Gene Dmel\Atg4

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General Information

Symbol

Dmel\Atg4

Species

D. melanogaster

Name

Autophagy-specific gene 4

Annotation symbol

CG4428

Feature type

protein_coding_gene

FlyBase ID

FBgn0031298

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

Cytogenetic map

21E4-21E4

Sequence location

2L:1,080,913..1,083,384 [+]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene Autophagy-specific gene 4 is referred to in FlyBase by the symbol Atg4 (CG4428, FBgn0031298). It has the cytological map location 21E4. Its sequence location is 2L:1080913..1083384. Its molecular function is described as cysteine-type endopeptidase activity. The biological processes in which it is involved are not known. 3 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

21E4-21E4

Limits computationally determined from genome sequence between P{lacW}l(2)k09610^k09610&P{lacW}S^k09538a and P{PZ}l(2)10685¹⁰⁶⁸⁵&P{lacW}Tango14^k00619

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

Left of (cM)

Right of (cM)

Notes

Molecular Map Data

Gene Order (in direction of increasing cytology)

References

Gene Order (overall orientation not stated)

References

Gene Model & Products

Please see the GBrowse view of Dmel\Atg4 for information on other features

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

Atg4-RA

FBtr0077953

NM_134719

2080

411

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

Atg4-PA

FBpp0077618

45.6

411

4.53

NP_608563

AAF51423

Additional Polypeptide Data & Comments

Reported size (kD)

Comments

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0031298

Crossreferences

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

•

Peptidase C54 (IPR005078)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Q9VPW2

Maps to

Does NOT map to

Identified with

LD26292

(BDGP Project Members, 2000-)

Mapped Features & Mutations

Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here

Type

Symbol & Location

Additional Notes

References

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

5753

Crossreferences

Expression Data

FlyBase-Curated Data

Transcript and
Protein data

Please see the FlyBase Gene Expression Report for details of gene expression from the literature.

Summary of Transcript Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

Summary of Polypeptide Expression

Stage

Tissue/Position

Reference

Marker for

Subcellular Localization

CV Term

Microarray Data

Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)

Untitled Document detailed view

AA942211
AI513962

External Data & Images

Linkouts

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

•

FBgn0031298

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0031298

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0031298

Alleles & Phenotypes

Summary of Allele Phenotypes

Phenotype manifest in

Allele

Classical Alleles ( 2 )

For All Classical Alleles Show

Allele of Atg4	Class	Mutagen	Stocks	Known lesion
Atg4^DG01403			1	--
Atg4^MB03551			1	--

Alleles Carried on Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Allele of Atg4	Class	Mutagen	Stocks	Known lesion
Atg4^GD11315		in vitro construct \| RNAi in vitro construct \| regulatory fusion	1	Yes

Aneuploid Aberrations

Useful deficiency

Df(2L)ast5

Useful duplication

Dp(2;2)M⁺Su²⁴⁺-1

Disrupted in

Df(2L)Exel6004

(Ryder, 2004.4.26)

Df(2L)Exel9037

(Ryder, 2004.4.26)

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

UAS construct

P{GD11315}

Insertions

Type of insertions

Name

Expression data

miscellaneous insertions

P{wHy}Atg4^DG01403

insertion of enhancer trap binary system

Mi{ET1}Atg4^MB03551

Related Comments

Please look at the allele reports for the complete phenotype data

Gene Ontology: Function, Process & Cellular Component ( 1 )

Molecular Function

CV term

Evidence

References

cysteine-type endopeptidase activity

inferred from sequence or structural similarity with SGD_LOCUS:ATG4; SGD:S0005167

(Thumm and Kadowaki, 2001)

Biological Process

CV term

Evidence

References

Cellular Component

CV term

Evidence

References

Sequence Ontology: Class of Gene

protein_coding_gene

nuclear_gene

Interactions & Pathways

Summary of Genetic Interactions

Interacts with

Please look at the allele data for full details of the genetic interactions

Atg4 allele

Gene

References

External Data

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

59536

Orthologs

Genome-wide drosophilid orthologs

Dana\GF15159

Dere\GG24763

Dgri\GH13687

Dmoj\GI17971

Dper\GL15485

Dpse\GA18177

Dsec\GM16788

Dsim\GD23066

Dvir\GJ16311

Dwil\GK24338

Dyak\GE17286

Curated drosophilid orthologs

Dpse\GA18177

Linkouts

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000019181
Anopheles gambiae (Ensembl)
ENSBTAP00000020474
Bos taurus (Ensembl)
ENSCAFP00000019248
Canis familiaris (Ensembl)
ENSCINP00000016004
Ciona intestinalis (Ensembl)
ENSGALP00000010165
Gallus gallus (Ensembl)
ENSP00000319732
Homo sapiens (Ensembl)
ENSP00000336547
Homo sapiens (Ensembl)
ENSMMUP00000009438
Macaca mulatta (Ensembl)
ENSMODP00000010772
Monodelphis domestica (Ensembl)
ENSPTRP00000038132
Pan troglodytes (Ensembl)
ENSRNOP00000025529
Rattus norvegicus (Ensembl)
GSTENP00004881001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000006516
Xenopus tropicalis (Ensembl)
WBGene00038967
Caenorhabditis briggsae (Wormbase)
WBGene00013595
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050522-430
Danio rerio (Zfin)
ZDB-GENE-050522-430
Danio rerio (Zfin)
DDB0218520
Dictyostelium discoideum (Dictybase)
MGI:1913865
Mus musculus (Informatics)
YNL223W
Saccharomyces cerevisiae (Yeastgenome)
SPAC19B12.08
Schizosaccharomyces pombe (Sanger)

Functional Complementation between Species

Partially functionally complements

Scer\ATG4

(Thumm and Kadowaki, 2001)

Inter-Species Misexpression Data

Produces phenotype in

Produces NO phenotype in

Stocks & Reagents

Stocks Listed in FlyBase ( 3 )

VDRC

v34843

w¹¹¹⁸ P{GD11315}v34843

Bloomington

23542

w¹¹¹⁸; Mi{ET1}Atg4^MB03551

20539

y¹ w^67c23; P{wHy}Atg4^DG01403

Genomic Clones ( 2 )

cDNA Clones ( 43 )

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

LD26292

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Affy Oligo

Linkouts

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0031298

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0031298

Antibody Information

Other Information

Discoverer

Etymology

Identification

Position Effect Variegation Data

Relationship to Other Genes

Source for database identity of

Source for identity of: Atg4 CG4428

(Scott et al., 2004)

Source for database merge of

Additional comments

Comments About Role

Comments About Molecular Function

Other Comments

External Crossreferences & Linkouts

Sequence Crossreferences

RefSeq (Transcripts)

•

NM_134719

RefSeq (Proteins)

•

NP_608563

DDBJ / EMBL / GenBank

•

UniProtKB/TrEMBL

•

Q9VPW2

Other Crossreferences

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

•

Peptidase C54 (IPR005078)

Linkouts

BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions

•

59536

DEDB - Drosophila exon database: splicing graphs

•

5753

DRSC - RNAi screening (Harvard): high-throughput cell culture data and design

•

FBgn0031298

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

•

FBgn0031298

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0031298

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0031298

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0031298

GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data

•

FBgn0031298

InParanoid orthologs - Eukaryotic orthologs

•

ENSANGP00000019181
Anopheles gambiae (Ensembl)
ENSBTAP00000020474
Bos taurus (Ensembl)
ENSCAFP00000019248
Canis familiaris (Ensembl)
ENSCINP00000016004
Ciona intestinalis (Ensembl)
ENSGALP00000010165
Gallus gallus (Ensembl)
ENSP00000319732
Homo sapiens (Ensembl)
ENSP00000336547
Homo sapiens (Ensembl)
ENSMMUP00000009438
Macaca mulatta (Ensembl)
ENSMODP00000010772
Monodelphis domestica (Ensembl)
ENSPTRP00000038132
Pan troglodytes (Ensembl)
ENSRNOP00000025529
Rattus norvegicus (Ensembl)
GSTENP00004881001
Tetraodon nigroviridis (Ensembl)
ENSXETP00000006516
Xenopus tropicalis (Ensembl)
WBGene00038967
Caenorhabditis briggsae (Wormbase)
WBGene00013595
Caenorhabditis elegans (Wormbase)
ZDB-CDNA-050522-430
Danio rerio (Zfin)
ZDB-GENE-050522-430
Danio rerio (Zfin)
DDB0218520
Dictyostelium discoideum (Dictybase)
MGI:1913865
Mus musculus (Informatics)
YNL223W
Saccharomyces cerevisiae (Yeastgenome)
SPAC19B12.08
Schizosaccharomyces pombe (Sanger)

PANTHER - Protein classification by function, families, and pathways

•

FBgn0031298

University of Chicago Dev. Expression

•

FBgn0031298

Synonyms & Secondary IDs ( 3 )

Reported As

Symbol Synonym

Atg4

CG4428

(Lee et al., 2003, Thumm and Kadowaki, 2001, )

Name Synonym

Autophagy-specific gene 4

(Scott et al., 2004)

Secondary FlyBase IDs

References ( 10 )

Research paper

Lee et al., 2003, Curr. Biol. 13(4): 350--357: Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. [FBrf0158810]
Thumm and Kadowaki, 2001, Molec. Genet. Genomics 266(4): 657--663: The loss of Drosophila APG4/AUT2 function modifies the phenotypes of cut and Notch signaling pathway mutants. [FBrf0145130]

Supplementary material

Scott et al., 2004, Dev. Cell 7:: Supplementary material. [FBrf0183440]
Giot et al., 2003, Science 302(5651):: Tables S1 to S7. [FBrf0166452]

Personal communication to FlyBase

Bellen, 2007.4.5, batch731.xml: batch731.xml [FBrf0191801]
Dickson et al., 2007.7.18, RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center: RNAi construct and insertion data submitted by the Vienna Drosophila RNAi Center [FBrf0200327]
Myrick et al., 2005.5.16, Deletion Generator Project genomic insertion collection.: Deletion Generator Project genomic insertion collection. [FBrf0188490]
Ryder, 2004.4.26, Exelixis CG deletion data.: Exelixis CG deletion data. [FBrf0184335]

FlyBase analysis

FlyBase, 1992-, FlyBase curation: FlyBase curation. [FBrf0105495]

Computer file

BDGP Project Members, 2000-, Berkeley Drosophila Genome Project.: Berkeley Drosophila Genome Project. [FBrf0125078]