FB2024_02 , released April 23, 2024
Gene: Dmel\Pex12
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General Information
Symbol
Dmel\Pex12
Species
D. melanogaster
Name
Peroxin 12
Annotation Symbol
CG3639
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031282
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Peroxin 12 (Pex12) encodes a peroxisome protein important for sperm development. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
21E2-21E2
Sequence location
Recombination map
2-1.5
RefSeq locus
NT_033779 REGION:815993..818096
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (12 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 protein transmembrane transporter activity
inferred from sequence or structural similarity with UniProtKB:Q04370
(Gene Ontology Curators, 2002-)
enables ubiquitin protein ligase activity
inferred from sequence or structural similarity with UniProtKB:Q04370
(Gene Ontology Curators, 2002-)
enables ubiquitin-protein transferase activity
inferred from biological aspect of ancestor with PANTHER:PTN000306679
(GO Reference Genome Project, 2011-)
enables zinc ion binding
inferred from electronic annotation with InterPro:IPR017375
(InterPro Project Members, 2004-)
Biological Process (5 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 (5 terms)
CV Term
Evidence
References
involved_in peroxisome organization
inferred from sequence or structural similarity with HGNC:8854
(Faust et al., 2012)
involved_in protein import into peroxisome matrix, receptor recycling
inferred from sequence or structural similarity with UniProtKB:Q04370
(Gene Ontology Curators, 2002-)
involved_in protein import into peroxisome matrix
inferred from biological aspect of ancestor with PANTHER:PTN000306679
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR017375
(InterPro Project Members, 2004-)
involved_in protein monoubiquitination
inferred from biological aspect of ancestor with PANTHER:PTN000306679
(GO Reference Genome Project, 2011-)
involved_in protein polyubiquitination
inferred from sequence or structural similarity with UniProtKB:Q04370
(Gene Ontology Curators, 2002-)
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
part_of peroxisomal importomer complex
inferred from biological aspect of ancestor with PANTHER:PTN000306679
(GO Reference Genome Project, 2011-)
is_active_in peroxisomal membrane
inferred from sequence or structural similarity with UniProtKB:Q04370
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000306679
(GO Reference Genome Project, 2011-)
located_in peroxisomal membrane
inferred from electronic annotation with InterPro:IPR017375
(InterPro Project Members, 2004-)
located_in peroxisome
inferred from sequence or structural similarity with HGNC:8854
(Faust et al., 2012)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the pex2/pex10/pex12 family. (Q9VPT5)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Peroxin 12 (Pex12) encodes a peroxisome protein important for sperm development. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
UNCLASSIFIED RING DOMAIN UBIQUITIN LIGASES -
This group comprises RING domain ubiquitin ligases that do not classify under other groups in 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).
PEROXISOMAL UBIQUITIN LIGASE RETROTRANSLOCON COMPLEX -
The peroxisomal ubiquitin ligase retrotranslocon complex is a transmembrane ubiquitin ligase complex that forms a pore through which the cargo receptor Pex5 is recycled from the peroxisome matrix to the cytosol. Pex5 is ubiquitinated by the E3 ligase activity of the subunits during recycling. Monoubiquitinated Pex5 is extracted from the matrix into the cytosol by the Membrane Extraction Complex ATPase complex. (Adappted from PMID:35768507 and PMID:37743160).
Protein Function (UniProtKB)
Component of a retrotranslocation channel required for peroxisome organization by mediating export of the PEX5 receptor from peroxisomes to the cytosol, thereby promoting PEX5 recycling (PubMed:21669930). The retrotranslocation channel is composed of PEX2, PEX10 and PEX12; each subunit contributing transmembrane segments that coassemble into an open channel that specifically allows the passage of PEX5 through the peroxisomal membrane (By similarity). PEX12 also regulates PEX5 recycling by activating the E3 ubiquitin-protein ligase activity of PEX10 (By similarity). When PEX5 recycling is compromised, PEX12 stimulates PEX10-mediated polyubiquitination of PEX5, leading to its subsequent degradation (By similarity).
(UniProt, Q9VPT5)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Pex12 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 Q9VPT5)

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

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pex12-RA
FBtr0078010
NM_134702
1040
297
Pex12-RB
FBtr0332972
NM_001272915
2104
297
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
Pex12-PA
FBpp0077675
34.5
297
9.09
Q9VPT5
NP_608546
AAF51456
Pex12-PB
FBpp0305188
34.5
297
9.09
Q9VPT5
NP_001259844
AGB92381
Polypeptides with Identical Sequences

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

297 aa isoforms: Pex12-PA, Pex12-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the PEX2-PEX10-PEX12 retrotranslocation channel.

(UniProt, Q9VPT5)
Domain

The three subunits of the retrotranslocation channel (PEX2, PEX10 and PEX12) coassemble in the membrane into a channel with an open 10 Angstrom pore. The RING-type zinc-fingers that catalyze PEX5 receptor ubiquitination are positioned above the pore on the cytosolic side of the complex.

The RING-type zinc-finger is degenerated and only coordinates one zinc ions, preventing E3 ubiquitin-protein ligase activity.

(UniProt, Q9VPT5)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Pex12 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).

-2.01

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
• membrane
(Aradska et al., 2015)
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\Pex12 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pex12
Transgenic constructs containing regulatory region of Pex12
Aberrations (Deficiencies and Duplications) ( 4 )
Inferred from experimentation ( 4 )
Gene disrupted in
Df(2L)Exel6002
(Ryder, 2004.4.26)
Df(2L)Exel7005
(Ryder, 2004.4.26)
Gene not disrupted in
Df(2L)Saf6Δ303
(Weake et al., 2009)
Gene partially disrupted in
Df(2L)MK01
(Blattner et al., 2017)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (4)
Hsap\PEX12
13 of 14
Yes
Yes
Hsap\PEX10
1 of 14
No
No
1  
Hsap\RNF130
1 of 14
No
No
Hsap\RNF145
1 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (4)
Rnor\Pex12
14 of 14
Yes
Yes
Rnor\Pex10
1 of 14
No
No
Rnor\Rnf130
1 of 14
No
No
Rnor\Rnf145
1 of 14
No
No
Mus musculus (laboratory mouse) (4)
Mmus\Pex12
13 of 14
Yes
Yes
Mmus\Pex10
1 of 14
No
No
Mmus\Rnf130
1 of 14
No
No
Mmus\Rnf145
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (5)
Xtro\pex12
7 of 13
Yes
Yes
Xtro\ppp3r1
6 of 13
No
No
Xtro\gpatch1
1 of 13
No
No
Xtro\pex10
1 of 13
No
No
Xtro\rnf145
1 of 13
No
No
Danio rerio (Zebrafish) (3)
Drer\pex12
14 of 14
Yes
Yes
Drer\pex10
1 of 14
No
No
Drer\rnf145b
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\prx-12
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP010497
11 of 12
Yes
Yes
Agam\AgaP_AGAP000928
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (2)
Atha\PEX12
13 of 13
Yes
Yes
Atha\PEX10
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\PEX12
10 of 13
Yes
Yes
Scer\PEX10
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\SPAPB17E12.03
9 of 12
Yes
Yes
Spom\pas4
1 of 12
No
No
Spom\SPCC548.05c
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Pex12. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (3)
CG13605
1 of 13
Pex2
1 of 13
Pex10
1 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 ( 2 )
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?
PEX12; peroxisomal biogenesis factor 12
13 of 14
601758
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
esyN Network Diagram
Interactions Browser
MIST Molecular Interaction Search Tool
Summary of Genetic Interactions
esyN Network Diagram
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Component of the PEX2-PEX10-PEX12 retrotranslocation channel.
(UniProt, Q9VPT5 )
Linkouts
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-1.5
Cytogenetic map
21E2-21E2
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
21E2-21E2
Limits computationally determined from genome sequence between P{lacW}l(2)k09610k09610&P{lacW}Sk09538a and P{PZ}l(2)1068510685&P{lacW}Tango14k00619
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

2-1.5

(FlyBase, 2016)

2-0.7

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (9)
Genomic Clones (12)
 

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

cDNA Clones (6)
 

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.

cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    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
        Nomenclature History
        Source for database identify of

        Source for identity of: pex12 CG3639

        (Chen et al., 2010)
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (7)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 34 )
        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.
        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.
        UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        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.
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Flygut - An atlas of the Drosophila adult midgut
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        References (42)