FlyBase Gene Report: Dmel\Atg4b

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

8 publicly available

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]

Other Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Atg4

Key Links

Genomic Location

Cytogenetic map

88F1-88F1

Sequence location

3R:15,353,720..15,356,924 [-]

Recombination map

3-57

RefSeq locus

NT_033777 REGION:15353720..15356924

Sequence

Get Decorated FASTA

Genomic Maps

GBrowse JBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

[Detailed GO annotations]

Gene Group (FlyBase)

AUTOPHAGY-RELATED GENES

Protein Family (UniProt)

Protein Signatures (InterPro)

Molecular Function (GO)
[Detailed GO annotations]

Experimental Evidence

Predictions / Assertions

cysteine-type endopeptidase activity

Summaries

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).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Atg4b or 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

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

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\Atg4b using the Feature Mapper tool.

External Data

Crossreferences

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

Atg4b_1

Linkouts

Gene Ontology (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

cysteine-type endopeptidase activity

inferred from sequence or structural similarity with SGD:S000005167

(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

autophagy

inferred from sequence or structural similarity with SGD:S000005167

(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

cytosol

inferred from sequence or structural similarity with SGD:S000005167

(FlyBase Curators, 2008--)

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)

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

View exonic expression by developmental stage for Dmel\Atg4b

View exonic expression by tissue for Dmel\Atg4b

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

FBgn0038325

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0038325

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG6194-RA

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG6194

Flygut - An atlas of the Drosophila adult midgut

FBgn0038325

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

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

Deletions and Duplications ( 1 )

Disrupted in

Df(3R)Exel6174

(Ryder, 2004.4.26)

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

viable

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Atg4b^GD11855

viable, with Scer\GAL4^Mef2.PR

Atg4b^GD11855

viable, with Scer\GAL4^pnr-MD237

Atg4b^GD11855

viable, with Scer\GAL4^tin.CΔ4

Atg4b^GD11855

Sterility

Allele

fertile

Other Phenotypes

Allele

visible, with Scer\GAL4^pnr-MD237

Atg4b^GD11855

Phenotype manifest in

Allele

chaeta | supernumerary, with Scer\GAL4^pnr-MD237

Atg4b^GD11855

trichogen cell, with Scer\GAL4^pnr-MD237

Atg4b^GD11855

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\ATG4D

13 of 15

Yes

Hsap\ATG4C

12 of 15

Yes

Hsap\ATG4A

5 of 15

Hsap\ATG4B

5 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (4)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Atg4d

13 of 15

Yes

Mmus\Atg4c

12 of 15

Yes

Mmus\Atg4a

5 of 15

Mmus\Atg4b

4 of 15

Rattus norvegicus (Norway rat) (5)

Rnor\Atg4d

9 of 13

Yes

Rnor\Atg4c

8 of 13

Yes

Rnor\Atg4b

4 of 13

Rnor\Atg4a

2 of 13

Rnor\LOC108348284

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (4)

Xtro\atg4c

11 of 12

Yes

Xtro\atg4d

8 of 12

Yes

Xtro\atg4b

4 of 12

Xtro\atg4a

3 of 12

Danio rerio (Zebrafish) (6)

Drer\atg4c

12 of 15

Yes

Drer\atg4da

11 of 15

Yes

Drer\atg4a

5 of 15

Drer\atg4b

5 of 15

Drer\atg4db

5 of 15

Yes

Drer\LOC101884161

2 of 15

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\atg-4.2

12 of 15

Yes

Cele\atg-4.1

5 of 15

Arabidopsis thaliana (thale-cress) (3)

Atha\AT3G59950

6 of 9

Yes

Atha\AT2G44140

5 of 9

Atha\AT2G44130

1 of 9

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\ATG4

9 of 15

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\atg4

7 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091905IW )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA19429

Drosophila persimilis

Dper\GL13755

Drosophila willistoni

Dwil\GK11310

Drosophila virilis

Dvir\GJ10670

Drosophila mojavensis

Dmoj\GI10728

Drosophila grimshawi

Dgri\GH16873

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506KS )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17016369

Glossina morsitans

Tsetse fly

Gmor\GMOY002013

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_12601

Aedes aegypti

Yellow fever mosquito

Aaeg\APG4A

Anopheles darlingi

American malaria mosquito

Adar\ADAC004585

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ002380

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W04D8 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA004926

Danaus plexippus

Monarch butterfly

Dple\DPOGS202319-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL007647

Apis florea

Little honeybee

Aflo\2165667716

Apis mellifera

Western honey bee

Amel\GB45197

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP14444

Bombus terrestris

Buff-tailed bumblebee

Bter\15211498

Linepithema humile

Argentine ant

Lhum\LH22618

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001f66

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_06708

Tribolium castaneum

Red flour beetle

Tcas\TC014208

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_10705

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X049W )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR007424

Ixodes scapularis

Black-legged tick

Isca\ISCW010488

Stegodyphus mimosarum

African social velvet spider

Smim\KFM59607.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur34g00150

Tetranychus urticae

Two-spotted spider mite

Turt\tetur07g07870

Tetranychus urticae

Two-spotted spider mite

Turt\tetur34g00290

Tetranychus urticae

Two-spotted spider mite

Turt\tetur34g00320

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_302128

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G065S )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Atg4cL

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000003328

Gallus gallus

Domestic chicken

Ggal\ATG4C

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (1)

Gene Symbol

Score

Source

Alignment

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 ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v7.1 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?

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

enhanceable

Atg4b

(Thumm and Kadowaki, 2001)

enhanceable

Atg4b

(Thumm and Kadowaki, 2001)

enhanceable

Atg4b

(Thumm and Kadowaki, 2001)

suppressible

Atg4b

(Thumm and Kadowaki, 2001)

suppressible

Atg4b

(Thumm and Kadowaki, 2001)

enhanceable

Atg4b

(Thumm and Kadowaki, 2001)

sno

enhanceable

Atg4b

(Thumm and Kadowaki, 2001)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

66931

DroID - A comprehensive database of gene and protein interactions.

FBgn0038325

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41868

MIST (genetic) - An integrated Molecular Interaction Database

Atg4b

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

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.

Macroautophagy

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-57

Cytogenetic map

88F1-88F1

Sequence location

3R:15,353,720..15,356,924 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

88F1-88F1

Limits computationally determined from genome sequence between P{lacW}MRG15^j6A3 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 (8)

Bloomington

18403

w¹¹¹⁸; PBac{WH}Atg4b^f01043

81793

y¹ v¹; P{TKO.GS04839}attP40

56046

y¹ v¹; P{TRiP.HMS04249}attP2

36340

y¹ w^*; P{lacW}Atg4b^P0997

FlyORF

F003145

M{UAS-Atg4b.ORF.3xHA.GW}ZH-86Fb

VDRC

v108299

P{KK102037}VIE-260B

v22293

w¹¹¹⁸; P{GD11855}v22293

v22294

w¹¹¹⁸; P{GD11855}v22294

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 sequences

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.

FBgn0038325

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0038325

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41868

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 ( 33 )

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.

41868

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0038325

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

FBgn0038325

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

Atg4b_1

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG6194

Flygut - An atlas of the Drosophila adult midgut

FBgn0038325

GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents

41868

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

TC014208

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

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

Dmel_CG6194

modMine - A data warehouse for the modENCODE project

FBgn0038325

Linkouts

BioGRID - A database of protein and genetic interactions.

66931

DroID - A comprehensive database of gene and protein interactions.

FBgn0038325

DRSC - Results frm RNAi screens

FBgn0038325

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0038325

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG6194-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0038325

FlyMine - An integrated database for Drosophila genomics

FBgn0038325

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

41868

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

MIST (genetic) - An integrated Molecular Interaction Database

Atg4b

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Macroautophagy

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

APG4

(Kourtis and Tavernarakis, 2009)

AUT2

(Kourtis and Tavernarakis, 2009)

Atg4

(Chakraborty et al., 2018, Kuo et al., 2018, Lei et al., 2017, Moy and Cherry, 2013, Chang and Neufeld, 2010, Zirin and Perrimon, 2010)

Atg4b

(Khezri and Rusten, 2019, Meltzer et al., 2019, O'Keefe and Denton, 2018, Galluzzi et al., 2017, Manent et al., 2017, Transgenic RNAi Project members, 2017-, Zhang and Baehrecke, 2015, Érdi et al., 2012)

CG6194

(Hosono et al., 2015, Érdi et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Mackay et al., 2012, Ni et al., 2010.12.1, Chittaranjan et al., 2009, Keleman et al., 2009.8.5, Czech et al., 2008, Liu and Lehmann, 2008)

DmAtg4-like

(Chittaranjan et al., 2009)

atg4

(Zhang et al., 2016)

Name Synonyms

Autophagy-related 4b

Autophagy-specific gene 4b

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (50)

Report Sections

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