FlyBase Gene Report: Dmel\Pex6

General Information

Symbol

Dmel\Pex6

Species

D. melanogaster

Name

Peroxin 6

Annotation Symbol

CG11919

Feature Type

protein_coding_gene

FlyBase ID

FBgn0033564

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

47C5-47C5

Sequence location

2R:10,879,974..10,883,202 [+]

Recombination map

2-63

RefSeq locus

NT_033778 REGION:10879974..10883202

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 (11 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR003959, InterPro:IPR003960

(InterPro Project Members, 2004-)

enables ATP hydrolysis activity

inferred from biological aspect of ancestor with PANTHER:PTN004603074

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR003959, InterPro:IPR003960

(InterPro Project Members, 2004-)

enables protein transporter activity

inferred from sequence or structural similarity with UniProtKB:Q13608

(Gene Ontology Curators, 2002-)

enables ubiquitin-modified protein reader activity

inferred from sequence or structural similarity with UniProtKB:Q13608

(Gene Ontology Curators, 2002-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in peroxisome organization

inferred from mutant phenotype

(Mast et al., 2011)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in peroxisome organization

inferred from sequence or structural similarity with UniProtKB:Q13608

(Faust et al., 2012)

involved_in protein import into peroxisome matrix, receptor recycling

inferred from sequence or structural similarity with UniProtKB:Q13608

(Gene Ontology Curators, 2002-)

involved_in protein import into peroxisome matrix

inferred from biological aspect of ancestor with PANTHER:PTN000554448

(GO Reference Genome Project, 2011-)

involved_in protein unfolding

inferred from sequence or structural similarity with UniProtKB:Q13608

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN000554448

(GO Reference Genome Project, 2011-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in peroxisome

inferred from direct assay

(Baron et al., 2016)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

is_active_in cytosol

inferred from biological aspect of ancestor with PANTHER:PTN000554448

(GO Reference Genome Project, 2011-)

is_active_in peroxisomal membrane

inferred from biological aspect of ancestor with PANTHER:PTN000554448

(GO Reference Genome Project, 2011-)

located_in peroxisome

inferred from sequence or structural similarity with UniProtKB:Q13608

(Faust et al., 2012)

Gene Group (FlyBase)

PEROXINS

UNCLASSIFIED ATPASES

PEROXISOMAL MEMBRANE EXTRACTION COMPLEX

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

ATP hydrolysis activity
RHEA 13065:

Summaries

Gene Group (FlyBase)

PEROXINS -: Peroxisomes are eukaryotic organelles critical for the metabolism of fatty acids, particularly very-long-chain fatty acids, and other metabolites. The peroxin genes encode proteins required for peroxisome biogenesis. (Adapted from FBrf0209624).
UNCLASSIFIED ATPASES -: This group comprises ATPases that do not classify under other groups in FlyBase.
PEROXISOMAL MEMBRANE EXTRACTION COMPLEX -: Peroxisomal membrane extraction complex is an ATPase chaperone complex that interacts with monoubiquitinated Pex5 cargo receptor in the peroxisomal ubiquitin ligase retrotranslocon complex. It promotes the ATP-dependent unfolding of Pex5 and extracts it into the cytosol. This drives peroxisomal matrix import cycle, allowing the cargo receptor to be available of further rounds import. (Adapted from PMID:36442669 and PMID:36117327.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Pex6 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 A1Z8D1)

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 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Pex6-RC

FBtr0339471

NM_001169643

2953

897

Pex6-RD

FBtr0339472

NM_001032232

2820

899

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

Pex6-PC

FBpp0308554

101.1

897

7.26

FBpp0308555

101.5

899

8.28

A1Z8D1

NP_001027403

AAF58736

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

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\Pex6 using the Feature Mapper tool.

External Data

Crossreferences

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

Pex6_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).

0.90

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 4

yolk

(Pridie and Simmonds, 2021)

embryonic cortex

(Pridie and Simmonds, 2021)

Additional Descriptive Data

A high level of Pex6 FISH signal is observed in the yolk and at the cortex of the syncytial blastoderm. During gastrulation, it is close to background levels.

(Pridie and Simmonds, 2021)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in peroxisome

inferred from direct assay

(Baron et al., 2016)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pex6 in JBrowse

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

View exonic expression by developmental stage for Dmel\Pex6

View exonic expression by tissue for Dmel\Pex6

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

3772165/tissue=All

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

FBgn0033564

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033564

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

FBgn0033564

Flygut - An atlas of the Drosophila adult midgut

FBgn0033564

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Pex6

Transgenic constructs containing regulatory region of Pex6

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 10 )

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

Pex6^EY09695

Sterility

Allele

fertile

Pex6^EY09695

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) (20)

Hsap\PEX6

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

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) (7)

Rnor\Pex6

10 of 14

Yes

Rnor\Atad2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (6)

Mmus\Pex6

9 of 14

Yes

Mmus\Atad2

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (16)

Xtro\pex6

8 of 13

Yes

Xtro\atad1

1 of 13

Xtro\atad2b

1 of 13

Yes

Xtro\atad2

1 of 13

Yes

Xtro\bcs1l

1 of 13

Xtro\fignl2

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (6)

Drer\pex6

10 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (15)

Cele\prx-6

11 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

Anopheles gambiae (African malaria mosquito) (17)

Agam\AgaP_AGAP001612

10 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (60)

Atha\PEX6

9 of 13

Yes

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

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) (16)

Scer\PEX6

9 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Schizosaccharomyces pombe (Fission yeast) (7)

Spom\pex6

9 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Pex6. 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) (20)

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

1 of 13

1 of 13

1 of 13

1 of 13

nmd

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

peroxisome biogenesis disorder 4A

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 3 )

Human Ortholog

Disease

Evidence

References

PEX6; peroxisomal biogenesis factor 6

model of Heimler syndrome 2

IEA

(FlyBase, 2019-)

model of peroxisome biogenesis disorder 4A

IEA

(FlyBase, 2019-)

model of Peroxisome biogenesis disorder 4B

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?

PEX6; peroxisomal biogenesis factor 6

10 of 14

601498

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

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

DroID - A comprehensive database of gene and protein interactions.

FBgn0033564

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.

Peroxisome

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-63

Cytogenetic map

47C5-47C5

Sequence location

2R:10,879,974..10,883,202 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

47C5-47C5

Limits computationally determined from genome sequence between P{lacW}l(2)k15826^k15826&P{EP}EP471 and P{EP}shn^EP2359&P{EP}shn^EP644

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-63

(FlyBase, 2016)

2-62.3

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

17593

y¹ w^67c23; P{EPgy2}Pex6^EY09695 Hao^EY09695

NIG-Fly

2RG-1045

y² VhaAC39-1^cho-1 v¹; P{U6-Pex6.NIG.sgRNA}attP40/CyO

VDRC

v32430

w¹¹¹⁸; P{GD8663}v32430

v32429

w¹¹¹⁸; P{GD8663}v32429/TM3

v318189

PBac{fTRG00692.sfGFP-TVPTBF}VK00033

Genomic Clones (15)

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

cDNA Clones (16)

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

GH14288

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.

FBgn0033564

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0033564

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Relationship to Other Genes

Source for database merge of

Additional comments

Dicistronic annotation CG30019 split out into separate annotations for each open reading frame, CG11919 and CG18003 in release 4.2 of the genome annotation.

(FlyBase Genome Annotators, 2005)

Nomenclature History

Source for database identify of

Source for identity of: Pex6 CG11919

(Mast et al., 2011)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG11919

(National Institute of Genetics Fly Stocks, 2022-, Baron et al., 2016, Sarov et al., 2016, Faust et al., 2012, Faust et al., 2012, Mast et al., 2011, Ellis and Carney, 2010)

CG30019

(Pedra et al., 2004, Giot et al., 2003)

DmCG11919

(Frohlich, 2001)

DmelPex6

(Mast et al., 2011)

PEX6

(Anderson-Baron and Simmonds, 2018, Baron et al., 2016, Faust et al., 2012)

Pex6

(Pridie and Simmonds, 2021, Anderson-Baron and Simmonds, 2018, Bhadra et al., 2016, Mast et al., 2011, FlyBase Genome Annotators, 2002-2003)

Name Synonyms

Peroxin 6

Secondary FlyBase IDs

FBgn0050019
FBtr0088229
FBpp0087324
FBtr0088230
FBpp0087325
FBtr0088231
FBpp0087326

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 39 )

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.

3772165

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.

A1Z8D1

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

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

A1Z8D1

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

3772165/tissue=All

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

FBgn0033564

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

FBgn0033564

FlyMine - An integrated database for Drosophila genomics

FBgn0033564

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

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

dme:Dmel_CG11919

MARRVEL_MODEL - MARRVEL (model organism gene)

3772165

Linkouts

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

FBgn0033564

DroID - A comprehensive database of gene and protein interactions.

FBgn0033564

DRSC - Results frm RNAi screens

FBgn0033564

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

Pex6_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033564

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0033564

Flygut - An atlas of the Drosophila adult midgut

FBgn0033564

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

TC002647

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

Peroxisome

References (34)

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

0.90

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