FlyBase Gene Report: Dmel\trsn

General Information

Symbol

Dmel\trsn

Species

D. melanogaster

Name

translin

Annotation Symbol

CG11761

Feature Type

protein_coding_gene

FlyBase ID

FBgn0033528

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

translin (trsn) encodes a protein that, together with the product of Trax, forms the Trsn/Trax complex, a ribonuclease that facilitates RNA-induced silencing complex (RISC) activation and has been implicated in many different processes, including starvation-induced sleep suppression. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

47A11-47A11

Sequence location

2R:10,479,011..10,480,111 [-]

Recombination map

2-62

RefSeq locus

NT_033778 REGION:10479011..10480111

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 (13 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables protein homodimerization activity

inferred from physical interaction with UniProtKB:Q7JVK6

(Suseendranathan et al., 2007)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

enables RNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000077814

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR033956

(InterPro Project Members, 2004-)

enables sequence-specific DNA binding

inferred from electronic annotation with InterPro:IPR002848, InterPro:IPR016068, InterPro:IPR036081

(InterPro Project Members, 2004-)

inferred from electronic annotation with InterPro:IPR002848, InterPro:IPR016068, InterPro:IPR016069, InterPro:IPR036081

(InterPro Project Members, 2004-)

enables single-stranded DNA binding

inferred from electronic annotation with InterPro:IPR033956

(InterPro Project Members, 2004-)

NOT enables RNA endonuclease activity

inferred from key residues

(Liu et al., 2009)

Biological Process (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in behavioral response to starvation

inferred from mutant phenotype

(Murakami et al., 2016)

involved_in negative regulation of circadian sleep/wake cycle, sleep

inferred from mutant phenotype

(Murakami et al., 2016)

involved_in protein stabilization

inferred from mutant phenotype

(Claussen et al., 2006)

involved_in regulatory ncRNA-mediated post-transcriptional gene silencing

inferred from mutant phenotype

(Liu et al., 2009)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in RNA metabolic process

inferred from electronic annotation with InterPro:IPR033956

(InterPro Project Members, 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Suseendranathan et al., 2007, Claussen et al., 2006)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000077814

(GO Reference Genome Project, 2011-)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000077815

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

UNCLASSIFIED PSEUDOENZYMES

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

UNCLASSIFIED PSEUDOENZYMES -: This group comprises pseudoenzymes that do not classify under other groups in FlyBase.

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\trsn 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 Q7JVK6)

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

PDB - An information portal to biological macromolecular structures

Comments on Gene Model

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

trsn-RA

FBtr0088306

NM_136747

864

235

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

trsn-PA

FBpp0087398

27.0

235

5.19

Q7JVK6

NP_610591

AAF58784

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

PDB - An information portal to biological macromolecular structures

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\trsn using the Feature Mapper tool.

External Data

Crossreferences

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

trsn_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).

1.83

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

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | faint | ubiquitous

(Fisher et al., 2012)

organism | ubiquitous

(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

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 4

organism | ubiquitous

• cytoplasm

(Suseendranathan et al., 2007)

embryonic stage 8 -- 9

embryonic neuroblast

(Suseendranathan et al., 2007)

third instar larval stage

ventral midline of embryo

(Suseendranathan et al., 2007)

embryonic/larval oenocyte

(Suseendranathan et al., 2007)

larval abdomen

(Suseendranathan et al., 2007)

embryonic/larval epidermis

Comment: in abdomen

(Suseendranathan et al., 2007)

adult stage | male

testis

(Suseendranathan et al., 2007)

spermatocyte

(Suseendranathan et al., 2007)

adult stage

adult brain

(Suseendranathan et al., 2007)

neuron

(Suseendranathan et al., 2007)

Additional Descriptive Data

trsn protein shows a uniform staining pattern in early embryos. In stage 8-9 embryos trsn is enriched in neuroblasts as they delaminae from the ectoderm. Later it is enriched in cells surrounding the tracheal pits. In third instar larvae, expression is observed in the ventral midline and also in the body wall. trsn protein is highly enriched in a cluster of six cells located laterally in each abdominal segment that are thought to be oenocytes. It is also expressed in epidermal cells in the abdominal segments. It is also observed in spermatocytes.

(Suseendranathan et al., 2007)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytosol

inferred from direct assay

(Suseendranathan et al., 2007, Claussen et al., 2006)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\trsn in JBrowse

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

View exonic expression by developmental stage for Dmel\trsn

View exonic expression by tissue for Dmel\trsn

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

FBgn0033528

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

36110/tissue=All

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

FBgn0033528

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033528

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

FBgn0033528

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

CG11761

Flygut - An atlas of the Drosophila adult midgut

FBgn0033528

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

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 trsn

Transgenic constructs containing regulatory region of trsn

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

viable

viable, with Scer\GAL4^Mef2.PR

trsn^GD1918

viable, with Scer\GAL4^pnr-MD237

trsn^GD1918

viable, with Scer\GAL4^tin.CΔ4

trsn^GD1918

Sterility

Allele

fertile

Other Phenotypes

Allele

abnormal jump response | recessive

trsn^EY06981

abnormal sleep | adult stage | :nutrition conditional | RU486 conditional, with Scer\GAL4^{elav.Switch.PO}

abnormal sleep | adult stage | nutrition conditional

abnormal sleep | adult stage | nutrition conditional, with Scer\GAL4^Lk.PK

abnormal sleep | adult stage | nutrition conditional, with Scer\GAL4^nSyb.PS

abnormal starvation stress response | adult stage

abnormal starvation stress response | adult stage, with Scer\GAL4^Lk.PK

abnormal starvation stress response | adult stage, with Scer\GAL4^nSyb.PS

abnormal starvation stress response | adult stage | RU486 conditional, with Scer\GAL4^{elav.Switch.PO}

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) (2)

Hsap\TSN

14 of 14

Yes

Hsap\TSNAX

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) (2)

Rnor\Tsn

13 of 14

Yes

Rnor\Tsnax

1 of 14

Mus musculus (laboratory mouse) (2)

Mmus\Tsn

13 of 14

Yes

Mmus\Tsnax

1 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\tsn

7 of 13

Yes

Xtro\tsnax

1 of 13

Xtro\XB5799768

1 of 13

Yes

Danio rerio (Zebrafish) (2)

Drer\tsn

14 of 14

Yes

Drer\tsnax

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (2)

Agam\AgaP_AGAP005538

12 of 12

Yes

Agam\AgaP_AGAP004585

1 of 12

Arabidopsis thaliana (thale-cress) (2)

Atha\AT2G37020

13 of 13

Yes

Atha\AT2G03780

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (2)

Spom\tsn1

12 of 12

Yes

Spom\SPCC736.09c

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:trsn. 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)

Trax

3 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?

TSN; translin

14 of 14

600575

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

trsn

two hybrid, pull down, molecular sieving, ion exchange chromatography, x-ray crystallography

(Hu et al., 2017.6.13, Kumar and Gupta, 2012)

trsn - Trax

two hybrid, chromatography technology, ion exchange chromatography, molecular sieving, western blot, molecular weight, Identification by mass spectrometry, mass spectrometry studies of complexes, x-ray crystallography, electron microscopy, experimental knowledge based, light scattering

(Mo et al., 2018, Hu et al., 2017.6.13, Guruharsha et al., 2011, Tian et al., 2011, Liu et al., 2009)

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.

61927

DroID - A comprehensive database of gene and protein interactions.

FBgn0033528

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

36110

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

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

Small interfering RNA (siRNA) biogenesis

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-62

Cytogenetic map

47A11-47A11

Sequence location

2R:10,479,011..10,480,111 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

47A11-47A11

Limits computationally determined from genome sequence between P{lacW}Hr46^k10308 and P{PZ}lola⁰⁰³⁴⁹&P{EP}lola^EP952

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-62

(FlyBase, 2016)

2-61.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

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

Bloomington

16774

y¹ w^67c23; P{EPgy2}trsn^EY06981

NIG-Fly

11761R-2

P{NIG.11761R}2

2RG-0120

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

VDRC

v108456

P{KK108391}VIE-260B

v9963

w¹¹¹⁸; P{GD1918}v9963

v342169

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD01701}attP40/CyO-GFP

Genomic Clones (11)

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

cDNA Clones (33)

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

GM27569

Other clones

DPiM_GM27569

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.

FBgn0033528

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0033528

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Suseendranathan et al., 2007)

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

Source for identity of translin CG11761 was sequence comparison ( date:031005 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Source for identity of: trsn translin

(Claussen et al., 2006)

Source for identity of: translin CG11761

(FlyBase, 1996-)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG11761

(National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Llamusi et al., 2013, Keleman et al., 2009.8.5, Strub et al., 2008, Giot et al., 2003)

TB-RBP

(Liu et al., 2009)

translin

trsn

(Zheng et al., 2023, Pennemann et al., 2021, Hu et al., 2017.6.13, Stahl et al., 2017, Murakami et al., 2016, Van Bortle et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Liu et al., 2009, Claussen et al., 2006)

Name Synonyms

TRANSLIN

(Suseendranathan et al., 2007)

Translin

(Nässel, 2021, Liu et al., 2019, Mo et al., 2018, Xiong et al., 2013)

testis-brain RNA binding protein

(Liu et al., 2009)

translin

(Murakami et al., 2016, Kumar and Gupta, 2012, Tian et al., 2011, Vazquez-Pianzola et al., 2011, Liu et al., 2009, Gupta et al., 2008, Suseendranathan et al., 2007, Claussen et al., 2006, Claussen et al., 2006, Sengupta et al., 2006)

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 ( 47 )

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.

36110

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.

Q7JVK6

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.

Q7JVK6

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0033528

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

36110/tissue=All

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

FBgn0033528

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

FBgn0033528

FlyMine - An integrated database for Drosophila genomics

FBgn0033528

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

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

dme:Dmel_CG11761

MARRVEL_MODEL - MARRVEL (model organism gene)

36110

PDB - An information portal to biological macromolecular structures

Linkouts

BioGRID - A database of protein and genetic interactions.

61927

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

FBgn0033528

DroID - A comprehensive database of gene and protein interactions.

FBgn0033528

DRSC - Results frm RNAi screens

FBgn0033528

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

trsn_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0033528

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0033528

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

CG11761

Flygut - An atlas of the Drosophila adult midgut

FBgn0033528

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

FBgn0033528

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

TC009885

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

36110

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

Small interfering RNA (siRNA) biogenesis

References (56)

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

1.83

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