FlyBase Gene Report: Dmel\CtsF

General Information

Symbol

Dmel\CtsF

Species

D. melanogaster

Name

Cathepsin F

Annotation Symbol

CG12163

Feature Type

protein_coding_gene

FlyBase ID

FBgn0260462

Gene Model Status

Current

Stock Availability

13 publicly available

Gene Summary

May have a role in autophagic cell death. (UniProt, Q9VN93)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

82F6-82F7

Sequence location

3R:5,237,651..5,251,745 [-]

Recombination map

3-47.5

RefSeq locus

NT_033777 REGION:5237651..5251745

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 (8 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables cysteine-type peptidase activity

inferred from direct assay

(Kocks et al., 2003)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables cysteine-type endopeptidase activity

inferred from biological aspect of ancestor with PANTHER:PTN000274640

(GO Reference Genome Project, 2011-)

enables cysteine-type peptidase activity

inferred from electronic annotation with InterPro:IPR000668, InterPro:IPR013128

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in proteolysis involved in protein catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN000274640

(GO Reference Genome Project, 2011-)

involved_in proteolysis

inferred from electronic annotation with InterPro:IPR000668

(InterPro Project Members, 2004-)

Cellular Component (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

located_in fusome

inferred from direct assay

(Lighthouse et al., 2008)

located_in perivitelline space

inferred from high throughput direct assay

(Lye et al., 2014)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in extracellular space

inferred from biological aspect of ancestor with PANTHER:PTN000274640

(GO Reference Genome Project, 2011-)

is_active_in lysosome

inferred from biological aspect of ancestor with PANTHER:PTN000274640

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

CATHEPSINS

Protein Family (UniProt)

Belongs to the peptidase C1 family. (Q9VN93)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

CATHEPSINS -: Lysosomal cysteine proteases, generally known as 'cathepsins', are optimally active in the slightly acidic milieu found in lysosomes. They comprise a group of papain-related enzymes, sharing similar amino acid sequences and folds. Most are endopeptidases, though some are aminopeptidases, aminodipeptidase or carboxydipeptidases. They are also extremely important processing enzymes and have several important specific and individual functions, often associated with restricted tissue localization. Cathepsins belong to MEROPS family C1, subfamily A. (Adapted from PMID:11532926.)

Protein Function (UniProtKB)

May have a role in autophagic cell death.

(UniProt, Q9VN93)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\CtsF 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 Q9VN93)

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

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

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

CtsF-RA

FBtr0078823

NM_169033

2299

614

CtsF-RB

FBtr0078822

NM_141264

1882

475

CtsF-RC

FBtr0303994

NM_169034

1425

350

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

CtsF-PA

FBpp0078465

69.0

614

7.00

FBpp0078464

53.5

475

8.15

FBpp0292963

37.7

350

4.19

D3PK81

NP_730902

AAF52056

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\CtsF 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).

-0.37

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

anterior endoderm anlage

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

organism | faint | ubiquitous

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | faint | ubiquitous

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in fusome

inferred from direct assay

(Lighthouse et al., 2008)

located_in perivitelline space

inferred from high throughput direct assay

(Lye et al., 2014)

Expression Deduced from Reporters

Reporter: P{PTT-GC}CtsF^CC00625

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female

germarium

• fusome

(Lighthouse et al., 2008)

adult stage | male

male germline cyst

(Lighthouse et al., 2008)

Reporter: PBac{754.P.FSVS-0}CtsF^CPTI002924

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult brain cell body rind | restricted

(Knowles-Barley, 2011.8.24)

superior medial protocerebrum

(Knowles-Barley, 2011.8.24)

superior lateral protocerebrum

(Knowles-Barley, 2011.8.24)

adult gnathal ganglion | faint | restricted

(Knowles-Barley, 2011.8.24)

fan-shaped body layer

(Knowles-Barley, 2011.8.24)

Reporter: PBac{754.P.FSVS-0}CtsF^CPTI003173

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

fan-shaped body layer | restricted

Comment: top layer of fan-shaped body

(Knowles-Barley, 2011.8.24)

adult brain | faint | ubiquitous

(Knowles-Barley, 2011.8.24)

adult brain cell body rind | restricted

Comment: selected cells in the adult brain cortex

(Knowles-Barley, 2011.8.24)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\CtsF in JBrowse

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

View exonic expression by developmental stage for Dmel\CtsF

View exonic expression by tissue for Dmel\CtsF

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

FBgn0260462

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

40628/tissue=All

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

FBgn0260462

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

FBgn0260462

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 15 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CtsF

Transgenic constructs containing regulatory region of CtsF

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)BSC176

(Christensen et al., 2007.10.29)

Gene partially disrupted in

Df(3R)rtp¹

(Mecklenburg et al., 2010)

Inferred from location ( 6 )

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

viable

CtsF^CC00625

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

CtsF^GD16992

viable, with Scer\GAL4^Mef2.PR

CtsF^GD16992

viable, with Scer\GAL4^pnr-MD237

CtsF^GD16992

viable, with Scer\GAL4^tin.CΔ4

CtsF^GD16992

Phenotype manifest in

Allele

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) (13)

Hsap\CTSF

12 of 14

Yes

Hsap\CTSW

5 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 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) (27)

Rnor\Ctsf

12 of 14

Yes

Rnor\Ctsw

5 of 14

Yes

4 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (27)

Mmus\Ctsf

11 of 14

Yes

Mmus\Ctsw

5 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Kng2

1 of 14

Yes

Mmus\Tinagl1

1 of 14

Mmus\Tinag

1 of 14

Xenopus tropicalis (Western clawed frog) (13)

Xtro\ctsf

7 of 13

Yes

Xtro\ctsw

4 of 13

Yes

Xtro\LOC105947118

3 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (31)

Drer\ctsf

12 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

Drer\si:dkey-239j18.3

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Drer\si:dkey-239j18.2

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Drer\si:dkey-228a15.1

1 of 14

Drer\tinagl1

1 of 14

Drer\wu:fa26c03

1 of 14

Drer\zgc:103438

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (30)

Cele\tag-196

12 of 14

Yes

Cele\R09F10.1

5 of 14

Yes

Cele\R07E3.1

4 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Anopheles gambiae (African malaria mosquito) (13)

Agam\AgaP_AGAP002879

7 of 12

Yes

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (39)

Atha\AT2G21430

10 of 13

Yes

Atha\AT3G54940

10 of 13

Yes

Atha\AT4G16190

10 of 13

Yes

Atha\RD19

10 of 13

Yes

5 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

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Yes

Atha\AT5G17140

2 of 13

Yes

Atha\CP1

2 of 13

Atha\XBCP3

2 of 13

Atha\ASY1

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

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:CtsF. 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) (15)

5 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

2 of 13

2 of 13

2 of 13

Cys

2 of 13

Swim

2 of 13

cer

1 of 13

CG6337

1 of 13

CG6357

1 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 ( 1 )

Human Ortholog

Disease

Evidence

References

CTSF; cathepsin F

model of neuronal ceroid lipofuscinosis 13

IEA

(FlyBase, 2019-)

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.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

CTSF; cathepsin F

12 of 14

603539

CEROID LIPOFUSCINOSIS, NEURONAL, 13 (KUFS TYPE); CLN13

neuronal ceroid lipofuscinosis 13

5 of 14

4 of 14

3 of 14

PYCNODYSOSTOSIS

pycnodysostosis

3 of 14

3 of 14

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

CtsF - CtsL1

experimental knowledge based

(Guruharsha et al., 2011)

CtsF - sima

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

suppressible

CtsF

(Bronstein et al., 2010)

enhanceable

CtsF

(Bronstein et al., 2010)

Chi

enhanceable

CtsF

(Bronstein et al., 2010)

Ssdp

enhanceable

CtsF

(Bronstein et al., 2010)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

65841

DroID - A comprehensive database of gene and protein interactions.

FBgn0260462

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

40628

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

Lysosome

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

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-47.5

Cytogenetic map

82F6-82F7

Sequence location

3R:5,237,651..5,251,745 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

82F6-82F7

Limits computationally determined from genome sequence between P{PZ}l(3)02733⁰²⁷³³ and P{EP}EP974

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-47.5

(FlyBase, 2016)

3-44.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (13)

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

Bloomington

51538

w^*; P{PTT-GC}CtsF^CC00625

15429

y¹ w^67c23; P{EPgy2}CtsF^EY02656

50865

w^*; P{PTT-GC}CtsF^YC0058/TM6C, Sb¹

33955

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00910}attP2

32769

y¹ w^*; Mi{MIC}CtsF^MI01609/TM3, Sb¹ Ser¹

19914

y¹ w^67c23; P{EPgy2}CtsF^EY04405/TM6C, Sb¹ Tb¹

13003

y¹ w^67c23; P{SUPor-P}CtsF^KG03153 CG33293^KG03153 ry⁵⁰⁶

Kyoto

115384

w¹¹¹⁸; PBac{754.P.FSVS-0}CtsF^CPTI002924

115393

w¹¹¹⁸; PBac{754.P.FSVS-0}CtsF^CPTI003173

NIG-Fly

HMS00910

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00910}attP2

VDRC

v107589

P{KK100598}VIE-260B

v12787

w¹¹¹⁸; P{GD4765}v12787

More stocks available...

Genomic Clones (23)

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

cDNA Clones (181)

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.

FBgn0260462

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260462

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Area matching Drosophila EST AA541045.

(Davies, 2001.3.15)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG12163 anon-WO0118547.305

(FlyBase, 1996-)

Additional comments

Release 3.1 annotation CG12163-RD split out from CG12163 into a distinct annotation, CG33293, in release 3.2 of the genome annotation.

(FlyBase Genome Annotators, 2004)

" NEST:bs35d06 " is within an intron of "CG12163" and transcribed in the same direction, suggesting that " NEST:bs35d06 " may represent a new exon of "CG12163".

(Andrews et al., 2000)

Source for merge of CG12163 anon-WO0118547.305 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: CtsF CG12163

(Kocks et al., 2003)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CTSF

(Kocks et al., 2003)

Cts8

(Kumar et al., 2013)

Cts9

(Kumar et al., 2013)

CtsF

(Tsarouhas et al., 2023, Hultmark and Andó, 2022, Gene Disruption Project members, 2018-)

anon-WO0118547.305

Name Synonyms

Cathepsin F

(Kocks et al., 2003)

Secondary FlyBase IDs

FBgn0046802
FBgn0062108
FBgn0037303

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 58 )

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.

40628

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.

Q9VN93

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9VN93

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

D3PK81

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.

Q9VN93

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0260462

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

40628/tissue=All

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

FBgn0260462

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

FBgn0260462

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

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

dme:Dmel_CG12163

MARRVEL_MODEL - MARRVEL (model organism gene)

40628

Linkouts

BioGRID - A database of protein and genetic interactions.

65841

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

FBgn0260462

DroID - A comprehensive database of gene and protein interactions.

FBgn0260462

DRSC - Results frm RNAi screens

FBgn0260462

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260462

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

FBgn0260462

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

TC009844

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

Lysosome

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

40628

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

References (74)

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

-0.37

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