FB2024_02 , released April 23, 2024
Gene: Dmel\Pgant3
Open Close
General Information
Symbol
Dmel\Pgant3
Species
D. melanogaster
Name
Polypeptide N-Acetylgalactosaminyltransferase 3
Annotation Symbol
CG4445
Feature Type
FlyBase ID
FBgn0027558
Gene Model Status
Stock Availability
Enzyme Name (EC)
polypeptide N-acetylgalactosaminyltransferase (2.4.1.41)
Gene Summary
Polypeptide N-Acetylgalactosaminyltransferase 3 (Pgant3) encodes a member of the UDP- GalNAc:polypeptide N-acetylgalactosaminyltransferase family. It catalyzes the transfer of a GalNAc sugar onto the hydroxyl groups of serine and threonine in secreted or membrane-bound proteins. Pgant3 product modulates secretion of extracellular matrix proteins and influences integrin-mediated cell adhesion during development. [Date last reviewed: 2018-09-27] (FlyBase Gene Snapshot)
Also Known As

BcDNA:GH09147

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-55
RefSeq locus
NT_033778 REGION:7057654..7061732
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
Biological Process (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN004287905
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in Golgi apparatus
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in Golgi apparatus
inferred from biological aspect of ancestor with PANTHER:PTN000187024
located_in Golgi stack
non-traceable author statement
Protein Family (UniProt)
Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily. (Q9Y117)
Catalytic Activity (EC/Rhea)
polypeptide N-acetylgalactosaminyltransferase activity
(1) L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+) + UDP (2.4.1.41)
(2) L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O- [N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP (2.4.1.41)
Summaries
Gene Snapshot
Polypeptide N-Acetylgalactosaminyltransferase 3 (Pgant3) encodes a member of the UDP- GalNAc:polypeptide N-acetylgalactosaminyltransferase family. It catalyzes the transfer of a GalNAc sugar onto the hydroxyl groups of serine and threonine in secreted or membrane-bound proteins. Pgant3 product modulates secretion of extracellular matrix proteins and influences integrin-mediated cell adhesion during development. [Date last reviewed: 2018-09-27]
Gene Group (FlyBase)
POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASES -
Polypeptide N-acetylgalactosaminyltransferase catalyze the transfer of N-Acetylgalactosamine (GalNAc) from UDP-GalNAc to serine and threonine acceptor sites and initiate mucin-type O-glycosylation. (Adapted from FBrf0151358 and FBrf0190815).
Protein Function (UniProtKB)
Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor (PubMed:12829714). It can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Prefers EA2 as substrate. Has weak activity toward Muc5AC-3, -13 and -3/13 substrates (PubMed:12829714). Plays a critical role in the regulation of integrin-mediated cell adhesion during wing development by influencing, via glycosylation, the secretion and localization of the integrin ligand Tig to the basal cell layer interface (PubMed:18835818, PubMed:20371600, PubMed:20807760, PubMed:22157008). Might have a role in protein O-glycosylation in the Golgi and thereby in establishing and/or maintaining a proper secretory apparatus structure (PubMed:20807760). Together with Pgant35A, regulates integrin levels and activity-dependent integrin signaling at the synapse in neurons and muscles (PubMed:25253852).
(UniProt, Q9Y117)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Pgant3 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 Q9Y117)

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 5.48

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

Gene model reviewed during 5.44

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0089061
2884
667
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
FBpp0088130
76.8
667
9.47
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
Domain

There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding.

The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity.

(UniProt, Q9Y117)
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\Pgant3 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).

-0.19

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in Golgi apparatus
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Pgant3 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 8 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pgant3
Transgenic constructs containing regulatory region of Pgant3
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (21)
5 of 14
Yes
No
5 of 14
Yes
No
4 of 14
No
No
3 of 14
No
No
3  
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
1  
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (20)
5 of 14
Yes
No
5 of 14
Yes
No
4 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
Yes
1 of 14
No
No
Mus musculus (laboratory mouse) (19)
5 of 14
Yes
No
5 of 14
Yes
No
4 of 14
No
No
4 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (23)
4 of 13
Yes
No
4 of 13
Yes
No
3 of 13
No
No
2 of 13
No
Yes
2 of 13
No
No
2 of 13
No
Yes
2 of 13
No
No
2 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Danio rerio (Zebrafish) (23)
5 of 14
Yes
No
4 of 14
No
No
4 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
3 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (9)
8 of 14
Yes
Yes
5 of 14
No
No
3 of 14
No
No
3 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
2 of 14
No
No
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (13)
10 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:Pgant3. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Drosophila melanogaster (Fruit fly) (13)
5 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
4 of 13
4 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.
    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)
    Interactions Browser

    Please see the Physical Interaction reports below for full details
    MIST Molecular Interaction Search Tool

    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement

    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
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
    KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
    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)
    2R
    Recombination map
    2-55
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    42E7-42E7
    Limits computationally determined from genome sequence between P{lacW}vimark16722 and P{lacW}cosk16101
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (17)
     

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

    cDNA Clones (120)
     

    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)
    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

        Area matching Drosophila ESTs AA978449 and AA940834. Gap of Unknown length.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: pgant3 anon-WO0118547.119

        Additional comments

        Source for merge of pgant3 anon-WO0118547.119 was sequence comparison ( date:051113 ).

        Nomenclature History
        Source for database identify of

        Source for identity of: pgant3 CG4445

        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (8)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 51 )
        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
        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.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        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
        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
        FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        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.
        References (55)