Human Gene TNPO1 (ENST00000337273.10_3) from GENCODE V47lift37
  Description: transportin 1, transcript variant 1 (from RefSeq NM_002270.4)
Gencode Transcript: ENST00000337273.10_3
Gencode Gene: ENSG00000083312.19_8
Transcript (Including UTRs)
   Position: hg19 chr5:72,112,488-72,210,215 Size: 97,728 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr5:72,112,565-72,201,237 Size: 88,673 Coding Exon Count: 24 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:72,112,488-72,210,215)mRNA (may differ from genome)Protein (898 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TNPO1_HUMAN
DESCRIPTION: RecName: Full=Transportin-1; AltName: Full=Importin beta-2; AltName: Full=Karyopherin beta-2; AltName: Full=M9 region interaction protein; Short=MIP;
FUNCTION: Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran- dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus (By similarity). Involved in nuclear import of M9- containing proteins. In vitro, binds directly to the M9 region of the heterogeneous nuclear ribonucleoproteins (hnRNP), A1 and A2 and mediates their nuclear import. Appears also to be involved in hnRNP A1/A2 nuclear export. Mediates the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones, and SRP19. In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev.
SUBUNIT: Binds HNRPA1, HNRPA2, HNRPDL, RPL23A, RPS7, RPL5, RAN and SRP19. Interacts with H2A, H2B, H3 and H4 histones. Binds to HIV-1 Rev.
INTERACTION: P62993:GRB2; NbExp=2; IntAct=EBI-286693, EBI-401755; P62826:RAN; NbExp=2; IntAct=EBI-286693, EBI-286642;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
SIMILARITY: Belongs to the importin beta family.
SIMILARITY: Contains 8 HEAT repeats.
SIMILARITY: Contains 1 importin N-terminal domain.
SEQUENCE CAUTION: Sequence=AAC50723.1; Type=Erroneous initiation; Sequence=AAH40340.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TNPO1
Diseases sorted by gene-association score: hiv-1 (3), dementia, frontotemporal (1), retinitis pigmentosa (1), amyotrophic lateral sclerosis 1 (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.62 RPKM in Cells - Cultured fibroblasts
Total median expression: 426.36 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.3077-0.406 Picture PostScript Text
3' UTR -1375.505715-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR001494 - Importin-beta_N

Pfam Domains:
PF03810 - Importin-beta N-terminal domain
PF13513 - HEAT-like repeat

SCOP Domains:
46458 - Globin-like
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain
48464 - ENTH/VHS domain
158553 - TAFH domain-like
47862 - Saposin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1QBK - X-ray MuPIT 2H4M - X-ray MuPIT 2OT8 - X-ray MuPIT 2QMR - X-ray MuPIT 2Z5J - X-ray MuPIT 2Z5K - X-ray MuPIT 2Z5M - X-ray MuPIT 2Z5N - X-ray MuPIT 2Z5O - X-ray MuPIT 4FDD - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q92973
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008139 nuclear localization sequence binding
GO:0008536 Ran GTPase binding
GO:0008565 protein transporter activity

Biological Process:
GO:0000060 protein import into nucleus, translocation
GO:0006607 NLS-bearing protein import into nucleus
GO:0006610 ribosomal protein import into nucleus
GO:0006886 intracellular protein transport
GO:0015031 protein transport
GO:0016032 viral process
GO:0035735 intraciliary transport involved in cilium assembly
GO:0043488 regulation of mRNA stability

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005929 cilium
GO:0031965 nuclear membrane
GO:0034399 nuclear periphery
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK299671 - Homo sapiens cDNA FLJ57425 complete cds, highly similar to Transportin-1.
U70322 - Human transportin (TRN) mRNA, complete cds.
AK301021 - Homo sapiens cDNA FLJ58732 complete cds, highly similar to Transportin-1.
AK308177 - Homo sapiens cDNA, FLJ98125.
BC040340 - Homo sapiens transportin 1, mRNA (cDNA clone MGC:17116 IMAGE:4178989), complete cds.
AB528475 - Synthetic construct DNA, clone: pF1KB8538, Homo sapiens TNPO1 gene for transportin 1, without stop codon, in Flexi system.
U72395 - Homo sapiens MIP mRNA, complete cds.
U72069 - Human karyopherin beta2 mRNA, complete cds.
JD131821 - Sequence 112845 from Patent EP1572962.
EU176628 - Synthetic construct Homo sapiens clone IMAGE:100011435; FLH180207.01L; RZPDo839F07254D transportin 1 (TNPO1) gene, encodes complete protein.
DL492592 - Novel nucleic acids.
CQ873870 - Sequence 289 from Patent WO2004076622.
DD413707 - Regulation of Mammalian Cells.
JD419238 - Sequence 400262 from Patent EP1572962.
JD077752 - Sequence 58776 from Patent EP1572962.
JD171255 - Sequence 152279 from Patent EP1572962.
JD126442 - Sequence 107466 from Patent EP1572962.
JD472999 - Sequence 454023 from Patent EP1572962.
JD234668 - Sequence 215692 from Patent EP1572962.
JD037222 - Sequence 18246 from Patent EP1572962.
JD284379 - Sequence 265403 from Patent EP1572962.
AK124768 - Homo sapiens cDNA FLJ42778 fis, clone BRAWH3005146.
AK055669 - Homo sapiens cDNA FLJ31107 fis, clone IMR322000152.
AL049378 - Homo sapiens mRNA; cDNA DKFZp586I1518 (from clone DKFZp586I1518).

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92973 (Reactome details) participates in the following event(s):

R-HSA-450400 ZFP36 (Tristetraproline, TTP) binds AU-rich elements in 3' UTR of target mRNAs
R-HSA-5624951 TNPO1 binds KIF17 dimer
R-HSA-450431 ZFP36 (TTP) recruits RNA degradation activities
R-HSA-450463 MK2 phosphorylates ZFP36 (Tristetraproline, TTP)
R-HSA-450394 p-S60,S186-ZFP36 (Tristetraproline, TTP) binds 14-3-3beta
R-HSA-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-5620924 Intraflagellar transport
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-5617833 Cilium Assembly
R-HSA-8953854 Metabolism of RNA
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: B4DVC6, ENST00000337273.1, ENST00000337273.2, ENST00000337273.3, ENST00000337273.4, ENST00000337273.5, ENST00000337273.6, ENST00000337273.7, ENST00000337273.8, ENST00000337273.9, KPNB2, MIP1, NM_002270, Q92957, Q92973, Q92975, TNPO1_HUMAN, TRN, uc317usm.1, uc317usm.2
UCSC ID: ENST00000337273.10_3
RefSeq Accession: NM_002270.4
Protein: Q92973 (aka TNPO1_HUMAN or TNP1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.