Human Gene TNPO3 (uc003vol.1)
  Description: transportin 3
RefSeq Summary (NM_012470): 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].
Transcript (Including UTRs)
   Position: hg18 chr7:128,382,184-128,482,434 Size: 100,251 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg18 chr7:128,384,545-128,482,060 Size: 97,516 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:128,382,184-128,482,434)mRNA (may differ from genome)Protein (923 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDMGIOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TNPO3_HUMAN
DESCRIPTION: RecName: Full=Transportin-3; AltName: Full=Importin-12; Short=Imp12; AltName: Full=Transportin-SR; Short=TRN-SR;
FUNCTION: Seems to function in nuclear protein import as nuclear transport receptor. In vitro, mediates the nuclear import of splicing factor SR proteins RBM4, SFRS1 and SFRS2, by recognizing phosphorylated RS domains.
SUBUNIT: Interacts with phosphorylated SFRS1 and SFRS2. Interacts with NUP62 and RBM4.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
SEQUENCE CAUTION: Sequence=AAD38537.1; Type=Frameshift; Positions=920;

-  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


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

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -134.00374-0.358 Picture PostScript Text
3' UTR -151.06523-0.289 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
IPR013598 - Exportin-1/Importin-b-like

Pfam Domains:
PF08389 - Exportin 1-like protein

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q9Y5L0
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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
Genome BrowserNo orthologGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details  Gene Details Gene Details
Gene Sorter  Gene Sorter Gene Sorter
MGI EnsemblFlyBase SGD
Protein Sequence Protein SequenceProtein Sequence Protein Sequence
Alignment AlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008139 nuclear localization sequence binding
GO:0008565 protein transporter activity
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding

Biological Process:
GO:0007165 signal transduction
GO:0015031 protein transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0031965 nuclear membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  BC068530 - Homo sapiens transportin 3, mRNA (cDNA clone IMAGE:5301701).
BC009923 - Homo sapiens transportin 3, mRNA (cDNA clone IMAGE:3508018), partial cds.
AK225999 - Homo sapiens mRNA for transportin 3 variant, clone: FCC109F07.
AF145029 - Homo sapiens transportin-SR (TRN-SR) mRNA, complete cds.
AJ133769 - Homo sapiens mRNA for nuclear transport receptor.
AK312580 - Homo sapiens cDNA, FLJ92955, highly similar to Homo sapiens transportin-SR (TRN-SR), mRNA.
BC172512 - Synthetic construct Homo sapiens clone IMAGE:100069206, MGC:199217 transportin 3 (TNPO3) mRNA, encodes complete protein.
BC156517 - Synthetic construct Homo sapiens clone IMAGE:100063123, MGC:190698 transportin 3 (TNPO3) mRNA, encodes complete protein.
AK022910 - Homo sapiens cDNA FLJ12848 fis, clone NT2RP2003391, highly similar to Transportin-3.
AK097374 - Homo sapiens cDNA FLJ40055 fis, clone TBAES2000352.
BC009221 - Homo sapiens transportin 3, mRNA (cDNA clone IMAGE:3927816), partial cds.
AK001263 - Homo sapiens cDNA FLJ10401 fis, clone NT2RM4000421, highly similar to Transportin-3.

-  Other Names for This Gene
  Alternate Gene Symbols: A4D1K9, IPO12, NM_012470, NP_036602, Q6NUM1, Q96G71, Q96GU9, Q9Y3R2, Q9Y5L0, TNPO3_HUMAN
UCSC ID: uc003vol.1
RefSeq Accession: NM_012470
Protein: Q9Y5L0 (aka TNPO3_HUMAN or TPO3_HUMAN)
CCDS: CCDS5809.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012470.2
exon count: 23CDS single in 3' UTR: no RNA size: 3669
ORF size: 2772CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 5306.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.