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    TNPO1 transportin 1 [ Homo sapiens (human) ]

    Gene ID: 3842, updated on 7-Apr-2024

    Summary

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    Official Symbol
    TNPO1provided by HGNC
    Official Full Name
    transportin 1provided by HGNC
    Primary source
    HGNC:HGNC:6401
    See related
    Ensembl:ENSG00000083312 MIM:602901; AllianceGenome:HGNC:6401
    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
    MIP; TRN; IPO2; MIP1; KPNB2
    Summary
    This gene encodes the beta subunit of the karyopherin receptor complex which interacts with nuclear localization signals to target nuclear proteins to the nucleus. The karyopherin receptor complex is a heterodimer of an alpha subunit which recognizes the nuclear localization signal and a beta subunit which docks the complex at nucleoporins. Alternate splicing of this gene results in several transcript variants encoding different proteins. [provided by RefSeq, Jun 2018]
    Expression
    Ubiquitous expression in thyroid (RPKM 18.9), testis (RPKM 17.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    5q13.2
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (72816661..72914388)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (73297810..73395474)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (72112488..72210215)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene TNPO1 divergent transcript Neighboring gene ribosomal protein L7 pseudogene 22 Neighboring gene H2B.L histone variant 1, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22654 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16085 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22656 Neighboring gene ribosomal protein L35a pseudogene 13 Neighboring gene microRNA 4804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16086 Neighboring gene FCHO2 divergent transcript Neighboring gene FCH and mu domain containing endocytic adaptor 2 Neighboring gene CTDNEP1 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity. Fare CM, et al. J Biol Chem, 2023 Feb. PMID 36529289, Free PMC Article
    2. Transportin-1 binds to the HIV-1 capsid via a nuclear localization signal and triggers uncoating. Fernandez J, et al. Nat Microbiol, 2019 Nov. PMID 31611641
    3. Influenza virus uses transportin 1 for vRNP debundling during cell entry. Miyake Y, et al. Nat Microbiol, 2019 Apr. PMID 30692667
    4. Karyopherin-β2 Recognition of a PY-NLS Variant that Lacks the Proline-Tyrosine Motif. Soniat M, et al. Structure, 2016 Oct 4. PMID 27618664, Free PMC Article
    5. Conformational heterogeneity of karyopherin beta2 is segmental. Cansizoglu AE, et al. Structure, 2007 Nov. PMID 17997969, Free PMC Article

    See all (218) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif containing ciliary targeting sequence.
      Title: Rab8 and TNPO1 are ciliary transport adaptors for GTPase Arl13b by interacting with its RVEP motif containing ciliary targeting sequence.
    2. Transportin 1 is a major nuclear import receptor of the nitric oxide synthase interacting protein.
      Title: Transportin 1 is a major nuclear import receptor of the nitric oxide synthase interacting protein.
    3. A minimal construct of nuclear-import receptor Karyopherin-beta2 defines the regions critical for chaperone and disaggregation activity.
      Title: A minimal construct of nuclear-import receptor Karyopherin-β2 defines the regions critical for chaperone and disaggregation activity.
    4. Tumor suppressor BAP1 nuclear import is governed by transportin-1.
      Title: Tumor suppressor BAP1 nuclear import is governed by transportin-1.
    5. Mechanism of karyopherin-beta2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X).
      Title: Mechanism of karyopherin-β2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X).
    6. TNPO1-mediated nuclear import of ARID1B promotes tumor growth in ARID1A-deficient gynecologic cancer.
      Title: TNPO1-mediated nuclear import of ARID1B promotes tumor growth in ARID1A-deficient gynecologic cancer.
    7. TNPO1-Mediated Nuclear Import of FUBP1 Contributes to Tumor Immune Evasion by Increasing NRP1 Expression in Cervical Cancer.
      Title: TNPO1-Mediated Nuclear Import of FUBP1 Contributes to Tumor Immune Evasion by Increasing NRP1 Expression in Cervical Cancer.
    8. C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers.
      Title: C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers.
    9. Lysine acetylation regulates the RNA binding, subcellular localization and inclusion formation of FUS.
      Title: Lysine acetylation regulates the RNA binding, subcellular localization and inclusion formation of FUS.
    10. HIV-1 resists MxB inhibition of viral Rev protein.
      Title: HIV-1 resists MxB inhibition of viral Rev protein.
    Submit: New GeneRIF Correction See all GeneRIFs (50)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, TNPO1, is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    rev importin beta specifically binds to the Rev nuclear localization signal (NLS, amino acids 35-50) and mediates the nuclear import of Rev PubMed
    rev Importin beta can inhibit the interaction of HIV-1 Rev with HIV-1 RRE RNA PubMed
    Tat tat The binding of HIV-1 Tat with importin beta is inhibited by RanGTP PubMed
    tat Importin beta binds to the HIV-1 Tat protein nuclear localization signal (NLS; amino acids 49-57) and mediates the nuclear import of Tat through a novel import pathway PubMed
    Vpr vpr HIV-1 Vpr causes increased levels of CyclinB1, Plk1, and Cdk1 in a complex with the nuclear transport and spindle assembly protein, importin beta PubMed
    vpr HIV-1 Vpr co-localizes with karyopherin beta and regulates karyopherin beta-mediated docking of the HIV-1 preintegration complex at the nuclear envelope, however multiple reports indicate the two proteins do not directly interact PubMed
    integrase gag-pol Some reports indicate a possible role for the interactions between karyopherin alpha and beta with HIV-1 integrase in the nuclear import of HIV-1 preintegration complexes (PIC), while other reports indicate integrase is not involved in PIC nuclear import PubMed
    gag-pol Karyopherin beta binds to complexes between HIV-1 integrase (integrase/GST fusion protein) and karyopherin alpha, but not to integrase alone PubMed
    gag-pol Karyopherin alpha and beta are reported to interact with HIV-1 integrase (IN) to facilitate nuclear import of IN, however a conflicting report indicates nuclear accumulation of IN does not involve karyopherin alpha, beta 1, or beta 2 mediated pathways PubMed
    matrix gag Karyopherin beta mediates the nuclear import of HIV-1 preintegration complexes through karyopherin alpha, which binds directly to nuclear localization signals in HIV-1 Matrix PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables nuclear import signal receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nuclear localization sequence binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein import into nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transportin-1
    Names
    M9 region interaction protein
    importin 2
    importin beta 2
    karyopherin (importin) beta 2
    karyopherin beta-2

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001364292.3 → NP_001351221.1  transportin-1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
      Source sequence(s)
      AC008953, AC008972, AC035140
      Consensus CDS
      CCDS4016.1
      UniProtKB/TrEMBL
      A0A7P0T944
      Conserved Domains (2) summary
      COG5215
      Location:24 → 759
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:95 → 116
      HEAT; HEAT repeat [structural motif]

    2. NM_001364293.3 → NP_001351222.1  transportin-1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
      Source sequence(s)
      AC008953, AC008972
      Consensus CDS
      CCDS4016.1
      UniProtKB/TrEMBL
      A0A7P0T944
      Conserved Domains (2) summary
      COG5215
      Location:24 → 759
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:95 → 116
      HEAT; HEAT repeat [structural motif]

    3. NM_001364294.3 → NP_001351223.1  transportin-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AC008953, AC008972
      Consensus CDS
      CCDS93733.1
      UniProtKB/TrEMBL
      A0A7P0T944, A0A7P0TBF0
      Related
      ENSP00000506620.1, ENST00000679378.1
      Conserved Domains (2) summary
      COG5215
      Location:24 → 733
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:95 → 116
      HEAT; HEAT repeat [structural motif]

    4. NM_001364295.3 → NP_001351224.1  transportin-1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC008953, AC008972, AC035140
      Consensus CDS
      CCDS93732.1
      UniProtKB/TrEMBL
      A0A7P0T944
      Related
      ENSP00000428899.1, ENST00000523768.5
      Conserved Domains (2) summary
      COG5215
      Location:67 → 717
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:87 → 115
      HEAT; HEAT repeat [structural motif]

    5. NM_001364296.2 → NP_001351225.1  transportin-1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC008953
      Conserved Domains (3) summary
      sd00044
      Location:95 → 116
      HEAT; HEAT repeat [structural motif]
      pfam03810
      Location:34 → 101
      IBN_N; Importin-beta N-terminal domain
      cl27876
      Location:23 → 188
      Cse1

    6. NM_002270.4 → NP_002261.3  transportin-1 isoform 1

      See identical proteins and their annotated locations for NP_002261.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC008972, AC035140, U70322, U72069
      Consensus CDS
      CCDS43329.1
      UniProtKB/Swiss-Prot
      B4DVC6, Q92957, Q92973, Q92975
      UniProtKB/TrEMBL
      A0A7P0T944
      Related
      ENSP00000336712.5, ENST00000337273.10
      Conserved Domains (2) summary
      COG5215
      Location:32 → 767
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:103 → 124
      HEAT; HEAT repeat [structural motif]

    7. NM_153188.4 → NP_694858.1  transportin-1 isoform 2

      See identical proteins and their annotated locations for NP_694858.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
      Source sequence(s)
      AC008953, AC008972, U70322, U72069
      Consensus CDS
      CCDS4016.1
      UniProtKB/TrEMBL
      A0A7P0T944
      Related
      ENSP00000425118.2, ENST00000506351.6
      Conserved Domains (2) summary
      COG5215
      Location:24 → 759
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:95 → 116
      HEAT; HEAT repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      72816661..72914388
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248501.3 → XP_005248558.1  transportin-1 isoform X2

      See identical proteins and their annotated locations for XP_005248558.1

      UniProtKB/TrEMBL
      A0A7P0T944
      Conserved Domains (2) summary
      COG5215
      Location:32 → 741
      KAP95; Karyopherin (importin) beta [Intracellular trafficking and secretion]
      sd00044
      Location:103 → 124
      HEAT; HEAT repeat [structural motif]

    2. XM_047417167.1 → XP_047273123.1  transportin-1 isoform X1

      UniProtKB/Swiss-Prot
      B4DVC6, Q92957, Q92973, Q92975

    3. XM_047417168.1 → XP_047273124.1  transportin-1 isoform X3

      UniProtKB/TrEMBL
      A0A7P0TBF0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      73297810..73395474
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352566.1 → XP_054208541.1  transportin-1 isoform X2

    2. XM_054352565.1 → XP_054208540.1  transportin-1 isoform X1

      UniProtKB/Swiss-Prot
      B4DVC6, Q92957, Q92973, Q92975

    3. XM_054352567.1 → XP_054208542.1  transportin-1 isoform X3

      UniProtKB/TrEMBL
      A0A7P0TBF0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92973.2 GenPept UniProtKB/Swiss-Prot:Q92973

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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