FB2022_02, released March 29, 2022

Gene: Dmel\Atg4b

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General Information
Symbol
Dmel\Atg4b
Species
D. melanogaster
Name
Autophagy-related 4b
Annotation Symbol
CG6194
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038325
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
Autophagy-related 4b (Atg4b) encodes a cysteine protease that cleaves the precursor product of Atg8a at the C-terminal region, thereby initiating autophagosome formation. [Date last reviewed: 2018-11-15] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Atg4

Key Links
Genomic Location
Cytogenetic map
88F1-88F1
Sequence location
Recombination map
3-57
RefSeq locus
NT_033777 REGION:15353720..15356924
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (3 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables Atg8-specific protease activity
inferred from sequence or structural similarity with UniProtKB:P53867
(Thumm and Kadowaki, 2001)
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in autophagy
inferred from sequence or structural similarity with UniProtKB:P53867
(Thumm and Kadowaki, 2001)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in cytosol
inferred from sequence or structural similarity with UniProtKB:P53867
(FlyBase Curators, 2008-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Autophagy-related 4b (Atg4b) encodes a cysteine protease that cleaves the precursor product of Atg8a at the C-terminal region, thereby initiating autophagosome formation. [Date last reviewed: 2018-11-15]
Gene Group (FlyBase)
AUTOPHAGY-RELATED GENES -
The Autophagy-related genes (Atg), characterized extensively in yeast, are a set of approximately twenty evolutionarily conserved genes required for autophagy. Autophagy (specifically, macroautophagy) is the process of bulk degradation of cytoplasmic material. It takes place by the assembly of a double membrane vesicle, the autophagosome, which delivers cargo to the lysosome for recycling. (Adapted from FBrf0219844 and FBrf020902).
ATG8 PROTEASES -
During macroautophagy/autophagy, ATG8-family proteases undergo 2 distinct proteolytic processing events. First, in support of phagophore growth, ATG8 is cleaved by ATG4 to expose a glycine at the COOH-terminus. The exposed glycine is then utilized in a series of ubiquitin-like reactions culminating in the covalent attachment of the ATG8-family protein to the phospholipid phosphatidylethanolamine (PE). Second, following autophagosome maturation, each ATG8 protein is recycled off the membrane by an ATG4-mediated cleavage that breaks the bond between glycine and PE. Thus, ATG4 is responsible for both early and late cleavage events on distinct pools (soluble and lipid-attached) of ATG8-related proteins. ATG8-family proteases are included within MEROPS family C54. (Adapted from PMID:29458288.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Atg4b 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VF80)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Atg4b-RA
FBtr0083115
NM_142195
2665
668
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
RefSeq ID
GenBank
Atg4b-PA
FBpp0082569
74.8
668
5.86
NP_650452
AAF55180
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
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\Atg4b 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
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

Comment: rapidly degraded

(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | faint | ubiquitous
(Fisher et al., 2012)
ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

(Fisher et al., 2012)
embryonic stage 9 -- 10
central brain primordium
(Fisher et al., 2012)
organism | faint | ubiquitous
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 11 -- 12
central brain primordium
(Fisher et al., 2012)
organism | faint | ubiquitous
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
organism | faint | ubiquitous
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
pupal stage
salivary gland
(Lee et al., 2003)
Additional Descriptive Data

The expression of this gene along with several others is induced in salivary glands in pupae at the time of head eversion. This stage is characterized by an increase in the ecdysone titer as well as large amounts of cell death in this tissue.

(Lee et al., 2003)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Atg4b in GBrowse 2
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
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
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 ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Atg4b
Transgenic constructs containing regulatory region of Atg4b
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3R)Exel6174
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\ATG4D
13 of 15
Yes
Yes
Hsap\ATG4C
12 of 15
No
Yes
Hsap\ATG4A
5 of 15
No
No
Hsap\ATG4B
5 of 15
No
No
1  
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Atg4d
13 of 15
Yes
Yes
Mmus\Atg4c
12 of 15
No
Yes
Mmus\Atg4a
5 of 15
No
No
Mmus\Atg4b
4 of 15
No
No
Rattus norvegicus (Norway rat) (5)
Rnor\Atg4d
9 of 13
Yes
Yes
Rnor\Atg4c
8 of 13
No
Yes
Rnor\Atg4b
4 of 13
No
No
Rnor\Atg4a
2 of 13
No
No
Rnor\LOC108348284
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
Xtro\atg4c
11 of 12
Yes
Yes
Xtro\atg4d
8 of 12
No
Yes
Xtro\atg4b
4 of 12
No
No
Xtro\atg4a
3 of 12
No
No
Danio rerio (Zebrafish) (6)
Drer\atg4c
12 of 15
Yes
Yes
Drer\atg4da
11 of 15
No
Yes
Drer\atg4a
5 of 15
No
No
Drer\atg4b
5 of 15
No
No
Drer\atg4db
5 of 15
No
Yes
Drer\LOC101884161
2 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\atg-4.2
12 of 15
Yes
Yes
Cele\atg-4.1
5 of 15
No
No
Arabidopsis thaliana (thale-cress) (3)
Atha\AT3G59950
6 of 9
Yes
No
Atha\AT2G44140
5 of 9
No
No
Atha\AT2G44130
1 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\ATG4
9 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\atg4
7 of 12
Yes
No
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Atg4a
7 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 ( 1 )
    Disease Associations of Human Orthologs (via DIOPT v8.0 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?
    ATG4D; autophagy related 4D cysteine peptidase
    13 of 15
    611340
        ATG4C; autophagy related 4C cysteine peptidase
        12 of 15
        611339
            ATG4A; autophagy related 4A cysteine peptidase
            5 of 15
            300663
                ATG4B; autophagy related 4B cysteine peptidase
                5 of 15
                611338
                     
                    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
                    Summary of Genetic Interactions
                    esyN Network Diagram
                    esyN Network Key:
                    Suppression
                    Enhancement
                    View in Interactions Browser
                    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
                    ct
                    enhanceable
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    Dl
                    enhanceable
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    dx
                    enhanceable
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    H
                    suppressible
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    N
                    suppressible
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    N
                    enhanceable
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    sno
                    enhanceable
                    Atg4b
                    (Thumm and Kadowaki, 2001)
                    External Data
                    Linkouts
                    BioGRID - A database of protein and genetic interactions.
                    DroID - A comprehensive database of gene and protein interactions.
                    MIST (genetic) - An integrated Molecular Interaction Database
                    Pathways
                    Signaling Pathways (FlyBase)
                    Metabolic Pathways
                    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                    External Data
                    Linkouts
                    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
                    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                    Genomic Location and Detailed Mapping Data
                    Chromosome (arm)
                    3R
                    Recombination map
                    3-57
                    Cytogenetic map
                    88F1-88F1
                    Sequence location
                    FlyBase Computed Cytological Location
                    Cytogenetic map
                    Evidence for location
                    88F1-88F1
                    Limits computationally determined from genome sequence between P{lacW}MRG15j6A3 and P{PZ}l(3)0653606536
                    Experimentally Determined Cytological Location
                    Cytogenetic map
                    Notes
                    References
                    Experimentally Determined Recombination Data
                    Location

                    3-57

                    (FlyBase, 2016)

                    3-56.1

                    (Comeron et al., 2012)
                    Left of (cM)
                    Right of (cM)
                    Notes
                    Stocks and Reagents
                    Stocks (7)
                    Genomic Clones (17)
                     

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

                    cDNA Clones (82)
                     

                    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 GBrowse 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
                      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                      Antibody Information
                      Laboratory Generated Antibodies
                       
                      Commercially Available Antibodies
                       
                      Other Information
                      Relationship to Other Genes
                      Source for database identify of

                      Source for identity of: Atg4b CG6194

                      (Érdi et al., 2012)
                      Source for database merge of
                      Additional comments
                      Other Comments
                      Origin and Etymology
                      Discoverer
                      Etymology
                      Identification
                      External Crossreferences and Linkouts ( 38 )
                      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/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.
                      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                      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
                      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                      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
                      FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                      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)
                      modMine - A data warehouse for the modENCODE project
                      Linkouts
                      BioGRID - A database of protein and genetic interactions.
                      DroID - A comprehensive database of gene and protein interactions.
                      DRSC - Results frm RNAi screens
                      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                      FlyMine - An integrated database for Drosophila genomics
                      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
                      MIST (genetic) - An integrated Molecular Interaction Database
                      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                      Synonyms and Secondary IDs (10)
                      Datasets (8)
                      Study focus (0)
                      Experimental Role
                      Project
                      Project Type
                      Title
                      Study result (8)
                      Result
                      Result Type
                      Title
                      scRNAseq_2020_Cattenoz_NI_seq_clustering
                      Clustering analysis of hemocytes from non-infested third instar larvae
                      scRNAseq_2020_Cattenoz_WI_seq_clustering
                      Clustering analysis of hemocytes from wasp-infested third instar larvae
                      scRNAseq_2020_Cho_NI72LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
                      scRNAseq_2020_Cho_NI96LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI120LG_seq_clustering
                      Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
                      scRNAseq_2020_Cho_WI96LG_seq_clustering
                      Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI96HL_seq_clustering
                      Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
                      scRNAseq_2020_Cho_NI120HL_seq_clustering
                      Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
                      References (62)