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    TNPO3 transportin 3 [ Homo sapiens (human) ]

    Gene ID: 23534, updated on 4-Jul-2021

    Summary

    Official Symbol
    TNPO3provided by HGNC
    Official Full Name
    transportin 3provided by HGNC
    Primary source
    HGNC:HGNC:17103
    See related
    Ensembl:ENSG00000064419 MIM:610032
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IPO12; TRNSR; LGMD1F; LGMDD2; MTR10A; TRN-SR; TRN-SR2
    Summary
    The protein encoded by this gene is a nuclear import receptor for serine/arginine-rich (SR) proteins such as the splicing factors SFRS1 and SFRS2. The encoded protein has also been shown to be involved in HIV-1 infection, apparently through interaction with the HIV-1 capsid protein. Several protein-coding and non-coding transcript variants have been found for this gene. [provided by RefSeq, Apr 2020]
    Expression
    Ubiquitous expression in testis (RPKM 16.7), thyroid (RPKM 13.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See TNPO3 in Genome Data Viewer
    Location:
    7q32.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (128954185..129055111, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128594239..128695165, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2205 Neighboring gene interferon regulatory factor 5 Neighboring gene RNA, 7SL, cytoplasmic 306, pseudogene Neighboring gene ornithine decarboxylase pseudogene Neighboring gene triosephosphate isomerase 1 pseudogene 2 Neighboring gene zinc finger protein 195-like

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
    GeneReviews: Not available
    Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX.
    GeneReviews: Not available
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    GeneReviews: Not available
    Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
    GeneReviews: Not available
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    GeneReviews: Not available
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    GeneReviews: Not available
    Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.
    GeneReviews: Not available
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    GeneReviews: Not available
    Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis.
    GeneReviews: Not available
    Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.
    GeneReviews: Not available
    GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
    GeneReviews: Not available
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    GeneReviews: Not available
    Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
    GeneReviews: Not available
    Limb-girdle muscular dystrophy, type 1F
    MedGen: C1842062 OMIM: 608423 GeneReviews: Not available
    Compare labs
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    GeneReviews: Not available
    Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.
    GeneReviews: Not available

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 LAI replication requires PSIP1 (LEDGF) and TNPO3 expression as shown through CRISPR/Cas9 genome editing in primary CD4+ T cells PubMed
    Knockdown of CPSF6, TNPO3, or NUP153 through siRNA leads to decreased CA and viral DNA nuclear entry PubMed
    shRNA knockdown of TNPO3 renders cells less permissive to HIV-1 WT; HIV-1 is enhanced by TNPO3 PubMed
    Knockdown of transportin 3 (TNPO3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
    Knockdown of transportin 3 (TNPO3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev disrupts both IN-TNPO3 and IN-importin alpha complexes PubMed
    rev The interaction of HIV-1 Rev with RAN or NUP98 hypothetically induces the binding of Rev to transportin 3 PubMed
    capsid gag TNPO3 is an export factor for both HIV-1 CA and tRNAs from the nucleus of infected cells PubMed
    gag HIV-1 inhibition by TNPO3 knockdown and CPSF6-358 is a CA-dependent manner and cytoplasmic localization of CPSF6-358 is required to inhibit HIV-1 PubMed
    gag TNPO3 directly interacts with in vitro-assembled HIV-1 CA-NC complexes. However, the other report that TNPO3 does not interact directly with HIV-1 CA tubes in vitro PubMed
    gag Cyclophilin A stabilizes the HIV-1 CA and antagonizes TNPO3 acceleration of uncoating in vitro PubMed
    gag HIV-1 N74D CA mutant remains partially dependent on TRN-SR2 for efficient infection when carrying the HIV envelope PubMed
    gag Residues N57, M66, Q67, K70, N74, and T107 in the N-terminal domain of HIV-1 CA are important for the binding to CPSF6. Mutations on these residues lead to the loss or reduction of dependency on TNPO3 and RanBP2 PubMed
    gag HIV-1 replication is dependent on TNPO3 expression and HIV-1 CA is the primary determinant for HIV-1 dependence upon TNPO3 PubMed
    gag Replacing HIV-1 CA with the corresponding MLV CA strikingly induce the chimera viruses insensitive to TNPO3 knockdown, suggesting that CA is a dominant viral determinant of TNPO3 dependency during HIV-1 infection PubMed
    gag HIV-1 CA and viral tRNAs bind to TNPO3 with greater affinity in the presence of RanGTP. The last 98 residues (amino acids 826-923) are important for CA and tRNA binding PubMed
    gag RanGTP inhibits the ability of TNPO3 to stimulate the uncoating of HIV-1 CA cores PubMed
    gag HIV-1 CA mutant with five amino acid substitutions (Q67H, K70R, H87P, T107N, and L111I) confers TNPO3-independence PubMed
    integrase gag-pol HIV-1 IN mutant R263A/K264A significantly reduces its ability of binding to TRN-SR2 and displays a block in nuclear import and integration PubMed
    gag-pol Site specific mutagenesis reveals that residues 185FKRK188 in the catalytic core domain (CCD) and 262RRK264 and K266/R269 in the C-terminal domain (CTD) in HIV-1 IN are important for its binding to TRN-SR2 PubMed
    gag-pol HIV-1 IN (amino acids 62-176) interacts with TRN-SR2 (amino acids 62-334) in yeast two-hybrid screen. TRN-SR2 imports the preintegration complex into the nucleus and TRN-SR2 knockdown inhibits early steps of HIV-1 replication PubMed
    gag-pol The binding between HIV-1 IN and TNPO3 is inhibited by RanGTP in a dose-dependent manner, leading to a TNPO3-RanGTP complex formation PubMed
    gag-pol R400E/R402E and Q761E/R762E substitutions in TNPO3 significantly impair its binding to HIV-1 IN. However, E304R and E391R/E392R have very little effect on the IN-TNPO3 interaction PubMed
    gag-pol Peptides (amino acids 170-191, 214-229, and 262-274) derived the C-terminal domain of HIV-1 IN bind to TRN-SR2 PubMed
    gag-pol HIV-1 Rev disrupts both IN-TNPO3 and IN-importin alpha complexes PubMed
    nucleocapsid gag TNPO3 directly interacts with in vitro-assembled HIV-1 CA-NC complexes PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables nuclear import signal receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small GTPase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein import into nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in annulate lamellae IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transportin-3
    Names
    imp12
    importin 12
    limb girdle muscular dystrophy 1F (autosomal dominant)
    transportin-SR

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_023428.1 RefSeqGene

      Range
      5001..105994
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001191028.3NP_001177957.2  transportin-3 isoform 2

      See identical proteins and their annotated locations for NP_001177957.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC018639, AC025594
      Consensus CDS
      CCDS55162.1
      UniProtKB/Swiss-Prot
      Q9Y5L0
      UniProtKB/TrEMBL
      B3KMX1
      Related
      ENSP00000418646.1, ENST00000471234.5
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:120248
      Xpo1; Exportin 1-like protein
    2. NM_001382216.1NP_001369145.1  transportin-3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) encodes the longest isoform (3).
      Source sequence(s)
      AC018639, AC025594
      Related
      ENSP00000487231.1, ENST00000627585.2
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    3. NM_001382217.1NP_001369146.1  transportin-3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:161275
      Xpo1; Exportin 1-like protein
    4. NM_001382218.1NP_001369147.1  transportin-3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    5. NM_001382219.1NP_001369148.1  transportin-3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    6. NM_001382220.1NP_001369149.1  transportin-3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    7. NM_001382221.1NP_001369150.1  transportin-3 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    8. NM_001382222.1NP_001369151.1  transportin-3 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    9. NM_001382223.1NP_001369152.1  transportin-3 isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein
    10. NM_012470.4NP_036602.1  transportin-3 isoform 1

      See identical proteins and their annotated locations for NP_036602.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC018639, AC025594
      Consensus CDS
      CCDS5809.1
      UniProtKB/Swiss-Prot
      Q9Y5L0
      UniProtKB/TrEMBL
      A0A024R794, B3KMX1
      Related
      ENSP00000265388.5, ENST00000265388.10
      Conserved Domains (2) summary
      smart00913
      Location:3396
      IBN_N; Importin-beta N-terminal domain
      pfam08389
      Location:121248
      Xpo1; Exportin 1-like protein

    RNA

    1. NR_034053.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon compared to variant 1, that causes a frameshift. An in-frame downstream translational start site is available, but it is probably not used due to an upstream ORF (uORF) with a strong Kozak consensus sequence, as well as two uORFs that overlap the putative downstream start site.
      Source sequence(s)
      AC018639, AC025594
    2. NR_167911.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    3. NR_167912.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    4. NR_167913.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    5. NR_167914.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    6. NR_167915.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    7. NR_167916.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    8. NR_167917.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    9. NR_167918.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    10. NR_167919.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    11. NR_167920.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    12. NR_167921.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    13. NR_167922.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    14. NR_167923.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    15. NR_167924.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    16. NR_167925.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    17. NR_167926.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594
    18. NR_167927.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC018639, AC025594

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

      Range
      128954185..129055111 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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