FB2024_03 , released June 25, 2024
Gene: Dmel\Pldn
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General Information
Symbol
Dmel\Pldn
Species
D. melanogaster
Name
Pallidin
Annotation Symbol
CG14133
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036192
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Pallidin (Pldn) encodes a core component of the biogenesis of lysosome-related organelles (BLOC-1) complex. It is involved in pigment granule biogenesis and synaptic vesicle recycling at the neuromuscular junction. [Date last reviewed: 2018-10-25] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
68D2-68D2
Sequence location
Recombination map
3-36
RefSeq locus
NT_037436 REGION:11689631..11691399
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 (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein binding
inferred from physical interaction with FLYBASE:Blos1; FB:FBgn0050077
(Cheli et al., 2010)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in eye pigment granule organization
inferred from mutant phenotype
(Cheli et al., 2010)
involved_in regulation of synaptic vesicle cycle
inferred from mutant phenotype
(Chen et al., 2017)
inferred from direct assay
(Chen et al., 2017)
involved_in synaptic vesicle recycling via endosome
inferred from mutant phenotype
(Chen et al., 2017)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in intracellular transport
inferred from biological aspect of ancestor with PANTHER:PTN001583105
(GO Reference Genome Project, 2011-)
Cellular Component (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
part_of BLOC-1 complex
inferred from genetic interaction with FLYBASE:Pldn; FB:FBgn0036192
(Chen et al., 2017)
inferred from genetic interaction with FLYBASE:Blos1; FB:FBgn0050077
(Chen et al., 2017)
is_active_in neuromuscular junction
inferred from mutant phenotype
(Chen et al., 2017)
inferred from direct assay
(Chen et al., 2017)
located_in postsynapse of neuromuscular junction
inferred from direct assay
(Chen et al., 2017)
located_in type I terminal bouton
inferred from direct assay
(Chen et al., 2017)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of BLOC-1 complex
inferred from biological aspect of ancestor with PANTHER:PTN001583105
(GO Reference Genome Project, 2011-)
inferred from sequence or structural similarity with HGNC:8549
(Cheli et al., 2010)
is_active_in transport vesicle
inferred from biological aspect of ancestor with PANTHER:PTN001583105
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the BLOC1S6 family. (Q9VTM0)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Pallidin (Pldn) encodes a core component of the biogenesis of lysosome-related organelles (BLOC-1) complex. It is involved in pigment granule biogenesis and synaptic vesicle recycling at the neuromuscular junction. [Date last reviewed: 2018-10-25]
Gene Group (FlyBase)
BIOGENESIS OF LYSOSOME-RELATED ORGANELLES COMPLEX-1 -
The BLOC (biogenesis of lysosome-related organelles complex) complexes are required for the biogenesis of specialized organelles of the endosomal-lysosomal system. In mammalian cells, BLOC-1 localizes to early endosomes and facilitates protein trafficking to melanosomes in melanocytes. In D.mel, BLOC-1 has been shown to be involved in pigment granule biogenesis. (Adapted from FBrf0192474).
Protein Function (UniProtKB)
Component of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) involved in pigment granule biogenesis and membrane trafficking in synapses (PubMed:20015953, PubMed:28317021). In response to high synaptic activity at neuromuscular junctions, plays a key role in promoting efficient synaptic vesicle recycling and re-formation through early endosomes (PubMed:28317021).
(UniProt, Q9VTM0)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Pldn 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 Q9VTM0)

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 5.53

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

Gene model reviewed during 5.45

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pldn-RB
FBtr0300097
NM_140237
952
167
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
Pldn-PB
FBpp0289374
19.0
167
9.62
Q9VTM0
NP_648494
AAF50027
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)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) composed of Blos1, Blos2, Blos3, Blos4, Dysb, Muted, Pldn and Snapin. Interacts with Blos1, Blos4 and Dysb.

(UniProt, Q9VTM0)
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\Pldn 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).

1.13

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of BLOC-1 complex
inferred from genetic interaction with FLYBASE:Pldn; FB:FBgn0036192
(Chen et al., 2017)
inferred from genetic interaction with FLYBASE:Blos1; FB:FBgn0050077
(Chen et al., 2017)
is_active_in neuromuscular junction
inferred from mutant phenotype
(Chen et al., 2017)
inferred from direct assay
(Chen et al., 2017)
located_in postsynapse of neuromuscular junction
inferred from direct assay
(Chen et al., 2017)
located_in type I terminal bouton
inferred from direct assay
(Chen et al., 2017)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pldn 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 ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pldn
Transgenic constructs containing regulatory region of Pldn
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
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) (1)
Hsap\BLOC1S6
8 of 14
Yes
Yes
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) (1)
Rnor\Bloc1s6
8 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Bloc1s6
8 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\bloc1s6
4 of 13
Yes
Yes
Xtro\rgl2
4 of 13
Yes
No
Danio rerio (Zebrafish) (1)
Drer\bloc1s6
9 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP005189
9 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Pldn. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 2 )
Potential Models Based on Orthology ( 1 )
Modifiers Based on Experimental Evidence ( 2 )
Allele
Disease
Interaction
References
PldnGD13391
model of  Hermansky-Pudlak syndrome 9
is ameliorated by per01
(Li et al., 2023)
PldnHMS05728
model of  Hermansky-Pudlak syndrome 9
is ameliorated by per01
(Li et al., 2023)
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?
BLOC1S6; biogenesis of lysosomal organelles complex 1 subunit 6
8 of 14
604310
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
Show neighbor-neighbor interactions:
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Other 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
Pldn - Blos1
two hybrid
(Cheli et al., 2010)
Pldn - Blos4
two hybrid
(Cheli et al., 2010)
Pldn - Dysb
two hybrid, anti tag coimmunoprecipitation, peptide massfingerprinting, western blot, anti bait coimmunoprecipitation, anti tag western blot
(Mullin et al., 2015, Cheli et al., 2010)
Summary of Genetic Interactions
esyN Network Diagram
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
esyN Network Key:
Suppression
Enhancement
Other 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
Arpc1
suppressible
Pldn
(Gokhale et al., 2016)
External Data
Subunit Structure (UniProtKB)
Component of the biogenesis of lysosome-related organelles complex-1 (BLOC-1) composed of Blos1, Blos2, Blos3, Blos4, Dysb, Muted, Pldn and Snapin. Interacts with Blos1, Blos4 and Dysb.
(UniProt, Q9VTM0 )
Linkouts
BioGRID - A database of protein and genetic interactions.
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
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3L
Recombination map
3-36
Cytogenetic map
68D2-68D2
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
68D2-68D2
Limits computationally determined from genome sequence between P{PZ}l(3)0123901239&P{lacW}l(3)01239j9B4 and P{PZ}CycA02461&P{PZ}CycA03946
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

3-36

(FlyBase, 2016)

3-30.1

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (6)
Genomic Clones (16)
 

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

cDNA Clones (3)
 

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
       

      polyclonal

      (Chen et al., 2017)
      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: pallidin CG14133

          (Cheli et al., 2010)

          Source for identity of: Pallidin pallidin

          (FlyBase, 2009-)

          Source for identity of: Pldn Pallidin

          (Gokhale et al., 2016)
          Nomenclature comments
          Etymology

          Named "Pallidin" after the human ortholog.

          (FlyBase, 2009-)
          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 ( 26 )
          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 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
          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
          BioGRID - A database of protein and genetic interactions.
          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
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (30)