FB2019_06, released Dec 19, 2019

Gene: Dmel\Tnpo

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General Information
Symbol
Dmel\Tnpo
Species
D. melanogaster
Name
Transportin
Annotation Symbol
CG7398
Feature Type
protein_coding_gene
FlyBase ID
FBgn0024921
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Snapshot
Transportin (Tnpo) encodes a protein involved in Hh signalling regulation by mediating the import of the transcription factor encoded by ci into the nucleus. [Date last reviewed: 2019-09-12]
Other Summaries
Also Known As
Trn, dTRN
Key Links
Genomic Location
Cytogenetic map
65A8-65A8
Sequence location
3L:6,193,480..6,200,385 [+]
Recombination map
3-16
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
GO Summary Ribbons
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
nuclear import signal receptor activity; nuclear localization sequence binding; Ran GTPase binding
Summaries
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).
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\Tnpo or the JBrowse view of Dmel\Tnpo 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
Comments on Gene Model
Low-frequency RNA-Seq exon junction(s) not annotated.
Gene model reviewed during 5.46
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-RA
FBtr0077000
NM_058020
5496
893
Tnpo-RB
FBtr0077001
NM_168160
4704
893
Tnpo-RC
FBtr0077002
NM_168161
4666
893
Tnpo-RD
FBtr0333059
NM_001274543
5414
893
Additional Transcript Data and Comments
Reported size (kB)
2.788 (longest cDNA)
(Siomi et al., 1998)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
Tnpo-PA
FBpp0076708
101.5
893
4.70
NP_477368
AAF50674
Tnpo-PB
FBpp0076709
101.5
893
4.70
NP_729154
AAN12089
Tnpo-PC
FBpp0076710
101.5
893
4.70
NP_729155
AAN12090
Tnpo-PD
FBpp0305273
101.5
893
4.70
NP_001261472
AGB94167
Polypeptides with Identical Sequences

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

893 aa isoforms: Tnpo-PA, Tnpo-PB, Tnpo-PC, Tnpo-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
893 (aa)
(Siomi et al., 1998)
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\Tnpo using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
Gene Ontology (9 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
nuclear import signal receptor activity
inferred from biological aspect of ancestor with PANTHER:PTN000055427
(assigned by GO_Central )
(Gaudet et al., 2011)
nuclear localization sequence binding
inferred from biological aspect of ancestor with PANTHER:PTN000055427
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with SGD:S000000221
(FlyBase Curators, 2008--)
Ran GTPase binding
inferred from electronic annotation with InterPro:IPR001494
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
larval lymph gland hemopoiesis
inferred from mutant phenotype
(Mondal et al., 2014)
regulation of protein import into nucleus
inferred from mutant phenotype
(Shi et al., 2014)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
protein import into nucleus
inferred from sequence or structural similarity with SGD:S000000221
(FlyBase Curators, 2008--)
inferred from biological aspect of ancestor with PANTHER:PTN000055427
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000055427
(assigned by GO_Central )
(Gaudet et al., 2011)
cytosol
inferred from sequence or structural similarity with SGD:S000000221
(FlyBase Curators, 2008--)
nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000055427
(assigned by GO_Central )
(Gaudet et al., 2011)
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Tnpo in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
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, and Transgenic Constructs
Classical and Insertion Alleles ( 3 )
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 Tnpo
Transgenic constructs containing regulatory region of Tnpo
Deletions and Duplications ( 1 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\TNPO1
13 of 15
Yes
Yes
 
 
Hsap\TNPO2
12 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Tnpo1
13 of 15
Yes
Yes
Mmus\Tnpo2
12 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Tnpo2
11 of 13
Yes
Yes
Rnor\Tnpo1
10 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\tnpo1
8 of 12
Yes
Yes
Xtro\tnpo2
7 of 12
No
Yes
Danio rerio (Zebrafish) (3)
Drer\tnpo2
11 of 15
Yes
Yes
Drer\tnpo1
9 of 15
No
Yes
Drer\LOC100005536
5 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\imb-2
13 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\TRN1
7 of 9
Yes
Yes
Atha\AT2G16960
2 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\KAP104
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\kap104
11 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190236 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\Tnpo
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00004179
Drosophila simulans
Dsim\GD28813
Drosophila sechellia
Dsec\GM14771
Drosophila erecta
Dere\GG15334
Drosophila yakuba
Dyak\GE21552
Drosophila ananassae
Dana\GF23533
Drosophila pseudoobscura pseudoobscura
Dpse\GA20324
Drosophila persimilis
Dper\GL22567
Drosophila willistoni
Dwil\GK16930
Drosophila virilis
Dvir\GJ13363
Drosophila mojavensis
Dmoj\GI12093
Drosophila grimshawi
Dgri\GH15155
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915015F )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17008372
Glossina morsitans
Tsetse fly
Gmor\GMOY001147
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_07512
Mayetiola destructor
Hessian fly
Mdes\Mdes001441
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL007521
Anopheles darlingi
American malaria mosquito
Adar\ADAC005021
Anopheles gambiae
Malaria mosquito
Agam\AGAP005892
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ000096
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00Y6 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA003635
Danaus plexippus
Monarch butterfly
Dple\DPOGS215758-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL014131
Apis florea
Little honeybee
Aflo\2443304180
Apis mellifera
Western honey bee
Amel\LOC408842
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP19315
Bombus terrestris
Buff-tailed bumblebee
Bter\15216658
Linepithema humile
Argentine ant
Lhum\LH12460
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:00271d
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG006021
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_03306
Tribolium castaneum
Red flour beetle
Tcas\TC001725
Pediculus humanus
Human body louse
Phum\PHUM308970
Rhodnius prolixus
Kissing bug
Rpro\RPRC011412
Rhodnius prolixus
Kissing bug
Rpro\RPRC010058
Cimex lectularius
Bed bug
Clec\CLEC005907
Cimex lectularius
Bed bug
Clec\CLEC000618
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI010129
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_10650
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00WF )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR013103
Ixodes scapularis
Black-legged tick
Isca\ISCW010530
Stegodyphus mimosarum
African social velvet spider
Smim\KFM58112.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM58113.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur27g01540
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_307700
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_301259
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G01O2 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Tnpo1_2
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Tnpo1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_005561gn
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000008100
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000021247
Gallus gallus
Domestic chicken
Ggal\TNPO1
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (5)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG8219
6 of 10
Apl
1 of 10
Arts
1 of 10
Fs(2)Ket
1 of 10
Karyβ3
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 ( 3 )
    Disease Associations of Human Orthologs (via DIOPT v7.1 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?
    TNPO1; transportin 1
    13 of 15
    602901
         
        TNPO2; transportin 2
        12 of 15
        603002
            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
            Tnpo
            Hsap\TNPO1
            (Jäckel et al., 2015)
            Interactions
            Summary of Physical Interactions
            esyN Network Diagram
            Show neighbor-neighbor interactions:
            Select Layout:
            Legend:
            Protein
            RNA
            Selected Interactor(s)
            Interactions Browser
            View in Interactions Browser
            Please see the Physical Interaction reports below for full details
            protein-protein
            Physical Interaction
            Assay
            References
            Tnpo - ci
            anti tag coimmunoprecipitation, anti tag western blot, pull down
            (Shi et al., 2014)
            Tnpo - sqd
            pull down, autoradiography
            (Norvell et al., 1999)
            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.
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            3L
            Recombination map
            3-16
            Cytogenetic map
            65A8-65A8
            Sequence location
            3L:6,193,480..6,200,385 [+]
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            65A8-65A8
            Limits computationally determined from genome sequence between P{PZ}l(3)0209402094 and P{lacW}l(3)L4060L4060
            Experimentally Determined Cytological Location
            Cytogenetic map
            Notes
            References
            Experimentally Determined Recombination Data
            Location
            3-16
            (FlyBase, 2016)
            3-14.4
            (Comeron et al., 2012)
            Left of (cM)
            Right of (cM)
            Notes
            Stocks and Reagents
            Stocks (9)
            Genomic Clones (18)
             

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

            cDNA Clones (154)
             

            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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

            cDNA clones, fully sequences
            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
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            Antibody Information
            Laboratory Generated Antibodies
             
            Commercially Available Antibodies
             
            Other Information
            Relationship to Other Genes
            Source for database identify of
            Source for identity of: Trn CG7398
            (Gabrielian, 1999.11)
            Source for identity of: Tnpo Trn
            (FlyBase, 2009-)
            Source for database merge of
            Additional comments
            Symbol changed from 'Trn' to 'Tnpo' (as of FB2017_04) to reduce confusion with the different gene 'trn' (tartan, FBgn0010452). The symbol of 'Trn' (Transportin) was changed because: (i) it has a smaller associated literature than 'trn' (tartan); (ii) it was named/characterized subsequently to 'trn' (tartan) (1998/FBrf0103092 vs 1993/FBrf0064397); (iii) it was originally named (FBrf0103092) based on its homology to the human 'transportin 1' gene, which now has the symbol 'TNPO1' and is also the symbol used for the orthologous gene in other vertebrates.
            (FlyBase, 2009-)
            Other Comments
            S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.
            (Stroschein-Stevenson et al., 2006)
            Trn has been cloned and sequenced.
            (Siomi et al., 1998)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 62 )
            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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
            Other crossreferences
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            Flygut - An atlas of the Drosophila adult midgut
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            modMine - A data warehouse for the modENCODE project
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            FLIGHT - Cell culture data for RNAi and other high-throughput technologies
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            FlyMine - An integrated database for Drosophila genomics
            InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Synonyms and Secondary IDs (15)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (65)