FlyBase Gene Report: Dmel\Arp6

General Information

Symbol

Dmel\Arp6

Species

D. melanogaster

Name

Actin-related protein 6

Annotation Symbol

CG11678

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011741

Gene Model Status

Current

Stock Availability

4 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Actr13E, Arp4, dArp6

Key Links

Genomic Location

Cytogenetic map

13E12-13E12

Sequence location

X:15,735,774..15,737,120 [-]

Recombination map

1-51

RefSeq locus

NC_004354 REGION:15735774..15737120

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 (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables chromatin binding

inferred from sequence or structural similarity with UniProtKB:Q9GZN1

(Gene Ontology Curators, 2002-)

enables nucleosome binding

inferred from biological aspect of ancestor with PANTHER:PTN000233887

(GO Reference Genome Project, 2011-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in transcription initiation-coupled chromatin remodeling

inferred from mutant phenotype

(Scacchetti et al., 2020)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in heterochromatin organization

inferred from sequence or structural similarity with UniProtKB:Q9GZN1

(Gene Ontology Curators, 2002-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in chromatin

inferred from direct assay

(Frankel et al., 1997)

located_in nucleus

inferred from direct assay

(Frankel et al., 1997)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

part_of Swr1 complex

inferred from biological aspect of ancestor with PANTHER:PTN000233887

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

ACTIN-RELATED PROTEINS

SWR1 COMPLEX

Protein Family (UniProt)

Belongs to the actin family. ARP6 subfamily. (P45890)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

ACTIN-RELATED PROTEINS -: Actin-related proteins (Arp) share significant sequence identity with actins. Arps broadly fall into two groups: nuclear Arps, involved in chromatin remodeling; and cytoplasmic Arps, associated with actin. (Adapted from PMID:21859859).
SWR1 COMPLEX -: In D.mel, the SWR1 complex is an ATP-dependent histone exchanger that incorporates the histone H2A variant, His2Av. (Adapted from FBrf0245697.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Arp6 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 P45890)

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 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Arp6-RA

FBtr0074203

NM_078610

1347

398

Additional Transcript Data and Comments

Reported size (kB)

1.35 (northern blot)

(Frankel et al., 1994)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Arp6-PA

FBpp0073983

45.4

398

4.71

P45890

NP_511165

AAF48499

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)

398 (aa); 45 (kD predicted)

(Frankel et al., 1994)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

P45890

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Arp6 using the Feature Mapper tool.

External Data

Crossreferences

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

Arp6_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).

-0.64

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

(Frankel et al., 1994)

Additional Descriptive Data

Arp6 transcripts are expressed throughout development with the highest levels in early embryos.

(Frankel et al., 1994)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in chromatin

inferred from direct assay

(Frankel et al., 1997)

located_in nucleus

inferred from direct assay

(Frankel et al., 1997)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Arp6 in JBrowse

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

View exonic expression by developmental stage for Dmel\Arp6

View exonic expression by tissue for Dmel\Arp6

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

FBgn0011741

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

32514/tissue=All

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

FBgn0011741

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011741

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

FBgn0011741

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

CG11678

Flygut - An atlas of the Drosophila adult midgut

FBgn0011741

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 3 )

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 Arp6

Transgenic constructs containing regulatory region of Arp6

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(1)Exel6250

(Ryder, 2004.4.26)

Inferred from location ( 11 )

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

Arp6^GD7361

viable, with Scer\GAL4^pnr-MD237

Arp6^GD7361

viable, with Scer\GAL4^tin.CΔ4

Arp6^GD7361

Sterility

Allele

female fertile, with Scer\GAL4^nanos.PG

Arp6^KK100286

female semi-sterile, with Scer\GAL4^nanos.PG

Arp6^GD7361

Other Phenotypes

Allele

abnormal flight, with Scer\GAL4^Mef2.PR

Arp6^GD7361

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) (27)

Hsap\ACTR6

14 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 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

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) (24)

Rnor\Actr6

14 of 14

Yes

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

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

Yes

Rnor\LOC102552318

1 of 14

Rnor\Potef

1 of 14

Mus musculus (laboratory mouse) (19)

Mmus\Actr6

13 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 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

Xenopus tropicalis (Western clawed frog) (13)

Xtro\actr6

8 of 13

Yes

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (21)

Drer\actr6

14 of 14

Yes

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

Drer\si:ch211-241j12.3

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

Caenorhabditis elegans (Nematode, roundworm) (11)

Cele\arp-6

14 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (12)

Agam\AgaP_AGAP005857

12 of 12

Yes

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

3 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (17)

Atha\ARP6

12 of 13

Yes

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

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (5)

Scer\ARP6

10 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\arp6

12 of 12

Yes

Spom\act1

2 of 12

Spom\arp5

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Arp6. 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) (14)

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

3 of 13

3 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 ( 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?

ACTR6; actin related protein 6

14 of 14

619729

ACTA1; actin alpha 1, skeletal muscle

3 of 14

102610

ACTA2; actin alpha 2, smooth muscle

3 of 14

102620

ACTB; actin beta

3 of 14

102630

Baraitser-Winter syndrome 1

ACTBL2; actin beta like 2

3 of 14

614835

ACTC1; actin alpha cardiac muscle 1

3 of 14

ACTIN, ALPHA, CARDIAC MUSCLE; ACTC1

ACTG1; actin gamma 1

3 of 14

102560

ACTG2; actin gamma 2, smooth muscle

3 of 14

102545

megacystis-microcolon-intestinal hypoperistalsis syndrome

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

Arp6 - Zaf1

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

Arp6 - ac

anti tag coimmunoprecipitation, anti tag western blot

(Hsiao et al., 2023)

Arp6 - ato

anti tag coimmunoprecipitation, anti tag western blot

(Hsiao et al., 2023)

Arp6 - sc

anti tag coimmunoprecipitation, anti tag western blot

(Hsiao et al., 2023)

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.

58864

DroID - A comprehensive database of gene and protein interactions.

FBgn0011741

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

32514

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

ATP-dependent chromatin remodeling

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P45890

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-51

Cytogenetic map

13E12-13E12

Sequence location

X:15,735,774..15,737,120 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

13E12-13E12

Limits computationally determined from genome sequence between P{EP}EP1489 and P{EP}BEST:RE35685^EP1581&P{EP}sd^EP1088

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-51

(FlyBase, 2016)

1-51.9

(Comeron et al., 2012)

(Frankel, 1994.4.18)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

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

Bloomington

65155

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05919}attP40

11678R-1

v108081

v17242

w¹¹¹⁸; P{GD7361}v17242/TM3

Genomic Clones (10)

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

cDNA Clones (23)

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

LD47054

Other clones

DPiM_LD47054

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.

FBgn0011741

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011741

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Frankel et al., 1994)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Actr13E colocalises with Su(var)205 in the centric heterochromatin throughout prepupal development and the two proteins undergo a series of changes in nuclear distribution that coincide with major shifts in nuclear functions.

(Frankel et al., 1997)

Actr13E is the most divergent actin related protein reported with an equally distant relationship to all known actin related proteins.

(Frankel et al., 1994)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Arp6 Actr13E

(FlyBase, 2009-)

Nomenclature comments

'Actr13E' renamed to 'Arp6' to rationalize the nomenclature of Actin-related protein (Arp) genes (by orthology with the mammalian and yeast genes). This gene was originally referred to as 'Arp4' (FBrf0087133, FBrf0098524), but this is misleading as subsequent studies have show that the gene is the ortholog of Arp6 (see FBrf0218773).

(FlyBase, 2009-)

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

ARP

(Frankel et al., 1994)

ARP(13E)

(Frankel et al., 1994)

ARP13E

(Goldstein and Gunawardena, 2000)

Acrp

Actr13E

(Czech et al., 2013, Handler et al., 2013, Handler et al., 2013, Japanese National Institute of Genetics, 2012.5.21)

Arp13E

(Mullins et al., 1996)

Arp4

(Li et al., 2002, Wallrath, 1998, Frankel et al., 1997)

Arp6

(Meyer-Nava et al., 2020, Schroeder et al., 2020, Kollmar, 2015.9.15, Kollmar and Odronitz, 2006)

CG11678

(Llamusi et al., 2013, Keleman et al., 2009.8.5, Perkins et al., 2009, Goldstein and Gunawardena, 2000)

actr13E

(Perkins and Tanentzapf, 2014)

arp4

(Frankel and Mooseker, 1996)

dArp6

(Li et al., 2002, Kato et al., 2001)

Name Synonyms

Actin-related protein 13E

Actin-related protein 6

actin-related protein

(Frankel, 1994.4.18)

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 ( 35 )

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.

32514

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.

P45890

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

P45890

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.

P45890

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0011741

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

32514/tissue=All

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

FBgn0011741

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

FBgn0011741

FlyMine - An integrated database for Drosophila genomics

FBgn0011741

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

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

dme:Dmel_CG11678

MARRVEL_MODEL - MARRVEL (model organism gene)

32514

Linkouts

BioGRID - A database of protein and genetic interactions.

58864

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

FBgn0011741

DroID - A comprehensive database of gene and protein interactions.

FBgn0011741

DRSC - Results frm RNAi screens

FBgn0011741

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

Arp6_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0011741

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011741

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

CG11678

Flygut - An atlas of the Drosophila adult midgut

FBgn0011741

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

TC008881

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

ATP-dependent chromatin remodeling

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

32514

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P45890

References (53)

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

-0.64

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