FlyBase Gene Report: Dmel\Mtr3

General Information

Symbol

Dmel\Mtr3

Species

D. melanogaster

Name

Mtr3

Annotation Symbol

CG8025

Feature Type

protein_coding_gene

FlyBase ID

FBgn0036916

Gene Model Status

Current

Stock Availability

5 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

dMtr3

Key Links

Genomic Location

Cytogenetic map

76D4-76D4

Sequence location

3L:19,912,405..19,913,715 [-]

Recombination map

3-46

RefSeq locus

NT_037436 REGION:19912405..19913715

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 (11 terms)

Molecular Function (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000237327

(GO Reference Genome Project, 2011-)

Biological Process (5 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in regulation of gene expression

inferred from mutant phenotype

(Kiss and Andrulis, 2010)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in nuclear mRNA surveillance

inferred from biological aspect of ancestor with PANTHER:PTN000237329

(GO Reference Genome Project, 2011-)

involved_in poly(A)-dependent snoRNA 3'-end processing

inferred from biological aspect of ancestor with PANTHER:PTN000237329

(GO Reference Genome Project, 2011-)

involved_in rRNA catabolic process

inferred from biological aspect of ancestor with PANTHER:PTN000237327

(GO Reference Genome Project, 2011-)

involved_in U4 snRNA 3'-end processing

inferred from biological aspect of ancestor with PANTHER:PTN000237329

(GO Reference Genome Project, 2011-)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Graham et al., 2006)

part_of exosome (RNase complex)

inferred from direct assay

(Forler et al., 2003)

part_of nuclear exosome (RNase complex)

inferred from direct assay

(Andrulis et al., 2002)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of cytoplasmic exosome (RNase complex)

inferred from biological aspect of ancestor with PANTHER:PTN000237328

(GO Reference Genome Project, 2011-)

part_of nuclear exosome (RNase complex)

inferred from sequence or structural similarity with SGD:S000003390

(Andrulis et al., 2002)

inferred from biological aspect of ancestor with PANTHER:PTN000237329

(GO Reference Genome Project, 2011-)

is_active_in nucleolus

inferred from biological aspect of ancestor with PANTHER:PTN000237329

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

NUCLEAR EXOSOME COMPLEX

CYTOPLASMIC EXOSOME COMPLEX

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

NUCLEAR EXOSOME COMPLEX -: The nuclear exosome is a 3'-5' exonuclease complex that is involved in the processing and degradation many types of RNAs, including mRNA, rRNA, snRNA, snoRNA and tRNA. In yeast and humans, the exosome has a barrel structure, the core of which is formed by a ring of six RNase PH domain subunits and a cap of three S1/KH-domain subunits. (Adapted from FBrf0210381 and PMID:27345150).
CYTOPLASMIC EXOSOME COMPLEX -: The cytoplasmic exosome is a 3'-5' exonuclease complex involved in the processing and degradation many types of RNA which include the removal of unstable and aberrant transcripts. In yeast and humans, the exosome has a barrel structure, the core of which is formed by a ring of six RNase PH domain subunits and a cap of three S1/KH-domain subunits. (Adapted from FBrf0210381 and PMID:27345150).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Mtr3 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 Q9VW53)

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 5.45

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Mtr3-RA

FBtr0074918

NM_140900

1253

326

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

Mtr3-PA

FBpp0074687

36.6

326

4.87

Q9VW53

NP_649157

AAF49096

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\Mtr3 using the Feature Mapper tool.

External Data

Crossreferences

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

Mtr3_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).

3.03

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Graham et al., 2006)

part_of exosome (RNase complex)

inferred from direct assay

(Forler et al., 2003)

part_of nuclear exosome (RNase complex)

inferred from direct assay

(Andrulis et al., 2002)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Mtr3 in JBrowse

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

View exonic expression by developmental stage for Dmel\Mtr3

View exonic expression by tissue for Dmel\Mtr3

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

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

40173/tissue=All

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

FBgn0036916

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036916

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

FBgn0036916

Flygut - An atlas of the Drosophila adult midgut

FBgn0036916

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Mtr3

Transgenic constructs containing regulatory region of Mtr3

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 5 )

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 - all die during P-stage, with Scer\GAL4^Mef2.PR

Mtr3^GD10662

partially lethal - majority die, with Scer\GAL4^pnr-MD237

Mtr3^GD10662

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

Mtr3^GD10662

viable, with Scer\GAL4^tin.CΔ4

Mtr3^GD10662

Other Phenotypes

Allele

visible, with Scer\GAL4^pnr-MD237

Mtr3^GD10662

Phenotype manifest in

Allele

trichogen cell, with Scer\GAL4^pnr-MD237

Mtr3^GD10662

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\EXOSC6

9 of 14

Yes

Hsap\EXOSC4

4 of 14

Hsap\EXOSC5

3 of 14

Hsap\PNPT1

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) (4)

Rnor\Exosc6

9 of 14

Yes

Rnor\Exosc4

4 of 14

Rnor\Exosc5

3 of 14

Rnor\Pnpt1

1 of 14

Mus musculus (laboratory mouse) (4)

Mmus\Exosc6

7 of 14

Yes

Mmus\Exosc4

4 of 14

Mmus\Exosc5

3 of 14

Mmus\Pnpt1

1 of 14

Xenopus tropicalis (Western clawed frog) (4)

Xtro\exosc6

6 of 13

Yes

Xtro\exosc4

1 of 13

Xtro\pnpt1

1 of 13

Xtro\renbp

1 of 13

Danio rerio (Zebrafish) (4)

Drer\exosc6

11 of 14

Yes

Drer\exosc4

3 of 14

Drer\exosc5

3 of 14

Drer\exosc8

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (6)

Cele\exos-4.2

8 of 14

Yes

3 of 14

3 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP011906

11 of 12

Yes

3 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (8)

Atha\RRP41L

9 of 13

Yes

5 of 13

3 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\MTR3

5 of 13

Yes

Scer\SKI6

5 of 13

Yes

Scer\RRP46

3 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\SPBC211.08c

6 of 12

Yes

Spom\rrp41

5 of 12

Spom\rrp46

3 of 12

Escherichia coli (enterobacterium) (2)

Ecol\rph

6 of 11

Yes

Ecol\pnp

1 of 11

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Mtr3. 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) (4)

7 of 13

5 of 13

1 of 13

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 ( 0 )

Human Ortholog

Disease

Evidence

References

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?

EXOSC6; exosome component 6

9 of 14

606490

EXOSC4; exosome component 4

4 of 14

606491

EXOSC5; exosome component 5

3 of 14

606492

CEREBELLAR ATAXIA, BRAIN ABNORMALITIES, AND CARDIAC CONDUCTION DEFECTS; CABAC

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

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

Mtr3 - CG33672

two hybrid

(Hu et al., 2017.6.13)

Mtr3 - Csl4

experimental knowledge based

(Guruharsha et al., 2011)

Mtr3 - Dis3

experimental knowledge based, anti tag coimmunoprecipitation, western blot

(Guruharsha et al., 2011, Graham et al., 2009)

Mtr3 - Rrp4

experimental knowledge based

(Guruharsha et al., 2011)

Mtr3 - Rrp40

experimental knowledge based

(Guruharsha et al., 2011)

Mtr3 - Rrp42

experimental knowledge based

(Guruharsha et al., 2011)

Mtr3 - Rrp6

experimental knowledge based

(Guruharsha et al., 2011)

Mtr3 - Ski6

experimental knowledge based

(Guruharsha et al., 2011)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

65441

DroID - A comprehensive database of gene and protein interactions.

FBgn0036916

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

40173

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.

RNA degradation

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

3-46

Cytogenetic map

76D4-76D4

Sequence location

3L:19,912,405..19,913,715 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

76D4-76D4

Limits computationally determined from genome sequence between P{lacW}l(3)L1243^L1243&P{lacW}Mi-2^j3D4 and P{PZ}eRF1⁰⁰¹⁰³

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-46

(FlyBase, 2016)

3-43.5

(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

91624

Mtr3² red¹ e⁴/TM6B, Sb¹ Tb¹

FlyORF

F002979

M{UAS-Mtr3.ORF.3xHA.GW}ZH-86Fb

NIG-Fly

8025R-2

P{NIG.8025R}2

VDRC

v26038

w¹¹¹⁸; P{GD10662}v26038

v26039

w¹¹¹⁸; P{GD10662}v26039

Genomic Clones (16)

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

cDNA Clones (16)

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

RE29317

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.

FBgn0036916

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0036916

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

New stable cell line derived from S2-unspecified : Stable S2 cell lines were created expressing copper-inducible epitope-tagged exosome subunits to examine the subcellular distribution of exosome complex components. Stable lines were created containing the following exosome subunits; Dis3, Rrp6, Mtr3, Rrp42, Rrp4, Ski6, Rrp46, Rrp40, and Csl4.
(Graham et al., 2006)

Other Comments

Identification: as a protein that copurifies with Spt6 protein.

(Andrulis et al., 2002)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Mtr3 CG8025

(Andrulis et al., 2002)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

CG8025

(Horan et al., 2015, Hosono et al., 2015, Graham et al., 2006, Giot et al., 2003, Andrulis et al., 2002)

Mtr3

(Choudhury et al., 2024, Kennison, 2020.10.22, Hu et al., 2017.6.13, Brewer-Jensen et al., 2016, Horan et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Guo et al., 2011, Avet-Rochex et al., 2010, Cooper et al., 2010, Kiss and Andrulis, 2010)

dMtr3

(Graham et al., 2009, Graham et al., 2006, Andrulis et al., 2002)

mtr3

(Flynt et al., 2010)

Name Synonyms

Mtr3

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 ( 36 )

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.

40173

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

BT021289

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.

Q9VW53

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.

Q9VW53

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

40173/tissue=All

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

FBgn0036916

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

FBgn0036916

FlyMine - An integrated database for Drosophila genomics

FBgn0036916

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

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

dme:Dmel_CG8025

MARRVEL_MODEL - MARRVEL (model organism gene)

40173

Linkouts

BioGRID - A database of protein and genetic interactions.

65441

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

FBgn0036916

DroID - A comprehensive database of gene and protein interactions.

FBgn0036916

DRSC - Results frm RNAi screens

FBgn0036916

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

Mtr3_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0036916

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0036916

Flygut - An atlas of the Drosophila adult midgut

FBgn0036916

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

FBgn0036916

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

TC008865

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

RNA degradation

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

40173

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

References (39)

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

3.03

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