FB2024_02 , released April 23, 2024
Gene: Dmel\Tnpo-SR
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General Information
Symbol
Dmel\Tnpo-SR
Species
D. melanogaster
Name
Transportin-Serine/Arginine rich
Annotation Symbol
CG2848
Feature Type
protein_coding_gene
FlyBase ID
FBgn0031456
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
Transportin-Serine/Arginine rich (Tnpo-SR) encodes a importin-beta family protein involved in the regulation of mRNA splicing. It contributes to the import into the nucleus of serine/arginine-rich (SR) proteins, which are involved in mRNA splicing. [Date last reviewed: 2019-09-12] (FlyBase Gene Snapshot)
All Summaries
Also Known As

Trn-SR, TNPO3

Key Links
Genomic Location
Cytogenetic map
23A3-23A5
Sequence location
Recombination map
2-7
RefSeq locus
NT_033779 REGION:2759924..2763889
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (7 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 small GTPase binding
inferred from electronic annotation with InterPro:IPR001494
(InterPro Project Members, 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in protein import into nucleus
inferred from direct assay
(Allemand et al., 2002)
involved_in regulation of mRNA splicing, via spliceosome
inferred from direct assay
(Allemand et al., 2002)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in intracellular protein transport
inferred from electronic annotation with InterPro:IPR001494
(InterPro Project Members, 2004-)
involved_in protein import into nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000270925
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
(Allemand et al., 2002)
located_in nucleus
inferred from direct assay
(Allemand et al., 2002)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000270925
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Transportin-Serine/Arginine rich (Tnpo-SR) encodes a importin-beta family protein involved in the regulation of mRNA splicing. It contributes to the import into the nucleus of serine/arginine-rich (SR) proteins, which are involved in mRNA splicing. [Date last reviewed: 2019-09-12]
Gene Group (FlyBase)
BETA IMPORTINS -
Importin-β family proteins are nucleocytoplasmic transport receptors that import and export proteins and RNAs through the nuclear pores. In some import/export pathways, importin-β directly interacts with the cargo. For cargo containing a classical nuclear localization (cNLS) signal, importin-α acts as an adaptor linking the cargo to importin-β. (Adapted from FBrf0235243, FBrf0131350 and PMID:21029754).
Summary (Interactive Fly)

an importin-ß family member responsible for transporting SR protein splice factors into the nucleus

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Tnpo-SR 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 Q9VQG0)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

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

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Tnpo-SR-RA
FBtr0077715
NM_134864
3307
932
Tnpo-SR-RB
FBtr0335126
NM_001273032
3586
932
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
Tnpo-SR-PA
FBpp0077399
105.8
932
5.69
Q9VQG0
NP_608708
AAF51214
Tnpo-SR-PB
FBpp0307125
105.8
932
5.69
Q9VQG0
NP_001259961
AGB92498
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

932 aa isoforms: Tnpo-SR-PA, Tnpo-SR-PB
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\Tnpo-SR using the Feature Mapper tool.

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

0.49

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
distribution deduced from reporter or direct label
Stage
Tissue/Position (including subcellular localization)
Reference
• nucleus
(Allemand et al., 2002)
Additional Descriptive Data

The Tnpo-SR proteinshows a uniform nuclear distribution in cultured S2 cells.

(Allemand et al., 2002)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
(Allemand et al., 2002)
located_in nucleus
inferred from direct assay
(Allemand et al., 2002)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Tnpo-SR in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Tnpo-SR
Transgenic constructs containing regulatory region of Tnpo-SR
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2L)Exel6277
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (4)
Hsap\TNPO3
14 of 14
Yes
Yes
2  
Hsap\IPO13
1 of 14
No
No
Hsap\XPO1
1 of 14
No
No
Hsap\XPOT
1 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (3)
Rnor\Tnpo3
14 of 14
Yes
Yes
Rnor\Ipo13
1 of 14
No
No
Rnor\Xpo1
1 of 14
No
No
Mus musculus (laboratory mouse) (3)
Mmus\Tnpo3
13 of 14
Yes
Yes
Mmus\Ipo13
1 of 14
No
No
Mmus\Xpo1
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\tnpo3
7 of 13
Yes
Yes
Xtro\cth
1 of 13
No
No
Xtro\xpo1
1 of 13
No
No
Xtro\xpot
1 of 13
No
Yes
Danio rerio (Zebrafish) (6)
Drer\tnpo3
14 of 14
Yes
Yes
Drer\ipo13a
1 of 14
No
No
Drer\ipo13b
1 of 14
No
No
Drer\xpo1a
1 of 14
No
No
Drer\xpo1b
1 of 14
No
No
Drer\xpot
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\tsr-1
14 of 14
Yes
Yes
Cele\T16G12.6
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP003576
11 of 12
Yes
Yes
Agam\AgaP_AGAP009571
1 of 12
No
No
Agam\AgaP_AGAP009929
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (4)
Atha\MOS14
12 of 13
Yes
Yes
Atha\AT1G12930
3 of 13
No
No
Atha\XPO1A
1 of 13
No
No
Atha\XPO1B
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\MTR10
12 of 13
Yes
Yes
Scer\CRM1
1 of 13
No
No
Scer\KAP122
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\mtr10
11 of 12
Yes
Yes
Spom\kap111
2 of 12
No
No
Spom\crm1
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Tnpo-SR. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (3)
CG10950
5 of 13
cdm
3 of 13
emb
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
TNPO3; transportin 3
model of  autosomal dominant limb-girdle muscular dystrophy type 2
IEA
(FlyBase, 2019-)
Modifiers Based on Experimental Evidence ( 2 )
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?
TNPO3; transportin 3
14 of 14
610032
 
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:
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser
View in Interactions Browser
Please see the Physical Interaction reports below for full details
MIST Molecular Interaction Search Tool
View in MIST tool (external link)
Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Tnpo-SR - Act5C
pull down, autoradiography, bimolecular fluorescence complementation, fluorescence microscopy
(Borkúti et al., 2022)
Summary of Genetic Interactions
esyN Network Diagram
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.
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-7
Cytogenetic map
23A3-23A5
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
23A3-23A5
Limits computationally determined from genome sequence between P{EP}EP832 and P{PZ}oho23B03575
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

2-7

(FlyBase, 2016)

2-6.2

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (10)
Genomic Clones (11)
 

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

cDNA Clones (22)
 

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.

    cDNA Clones, End Sequenced (ESTs)
    BDGP DGC clones
    Other clones
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    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: Trn-SR anon- EST:Posey294

        (Ashburner, 2004.6.30)
        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: Trn-SR CG2848

        (Allemand et al., 2002)

        Source for identity of: Tnpo-SR Trn-SR

        (FlyBase, 2009-)
        Nomenclature comments

        Symbol changed from 'Trn-SR' to 'Tnpo-SR' (as of FB2017_04) to be consistent with the symbol change of 'Trn' to 'Tnpo' (which was done to minimise confusion with the different gene 'trn' (tartan, FBgn0010452).

        (FlyBase, 2009-)
        Etymology
        Synonyms and Secondary IDs (9)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 42 )
        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.
        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.
        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.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        FlyMine - An integrated database for Drosophila genomics
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (55)