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Aliases for TNPO3 Gene

Aliases for TNPO3 Gene

  • Transportin 3 2 3 5
  • Limb Girdle Muscular Dystrophy 1F (Autosomal Dominant) 2 3
  • Transportin-SR 3 4
  • Importin 12 2 3
  • TRN-SR 3 4
  • Imp12 3 4
  • IPO12 3 4
  • Transportin-3 3
  • Importin-12 4
  • TRN-SR2 3
  • MTR10A 3
  • LGMD1F 3
  • TRNSR 3

External Ids for TNPO3 Gene

Previous HGNC Symbols for TNPO3 Gene

  • LGMD1F

Previous GeneCards Identifiers for TNPO3 Gene

  • GC07M128149
  • GC07M128148
  • GC07M128188
  • GC07M128382
  • GC07M128594
  • GC07M122955

Summaries for TNPO3 Gene

Entrez Gene Summary for TNPO3 Gene

  • 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. Two transcript variants encoding different isoforms as well as a noncoding transcript have been found for this gene.[provided by RefSeq, Jul 2010]

GeneCards Summary for TNPO3 Gene

TNPO3 (Transportin 3) is a Protein Coding gene. Diseases associated with TNPO3 include Muscular Dystrophy, Limb-Girdle, Type 1F and Autosomal Dominant Limb-Girdle Muscular Dystrophy Type 1G. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is IPO13.

UniProtKB/Swiss-Prot for TNPO3 Gene

  • 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.

Gene Wiki entry for TNPO3 Gene

Additional gene information for TNPO3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TNPO3 Gene

Genomics for TNPO3 Gene

GeneHancer (GH) Regulatory Elements for TNPO3 Gene

Promoters and enhancers for TNPO3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J129053 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 661.7 +0.4 368 2.9 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 TNPO3 GC07P129056 TPI1P2 ENSG00000243679 ENSG00000242588 ENSG00000243302 ENSG00000230715 NRF1 RPS10P15 ENSG00000229413
GH07J128737 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 33.9 +314.5 314470 6.6 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CALU ENSG00000243302 ENSG00000230715 ENSG00000243679 ENSG00000242588 TNPO3 RPS10P15 ENSG00000229413 CDC26P1 OPN1SW
GH07J129122 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 43 -67.7 -67653 1.6 PKNOX1 STAT5A BMI1 YBX1 BATF IRF4 ZNF207 ATF7 BCLAF1 IKZF2 TNPO3 ENSG00000242588 TSPAN33 RBM28 ENSG00000242162 TPI1P2 ENSG00000243302 ENSG00000243230 AHCYL2 ENSG00000230715
GH07J128862 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 23.8 +192.0 191968 2.4 HDGF HNRNPUL1 PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ATP6V1F FLNC-AS1 ENSG00000243302 ENSG00000230715 ENSG00000243679 ENSG00000242588 TNPO3 ENSG00000229413 RPS10P15 ENSG00000273270
GH07J128341 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.2 +711.9 711932 2.6 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 RBM28 RNU7-27P GC07P128370 ZNF800 GCC1 ENSG00000243679 ENSG00000230715 ENSG00000243302 ENSG00000224138 ENSG00000242588
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TNPO3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TNPO3 gene promoter:
  • SRF (504 AA)
  • SRF
  • Pax-5
  • USF-1
  • CREB
  • deltaCREB
  • USF1
  • ISGF-3
  • AP-1
  • MAZR

Genomic Locations for TNPO3 Gene

Genomic Locations for TNPO3 Gene
chr7:128,954,180-129,055,173
(GRCh38/hg38)
Size:
100,994 bases
Orientation:
Minus strand
chr7:128,594,234-128,695,227
(GRCh37/hg19)
Size:
100,994 bases
Orientation:
Minus strand

Genomic View for TNPO3 Gene

Genes around TNPO3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNPO3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNPO3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNPO3 Gene

Proteins for TNPO3 Gene

  • Protein details for TNPO3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5L0-TNPO3_HUMAN
    Recommended name:
    Transportin-3
    Protein Accession:
    Q9Y5L0
    Secondary Accessions:
    • A4D1K9
    • C9IZM0
    • Q6NUM1
    • Q96G71
    • Q96GU9
    • Q9Y3R2

    Protein attributes for TNPO3 Gene

    Size:
    923 amino acids
    Molecular mass:
    104203 Da
    Quaternary structure:
    • Interacts with phosphorylated SFRS1 and SFRS2. Interacts with NUP62 and RBM4.
    SequenceCaution:
    • Sequence=AAD38537.1; Type=Frameshift; Positions=920; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TNPO3 Gene

    Alternative splice isoforms for TNPO3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TNPO3 Gene

Post-translational modifications for TNPO3 Gene

  • Ubiquitination at isoforms=2, 3, 5628
  • Modification sites at PhosphoSitePlus

Other Protein References for TNPO3 Gene

No data available for DME Specific Peptides for TNPO3 Gene

Domains & Families for TNPO3 Gene

Gene Families for TNPO3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TNPO3 Gene

Suggested Antigen Peptide Sequences for TNPO3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TNPO3: view

No data available for UniProtKB/Swiss-Prot for TNPO3 Gene

Function for TNPO3 Gene

Molecular function for TNPO3 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for TNPO3 Gene

Gene Ontology (GO) - Molecular Function for TNPO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005488 binding IEA --
GO:0005515 protein binding IPI 12628928
GO:0008139 nuclear localization sequence binding IBA --
GO:0008565 protein transporter activity IBA --
GO:0038023 signaling receptor activity TAS 10366588
genes like me logo Genes that share ontologies with TNPO3: view
genes like me logo Genes that share phenotypes with TNPO3: view

Human Phenotype Ontology for TNPO3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TNPO3 Gene

miRTarBase miRNAs that target TNPO3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNPO3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TNPO3 Gene

Localization for TNPO3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNPO3 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TNPO3 gene
Compartment Confidence
nucleus 4
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TNPO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IBA --
GO:0031965 nuclear membrane IBA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with TNPO3: view

Pathways & Interactions for TNPO3 Gene

SuperPathways for TNPO3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TNPO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006606 protein import into nucleus IBA --
GO:0007165 signal transduction IEA --
GO:0015031 protein transport IEA --
GO:0035048 obsolete splicing factor protein import into nucleus IDA --
genes like me logo Genes that share ontologies with TNPO3: view

No data available for Pathways by source and SIGNOR curated interactions for TNPO3 Gene

Drugs & Compounds for TNPO3 Gene

No Compound Related Data Available

Transcripts for TNPO3 Gene

mRNA/cDNA for TNPO3 Gene

Unigene Clusters for TNPO3 Gene

Transportin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNPO3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TNPO3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2:
SP3: - -
SP4: - - - -
SP5:

ExUns: 23 ^ 24 ^ 25
SP1:
SP2: -
SP3:
SP4:
SP5:

Relevant External Links for TNPO3 Gene

GeneLoc Exon Structure for
TNPO3
ECgene alternative splicing isoforms for
TNPO3

Expression for TNPO3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TNPO3 Gene

Protein differential expression in normal tissues from HIPED for TNPO3 Gene

This gene is overexpressed in Bone (50.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TNPO3 Gene



Protein tissue co-expression partners for TNPO3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TNPO3 Gene:

TNPO3

SOURCE GeneReport for Unigene cluster for TNPO3 Gene:

Hs.193613

mRNA Expression by UniProt/SwissProt for TNPO3 Gene:

Q9Y5L0-TNPO3_HUMAN
Tissue specificity: Expressed in skeletal muscle.

Evidence on tissue expression from TISSUES for TNPO3 Gene

  • Intestine(4.5)
  • Nervous system(4.4)
  • Liver(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TNPO3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • lymphatic
  • skeletal muscle
  • skeleton
Regions:
Thorax:
  • clavicle
  • scapula
Abdomen:
  • biliary tract
  • liver
  • spleen
Pelvis:
  • pelvis
Limb:
  • arm
  • forearm
  • humerus
  • lower limb
  • shin
  • shoulder
  • thigh
  • upper limb
General:
  • blood
  • coagulation system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with TNPO3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TNPO3 Gene

Orthologs for TNPO3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TNPO3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TNPO3 34 33
  • 99.71 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TNPO3 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TNPO3 34 33
  • 94.9 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TNPO3 34 33
  • 94.66 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TNPO3 34
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tnpo3 33
  • 90.9 (n)
mouse
(Mus musculus)
Mammalia Tnpo3 16 34 33
  • 90.79 (n)
chicken
(Gallus gallus)
Aves TNPO3 34 33
  • 77.27 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TNPO3 34
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tnpo3 33
  • 76.25 (n)
Str.15240 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.29508 33
zebrafish
(Danio rerio)
Actinopterygii tnpo3 34 33
  • 73.06 (n)
OneToOne
zgc55409 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6715 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003576 33
  • 50.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Trn-SR 34 33
  • 50.62 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea tsr-1 34 33
  • 43.91 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MTR10 36 34 33
  • 40.93 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR115C 33
  • 39.59 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A02321g 33
  • 39.02 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G62600 33
  • 40.77 (n)
rice
(Oryza sativa)
Liliopsida Os10g0477800 33
  • 42.33 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10940 34
  • 47 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU06355 33
  • 41.85 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mtr10 33
  • 40.98 (n)
Species where no ortholog for TNPO3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TNPO3 Gene

ENSEMBL:
Gene Tree for TNPO3 (if available)
TreeFam:
Gene Tree for TNPO3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TNPO3: view image

Paralogs for TNPO3 Gene

Paralogs for TNPO3 Gene

Pseudogenes.org Pseudogenes for TNPO3 Gene

genes like me logo Genes that share paralogs with TNPO3: view

Variants for TNPO3 Gene

Sequence variations from dbSNP and Humsavar for TNPO3 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs137891112 uncertain-significance, Limb-girdle muscular dystrophy, type 1F 128,990,050(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs142268279 uncertain-significance, likely-benign, not specified, Limb-girdle muscular dystrophy, type 1F 129,018,044(-) G/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs149434536 benign, not specified, Limb-girdle muscular dystrophy, type 1F 128,967,339(-) G/A/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs190759031 benign, not specified, Limb-girdle muscular dystrophy, type 1F 128,970,321(-) T/A/G intron_variant
rs35060568 benign, not specified, Limb-girdle muscular dystrophy, type 1F 128,975,843(-) C/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for TNPO3 Gene

Variant ID Type Subtype PubMed ID
esv2670312 CNV deletion 23128226
esv2735137 CNV deletion 23290073
esv2761368 CNV gain 21179565
esv3572135 CNV loss 25503493
nsv1025216 CNV loss 25217958
nsv507416 OTHER sequence alteration 20534489
nsv831125 CNV loss 17160897

Variation tolerance for TNPO3 Gene

Residual Variation Intolerance Score: 2.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.16; 23.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNPO3 Gene

Human Gene Mutation Database (HGMD)
TNPO3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNPO3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNPO3 Gene

Disorders for TNPO3 Gene

MalaCards: The human disease database

(20) MalaCards diseases for TNPO3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy, limb-girdle, type 1f
  • lgmd1f
autosomal dominant limb-girdle muscular dystrophy type 1g
  • limb-girdle muscular dystrophy, type 1g
autosomal dominant limb-girdle muscular dystrophy
  • limb-girdle muscular dystrophies, autosomal dominant
limb-girdle muscular dystrophy
  • lgmd
primary biliary cholangitis
  • pbc
- elite association - COSMIC cancer census association via MalaCards
Search TNPO3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TNPO3_HUMAN
  • Limb-girdle muscular dystrophy 1F (LGMD1F) [MIM:608423]: An autosomal dominant myopathy characterized by proximal muscle weakness primarily affecting the lower limbs, but also affecting the upper limbs in most patients. Affected individuals also have distal muscle weakness of the hands and lower leg muscles. The disease has generally a benign clinical course but some individuals with childhood or juvenile onset manifest severe widespread myopathy, leading to wheelchair dependency and respiratory insufficiency. Muscle biopsy shows dystrophic changes with abnormal nuclei, rimmed vacuoles, and filamentous inclusions. {ECO:0000269 PubMed:23667635}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TNPO3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TNPO3: view

No data available for Genatlas for TNPO3 Gene

Publications for TNPO3 Gene

  1. A human importin-beta family protein, transportin-SR2, interacts with the phosphorylated RS domain of SR proteins. (PMID: 10713112) Lai MC … Tarn WY (The Journal of biological chemistry 2000) 2 3 4 22 58
  2. Transportin-SR, a nuclear import receptor for SR proteins. (PMID: 10366588) Kataoka N … Dreyfuss G (The Journal of cell biology 1999) 2 3 4 22 58
  3. Next-generation sequencing identifies transportin 3 as the causative gene for LGMD1F. (PMID: 23667635) Torella A … Nigro V (PloS one 2013) 2 3 4 58
  4. Association of a functional polymorphism in the IRF5 region with systemic sclerosis in a Japanese population. (PMID: 19479858) Ito I … Tsuchiya N (Arthritis and rheumatism 2009) 3 22 44 58
  5. Transportin-SR2 mediates nuclear import of phosphorylated SR proteins. (PMID: 11517331) Lai MC … Tarn WY (Proceedings of the National Academy of Sciences of the United States of America 2001) 3 4 22 58

Products for TNPO3 Gene

Sources for TNPO3 Gene

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