FlyBase Gene Report: Dmel\PheRS-m

General Information

Symbol

Dmel\PheRS-m

Species

D. melanogaster

Name

Phenylalanyl-tRNA synthetase, mitochondrial

Annotation Symbol

CG13348

Feature Type

protein_coding_gene

FlyBase ID

FBgn0275436

Gene Model Status

Current

Stock Availability

5 publicly available

Enzyme Name (EC)

phenylalanine--tRNA ligase (6.1.1.20)

Gene Summary

Is responsible for the charging of tRNA(Phe) with phenylalanine in mitochondrial translation. (UniProt, O16129)

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

Aats-phe, mitochondrial phenylalanyl-tRNA synthetase, PheRS

Key Links

Genomic Location

Cytogenetic map

50C20-50C20

Sequence location

2R:13,968,308..13,969,902 [+]

Recombination map

2-68

RefSeq locus

NT_033778 REGION:13968308..13969902

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 (7 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables phenylalanine-tRNA ligase activity

inferred from mutant phenotype

(Fan et al., 2021)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables ATP binding

inferred from electronic annotation with InterPro:IPR002319, InterPro:IPR004530

(InterPro Project Members, 2004-)

enables phenylalanine-tRNA ligase activity

inferred from sequence or structural similarity with UniProtKB:O95363

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN000165932

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR004530

(InterPro Project Members, 2004-)

inferred from sequence or structural similarity with UniProtKB:P08425

(Gray et al., 1998)

traceable author statement

(Lu et al., 2015)

enables tRNA binding

inferred from sequence or structural similarity with UniProtKB:O95363

(Gene Ontology Curators, 2002-)

inferred from electronic annotation with InterPro:IPR002319

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in phenylalanyl-tRNA aminoacylation

inferred from mutant phenotype

(Fan et al., 2021)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in phenylalanyl-tRNA aminoacylation

inferred from electronic annotation with InterPro:IPR004530

(InterPro Project Members, 2004-)

inferred from sequence or structural similarity with UniProtKB:O95363

(Gene Ontology Curators, 2002-)

traceable author statement

(Lu et al., 2015)

inferred from biological aspect of ancestor with PANTHER:PTN000165932

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with UniProtKB:P08425

(Gray et al., 1998)

involved_in tRNA processing

inferred from sequence or structural similarity with UniProtKB:O95363

(Gene Ontology Curators, 2002-)

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:PTN000165932

(GO Reference Genome Project, 2011-)

located_in cytoplasm

inferred from electronic annotation with InterPro:IPR004530

(InterPro Project Members, 2004-)

is_active_in mitochondrion

inferred from biological aspect of ancestor with PANTHER:PTN000165999

(GO Reference Genome Project, 2011-)

located_in mitochondrion

inferred from sequence or structural similarity with UniProtKB:P08425

(Gray et al., 1998)

traceable author statement

(Lu et al., 2015)

Gene Group (FlyBase)

MITOCHONDRIAL AMINOACYL-TRNA SYNTHETASES

Protein Family (UniProt)

Belongs to the class-II aminoacyl-tRNA synthetase family. (O16129)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

phenylalanine-tRNA ligase activity

tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+) (6.1.1.20)

RHEA 19413:

Summaries

Gene Group (FlyBase)

MITOCHONDRIAL AMINOACYL-TRNA SYNTHETASES -: Mitochondrial aminoacyl-tRNA synthetases catalyze the ligation of amino acids to their cognate tRNAs in mitochondria. They are encoded by nuclear genes and are imported into mitochondria with the guidance of a 'mitochondrial targeting sequence'. (Adapted from FBrf0230668.)

Protein Function (UniProtKB)

Is responsible for the charging of tRNA(Phe) with phenylalanine in mitochondrial translation.

(UniProt, O16129)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\PheRS-m 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 O16129)

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

Gene model reviewed during 5.50

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

PheRS-m-RA

FBtr0087594

NM_057935

1526

453

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

PheRS-m-PA

FBpp0086720

52.0

453

7.18

O16129

NP_477283

AAF58310

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\PheRS-m using the Feature Mapper tool.

External Data

Crossreferences

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

Aats-phe_1

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).

1.85

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

larval muscle system

(Seshaiah and Andrew, 1999)

embryonic stage 11 -- 12

dorsal pharyngeal muscle primordium

(Fisher et al., 2012)

somatic muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)

trunk visceral muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

dorsal pharyngeal muscle cell

(Fisher et al., 2012)

larval muscle system

(Fisher et al., 2012)

larval somatic muscle cell

(Fisher et al., 2012)

larval visceral muscle cell

(Fisher et al., 2012)

Additional Descriptive Data

PheRS-m transcripts are expressed at a high level in embryonic muscle precursors.

(Seshaiah and Andrew, 1999)

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\PheRS-m in JBrowse

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

View exonic expression by developmental stage for Dmel\PheRS-m

View exonic expression by tissue for Dmel\PheRS-m

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

FBgn0275436

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

36547/tissue=All

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

FBgn0275436

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0020766

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

FBgn0275436

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

CG13348

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

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 PheRS-m

Transgenic constructs containing regulatory region of PheRS-m

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2R)Exel7129

(Ryder, 2004.4.26)

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

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

PheRS-m^GD14808

lethal, with Scer\GAL4^Mef2.PR

PheRS-m^GD14808

lethal - all die before end of first instar larval stage

PheRS-m^C19X

lethal - all die before end of second instar larval stage, with Scer\GAL4^da.PU

PheRS-m^HMC05742

lethal - all die before end of second instar larval stage | recessive

PheRS-m^KO

lethal - all die during embryonic stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

PheRS-m^GD14808

partially lethal - majority die, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

partially lethal - majority live

PheRS-m^D127Y

viable, with Scer\GAL4^pnr-MD237

PheRS-m^GD14808

viable, with Scer\GAL4^tin.CΔ4

PheRS-m^GD14808

Other Phenotypes

Allele

abnormal adult locomotory behavior | dominant | female | progressive

PheRS-m^C19X

abnormal adult locomotory behavior | progressive | recessive

PheRS-m^D127Y

abnormal developmental rate | codominant

PheRS-m^D127Y

abnormal developmental rate | dominant

PheRS-m^C19X

abnormal developmental rate | larval stage, with Scer\GAL4^da.PU

PheRS-m^HMC05742

abnormal developmental rate | larval stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

abnormal developmental rate | larval stage | recessive

PheRS-m^KO

abnormal neuroanatomy | adult stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

abnormal size | adult stage

PheRS-m^D127Y

bang sensitive, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

decreased body size | larval stage

PheRS-m^KO

decreased body size | larval stage, with Scer\GAL4^da.PU

PheRS-m^HMC05742

decreased cell size | cell autonomous | somatic clone, with Scer\GAL4^Act5C.PP

PheRS-m^NIG.13348R

decreased rate of feeding behavior | codominant | second instar larval stage

PheRS-m^D127Y

decreased rate of feeding behavior | first instar larval stage

PheRS-m^C19X

decreased rate of feeding behavior | larval stage

PheRS-m^C19X

decreased rate of feeding behavior | semidominant | third instar larval stage

PheRS-m^D127Y

decreased size | adult stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

majority die during P-stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

short lived, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

short lived | dominant

PheRS-m^C19X

short lived | semidominant

PheRS-m^D127Y

visible, with Scer\GAL4^pnr-MD237

PheRS-m^GD14808

visible | adult stage

PheRS-m^D127Y

visible | adult stage, with Scer\GAL4^eya.enh1+E+2

PheRS-m^HMC05742

Phenotype manifest in

Allele

adult brain, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

eye, with Scer\GAL4^eya.enh1+E+2

PheRS-m^HMC05742

indirect flight muscle | adult stage

lysosome & larval fat body | somatic clone | cell autonomous, with Scer\GAL4^Act5C.PP

PheRS-m^NIG.13348R

mitochondrial chromosome | increased number | larval stage

PheRS-m^KO

mitochondrial chromosome | increased number | larval stage, with Scer\GAL4^da.PU

PheRS-m^HMC05742

mitochondrial crista | adult stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

mitochondrion | adult stage

mitochondrion | adult stage, with Scer\GAL4^elav.PU

PheRS-m^HMC05742

trichogen cell, with Scer\GAL4^pnr-MD237

PheRS-m^GD14808

wing

PheRS-m^D127Y

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\FARS2

14 of 14

Yes

Hsap\FARSA

2 of 14

Hsap\FDXACB1

2 of 14

Yes

Hsap\KIF14

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) (3)

Rnor\Fars2

14 of 14

Yes

Rnor\Farsa

2 of 14

Rnor\Fdxacb1

2 of 14

Yes

Mus musculus (laboratory mouse) (3)

Mmus\Fars2

14 of 14

Yes

Mmus\Farsa

2 of 14

Mmus\Fdxacb1

2 of 14

Yes

Xenopus tropicalis (Western clawed frog) (3)

Xtro\fars2

7 of 13

Yes

Xtro\XB1017155

2 of 13

Xtro\farsa

1 of 13

Danio rerio (Zebrafish) (3)

Drer\fars2

13 of 14

Yes

Drer\fdxacb1

2 of 14

Yes

Drer\farsa

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\fars-2

13 of 14

Yes

Cele\fars-1

1 of 14

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP012096

12 of 12

Yes

Agam\AgaP_AGAP002653

2 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\AT3G58140

13 of 13

Yes

Atha\AT4G39280

2 of 13

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\MSF1

13 of 13

Yes

Scer\FRS2

2 of 13

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\SPCC736.03c

11 of 12

Yes

Spom\frs2

2 of 12

Escherichia coli (enterobacterium) (1)

Ecol\pheS

4 of 11

Yes

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:PheRS-m. 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)

α-PheRS

4 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 4 )

Allele

Disease

Evidence

References

PheRS-m^HMC05742

model of developmental and epileptic encephalopathy

CEC

(Fan et al., 2021)

PheRS-m^KO

model of developmental and epileptic encephalopathy

CEC

(Fan et al., 2021)

model of neonatal period electroclinical syndrome

CEA with Hsap\FARS2^G309S.UAS

(Fan et al., 2021)

model of hereditary spastic paraplegia

CEA with Hsap\FARS2^D142Y.UAS

(Fan et al., 2021)

PheRS-m^C19X

model of hereditary spastic paraplegia 77

CEA

(Mo et al., 2023)

PheRS-m^D127Y

model of hereditary spastic paraplegia 77

CEA

(Mo et al., 2023)

Potential Models Based on Orthology ( 2 )

Human Ortholog

Disease

Evidence

References

FARS2; phenylalanyl-tRNA synthetase 2, mitochondrial

model of combined oxidative phosphorylation deficiency 14

IEA

(FlyBase, 2019-)

model of hereditary spastic paraplegia 77

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?

FARS2; phenylalanyl-tRNA synthetase 2, mitochondrial

14 of 14

611592

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.

Dmel gene

Ortholog showing functional complementation

Supporting References

PheRS-m

Hsap\FARS2

(Fan et al., 2021)

Interactions

Summary of Physical Interactions

esyN Network Diagram

Show neighbor-neighbor interactions:

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(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

PheRS-m - Hsp60A

experimental knowledge based

(Guruharsha et al., 2011)

PheRS-m - JMJD6

experimental knowledge based

(Guruharsha et al., 2011)

PheRS-m - mts

experimental knowledge based

(Guruharsha et al., 2011)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

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

36547

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

tRNA charging

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

Aminoacyl-tRNA biosynthesis

External Data

Linkouts

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

Aminoacyl-tRNA biosynthesis

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-68

Cytogenetic map

50C20-50C20

Sequence location

2R:13,968,308..13,969,902 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

50C20-50C20

Limits computationally determined from genome sequence between P{lacW}Cp1^k15819&P{EP}CG6701^EP2054 and P{lacW}mam^k05821

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-68

(FlyBase, 2016)

2-73.5

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

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

Bloomington

26972

y¹ w^*; P{EP}PheRS-m^G19615/CyO

64869

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05742}attP40

13348R-2

v107079

v36554

w¹¹¹⁸; P{GD14808}v36554

Genomic Clones (16)

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

cDNA Clones (40)

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

LD27389

Other clones

DPiM_LD27389

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.

FBgn0275436

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

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

Source for merge of: Aats-phe-m Aats-phe

(Bullard et al., 1999)

Additional comments

FlyBase curator comment: BLAST analysis of the sequence given in Fig2 of FBrf0108640 shows that the "Drosophila mtPheRS" gene (= 'Aats-phe-m' in FlyBase) corresponds to the CG13348 annotation (aka 'Aats-phe').

(Bullard et al., 1999)

Nomenclature History

Source for database identify of

Source for identity of: PheRS-m Aats-phe-m

(Lu et al., 2015)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (13)

Reported As

Symbol Synonym

Aats-phe

(Lindström et al., 2017, Altenhein et al., 2006)

Aats-phe-m

CG13348

(Fan et al., 2021, Hosono et al., 2015, Lu et al., 2015, Keleman et al., 2009.8.5, Perkins et al., 2009)

FRS

(Seshaiah and Andrew, 1999)

PheRS

(Arsham and Neufeld, 2009, Seshaiah and Andrew, 1999.7.29)

PheRS-m

(Lu et al., 2015)

Pts

(Gray et al., 1998)

dFARS

(Wu et al., 2019)

dFARS2

(Fan et al., 2021)

mtPheRS

(Bullard et al., 1999)

Name Synonyms

Phenylalanyl-tRNA synthetase

(Gray et al., 1998)

Phenylalanyl-tRNA synthetase, mitochondrial

(Lu et al., 2015)

mitochondrial phenylalanyl-tRNA synthetase

(Bullard et al., 1999)

Secondary FlyBase IDs

FBgn0027628
FBgn0028548
FBgn0020766

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 37 )

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.

36547

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.

O16129

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

O16129

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.

O16129

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0275436

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

36547/tissue=All

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

FBgn0275436

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

FBgn0275436

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

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

dme:Dmel_CG13348

MARRVEL_MODEL - MARRVEL (model organism gene)

36547

Linkouts

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

FBgn0275436

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

Aats-phe_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0020766

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0275436

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

tRNA charging

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

CG13348

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

TC010176

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

Aminoacyl-tRNA biosynthesis

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

Aminoacyl-tRNA biosynthesis

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

36547

References (45)

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

1.85

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