FlyBase Gene Report: Dmel\Atg4a

General Information

Symbol

Dmel\Atg4a

Species

D. melanogaster

Name

Autophagy-related 4a

Annotation Symbol

CG4428

Feature Type

protein_coding_gene

FlyBase ID

FBgn0031298

Gene Model Status

Current

Stock Availability

12 publicly available

Gene Summary

Autophagy-related 4a (Atg4a) encodes a protein involved in autophagy. [Date last reviewed: 2019-06-27] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Atg4

Key Links

Genomic Location

Cytogenetic map

21E4-21E4

Sequence location

2L:1,080,911..1,085,380 [+]

Recombination map

2-1.5

RefSeq locus

NT_033779 REGION:1080911..1085380

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

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

Function

Gene Ontology (GO) Annotations (12 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables cysteine-type endopeptidase activity

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:K8ESC5

(Gene Ontology Curators, 2002-)

enables cysteine-type peptidase activity

inferred from electronic annotation with InterPro:IPR005078, InterPro:IPR046792

(InterPro Project Members, 2004-)

enables protein-phosphatidylethanolamide deconjugating activity

inferred from sequence or structural similarity with UniProtKB:P53867

(Thumm and Kadowaki, 2001)

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR046792

(InterPro Project Members, 2004-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in macroautophagy

inferred from mutant phenotype

(Xu et al., 2015, Lőw et al., 2013, Pircs et al., 2012)

NOT involved_in larval midgut cell programmed cell death

inferred from mutant phenotype

(Chang et al., 2013)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

involved_in aggrephagy

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

involved_in autophagosome assembly

inferred from sequence or structural similarity with UniProtKB:Q9Y4P1

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

involved_in mitophagy

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:Q9Y4P1

(Gene Ontology Curators, 2002-)

involved_in piecemeal microautophagy of the nucleus

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

involved_in protein processing

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN002503342

(GO Reference Genome Project, 2011-)

located_in cytosol

inferred from sequence or structural similarity with UniProtKB:P53867

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

AUTOPHAGY-RELATED GENES

ATG8 PROTEASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Autophagy-related 4a (Atg4a) encodes a protein involved in autophagy. [Date last reviewed: 2019-06-27]

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 proteins 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

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Atg4a 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 Q9VPW2)

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

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

Gene model reviewed during 5.45

Antisense UTR: extended 3' UTR (one isoform) overlaps CDS of CG4629 on the opposite strand.

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Atg4a-RA

FBtr0077953

NM_134719

2076

411

Atg4a-RB

FBtr0332569

NM_001272923

4075

410

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

Atg4a-PA

FBpp0077618

45.6

411

4.53

FBpp0304824

45.5

410

4.56

M9PBM3

NP_001259852

AGB92389

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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\Atg4a using the Feature Mapper tool.

External Data

Crossreferences

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).

-1.02

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 | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\Atg4a in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\Atg4a

View exonic expression by tissue for Dmel\Atg4a

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

FBgn0031298

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33283/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0031298

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0031298

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0031298

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

CG4428

Flygut - An atlas of the Drosophila adult midgut

FBgn0031298

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

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 Atg4a

Transgenic constructs containing regulatory region of Atg4a

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(2L)Exel6004

(Ryder, 2004.4.26)

Df(2L)Exel9037

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

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

Atg4a^GD11315

partially lethal, with Scer\GAL4^tin.CΔ4

Atg4a^GD11315

viable, with Scer\GAL4^pnr-MD237

Atg4a^GD11315

Other Phenotypes

Allele

abnormal locomotor behavior | adult stage, with Scer\GAL4^Mef2.PU

Atg4a^KK108570

abnormal starvation stress response | larval stage, with Scer\GAL4^Cg.PU

Atg4a^HMS01482

abnormal starvation stress response | late third instar larval stage | somatic clone, with Scer\GAL4^Act5C.PP

Atg4a^C98A.UAS

increased occurrence of cell division | adult stage, with Scer\GAL4^NP0001

Atg4a^HMS01482

some die during pupal stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Atg4a^GD11315

Phenotype manifest in

Allele

adult gut, with Scer\GAL4^NP0001

Atg4a^HMS01482

autophagosome | somatic clone | third instar larval stage, with Scer\GAL4^Act5C.PP

Atg4a^C98A.UAS

embryonic/larval fat body | larval stage, with Scer\GAL4^Cg.PU

Atg4a^HMS01482

embryonic/larval fat body | somatic clone | third instar larval stage, with Scer\GAL4^Act5C.PP

Atg4a^C98A.UAS

lysosome | somatic clone | third instar larval stage, with Scer\GAL4^Act5C.PP

Atg4a^C98A.UAS

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (4)

Hsap\ATG4A

14 of 14

Yes

Hsap\ATG4B

13 of 14

Yes

Hsap\ATG4C

7 of 14

Hsap\ATG4D

7 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (4)

Rnor\Atg4b

13 of 14

Yes

Rnor\Atg4a

10 of 14

Yes

Rnor\Atg4c

7 of 14

Rnor\Atg4d

7 of 14

Mus musculus (laboratory mouse) (5)

Mmus\Atg4a

14 of 14

Yes

Mmus\Atg4b

12 of 14

Yes

Mmus\Atg4a-ps

11 of 14

Yes

Mmus\Atg4c

7 of 14

Mmus\Atg4d

7 of 14

Xenopus tropicalis (Western clawed frog) (6)

Xtro\atg4a

11 of 13

Yes

Xtro\atg4b

7 of 13

Yes

Xtro\atg4c

5 of 13

Xtro\atg4d

5 of 13

Xtro\ccser2

1 of 13

Yes

Xtro\paqr3

1 of 13

Danio rerio (Zebrafish) (6)

Drer\atg4a

14 of 14

Yes

Drer\atg4b

13 of 14

Yes

7 of 14

7 of 14

6 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\atg-4.1

13 of 14

Yes

Cele\atg-4.2

7 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP008497

12 of 12

Yes

Agam\AgaP_AGAP004023

5 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\AT2G44140

11 of 13

Yes

Atha\AT3G59950

11 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\ATG4

11 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\atg4

10 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Atg4a. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (1)

Atg4b

10 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 ( 1 )

Allele

Disease

Interaction

References

Atg4a^KK108570

ameliorates myotonic dystrophy type 1

modeled by Zzzz\CTG^i480.UAS.cGa

(Bargiela et al., 2015)

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?

ATG4A; autophagy related 4A cysteine peptidase

14 of 14

300663

ATG4B; autophagy related 4B cysteine peptidase

13 of 14

611338

ATG4C; autophagy related 4C cysteine peptidase

7 of 14

611339

ATG4D; autophagy related 4D cysteine peptidase

7 of 14

611340

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:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

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

Atg4a - CG8654

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Cyp6a13

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Cyp6d4

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Cyp9f2

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Fer1HCH

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Flad1

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Hmgs

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Hsp60A

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - JMJD6

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Lst8

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - MRG15

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - ND-75

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - SPE

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Sil1

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - Tap42

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - exu

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - hiro

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - igl

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - mts

experimental knowledge based

(Guruharsha et al., 2011)

Atg4a - nwk

experimental knowledge based

(Guruharsha et al., 2011)

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

Atg4a

suppressible

Atg8a

(Pircs et al., 2012)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Dcp-1

suppressible

Atg4a

(Kim et al., 2010)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59536

DroID - A comprehensive database of gene and protein interactions.

FBgn0031298

MIST (genetic) - An integrated Molecular Interaction Database

33283

MIST (protein-protein) - An integrated Molecular Interaction Database

33283

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

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.

Macroautophagy

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-1.5

Cytogenetic map

21E4-21E4

Sequence location

2L:1,080,911..1,085,380 [+]

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

2-1.5

(FlyBase, 2016)

2-1.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (12)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

23542

w¹¹¹⁸; Mi{ET1}Atg4a^MB03551

28367

y¹ v¹; P{TRiP.JF03003}attP2

81430

y¹ v¹; P{TKO.GS04627}attP40

44421

y¹ v¹; P{TRiP.GLC01355}attP40

83221

y¹ w^*; TI{CRIMIC.TG4.1}Atg4a^{CR00969-TG4.1}/SM6a

35740

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01482}attP2

602261

y¹ w^*; TI{CRIMIC.TG4.1}Atg4a^{CR71048-KO-TG4.1}/SM6a

NIG-Fly

M2L-2085

y¹ w¹¹¹⁸; Atg4a^SK4 P{neoFRT}40A/CyO-Tb

M2L-2086

y¹ w¹¹¹⁸; Atg4a^SK7 P{neoFRT}40A/CyO-Tb

2LG-1663

y² VhaAC39-1^cho-1 v¹; P{U6-Atg4a.NIG.sgRNA}attP40/CyO

VDRC

v107317

P{KK108570}VIE-260B

v34843

w¹¹¹⁸ P{GD11315}v34843

Genomic Clones (6)

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

cDNA Clones (89)

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

LD26292

Other clones

DPiM_LD26292

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.

FBgn0031298

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0031298

Antibody Information

Laboratory Generated Antibodies

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: Atg4 CG4428

(Scott et al., 2004)

Source for identity of: Atg4a Atg4

(Érdi et al., 2012)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

APG4

(Kourtis and Tavernarakis, 2009)

ATG4

(Song et al., 2020, Barth et al., 2012, Wu et al., 2009)

AUT2

(Kourtis and Tavernarakis, 2009)

CG4428

(National Institute of Genetics Fly Stocks, 2022-, Érdi et al., 2012, Pircs et al., 2012, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Perkins et al., 2009, Lee et al., 2003, Thumm and Kadowaki, 2001)

atg4

(Singh and Chowdhuri, 2018, Zhang et al., 2016, Kwon et al., 2013, Chen et al., 2012, Kim et al., 2010, Shelly et al., 2009)

Name Synonyms

Autophagy-related 4a

Autophagy-specific gene 4

(Scott et al., 2004)

Autophagy-specific gene 4a

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 40 )

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.

33283

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.

Q9VPW2

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.

Q9VPW2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0031298

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33283/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0031298

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0031298

FlyMine - An integrated database for Drosophila genomics

FBgn0031298

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

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

dme:Dmel_CG4428

MARRVEL_MODEL - MARRVEL (model organism gene)

33283

Linkouts

BioGRID - A database of protein and genetic interactions.

59536

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

FBgn0031298

DroID - A comprehensive database of gene and protein interactions.

FBgn0031298

DRSC - Results frm RNAi screens

FBgn0031298

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0031298

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0031298

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

CG4428

Flygut - An atlas of the Drosophila adult midgut

FBgn0031298

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0031298

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

TC013405

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

MIST (genetic) - An integrated Molecular Interaction Database

33283

MIST (protein-protein) - An integrated Molecular Interaction Database

33283

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

Macroautophagy

References (101)

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

-1.02

Report Sections