EP}CG33967^EP666

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

88C9-88C10

(Akhmanova, 1996.4.22)

88C-88C

(determined by in situ hybridisation)

(Akhmanova et al., 1996)

Experimentally Determined Recombination Data

Location

3-55

(FlyBase, 2016)

3-54.2

(Comeron et al., 2012)

(Akhmanova, 1996.4.22)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

51172

y¹ v¹; P{TRiP.HMJ21134}attP40

15970

y¹ w^67c23; P{EPgy2}His4r^EY06726

34816

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00126}attP2

Kyoto

141607

y^* w^*; P{FRT(w^hs)}2A P{neoFRT}82B PBac{SAstopDsRed}LL05512 P{Car20y}96E/TM6B, Tb¹

NIG-Fly

HMJ21134

y¹ v¹; P{TRiP.HMJ21134}attP40/CyO

VDRC

v330514

P{VSH330514}attP40

Genomic Clones (22)

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

cDNA Clones (421)

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.

FBgn0013981

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0013981

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

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)

Identification and characterisation of histone H4 replacement genes from D.melanogaster and D.hydei.

(Akhmanova et al., 1996)

Relationship to Other Genes

Source for database merge of

Source for merge of: His4r BcDNA:RH52884

(FlyBase, 1996-)

Additional comments

Source for merge of His4r BcDNA:RH52884 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

BcDNA:RH52884

CG3379

(Meadows, 2018.4.4, Kolkhof et al., 2017, Rosa-Ferreira et al., 2015, Jaspers et al., 2012, Cammarato et al., 2011, Ni et al., 2011.7.19, Müller et al., 2010, Ni et al., 2010.12.1)

FBtr0082962

(Li et al., 2012)

H4r

(Ábrahám et al., 2022, Llorens-Giralt et al., 2021, Matsuo, 2021, Horard and Loppin, 2015, Rathke et al., 2014, Akhmanova, 1996.4.22, Akhmanova, 1996.4.22, Akhmanova et al., 1996)

His4-88CD

His4R

(Goldstein and Ahmad, 2005)

Name Synonyms

Histone H4 replacement

(Jaspers et al., 2012, Cammarato et al., 2011, Pedersen et al., 2010)

Secondary FlyBase IDs

FBgn0064800

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 70 )

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.

41773

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.

P84040

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

P84040

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

A0A0B4KFZ9

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.

P84040

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

41773/tissue=All

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

FBgn0013981

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

FBgn0013981

FlyMine - An integrated database for Drosophila genomics

FBgn0013981

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

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

dme:Dmel_CG3379

MARRVEL_MODEL - MARRVEL (model organism gene)

41773

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

66847

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

FBgn0013981

DroID - A comprehensive database of gene and protein interactions.

FBgn0013981

DRSC - Results frm RNAi screens

FBgn0013981

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

His4r_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0013981

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0013981

Flygut - An atlas of the Drosophila adult midgut

FBgn0013981

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

TC034494

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

41773

References (71)

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

0.11

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