Human Gene TPR (uc001grv.3) Description and Page Index
  Description: Homo sapiens translocated promoter region, nuclear basket protein (TPR), mRNA.
RefSeq Summary (NM_003292): This gene encodes a large coiled-coil protein that forms intranuclear filaments attached to the inner surface of nuclear pore complexes (NPCs). The protein directly interacts with several components of the NPC. It is required for the nuclear export of mRNAs and some proteins. Oncogenic fusions of the 5' end of this gene with several different kinase genes occur in some neoplasias. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803613.253555.1, SRR1803616.28520.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000367478.9/ ENSP00000356448.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:186,280,786-186,344,457 Size: 63,672 Total Exon Count: 51 Strand: -
Coding Region
   Position: hg19 chr1:186,283,103-186,344,160 Size: 61,058 Coding Exon Count: 51 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:186,280,786-186,344,457)mRNA (may differ from genome)Protein (2363 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TPR_HUMAN
DESCRIPTION: RecName: Full=Nucleoprotein TPR;
FUNCTION: Component of the cytoplasmic fibrils of the nuclear pore complex implicated in nuclear protein import. Its N-terminus is involved in activation of oncogenic kinases. Plays a role in the mitotic spindle checkpoint.
SUBUNIT: Interacts with MAD1L1 and MAD2L1.
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side. Chromosome, centromere, kinetochore. Note=The assembly of the NPC is a stepwise process in which Trp-containing peripheral structures assemble after other components, including p62. Detected at kinetochores during prometaphase.
TISSUE SPECIFICITY: Highest in testis, lung, thymus, spleen and brain, lower levels in heart, liver and kidney.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in TPR are a cause of thyroid papillary carcinoma (TPC) [MIM:188550]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=Chromosomal aberrations involving TPR are found in thyroid papillary carcinomas. Intrachromosomal rearrangement that links the 5'-end of the TPR gene to the protein kinase domain of NTRK1 forms the fusion protein TRK-T1. TRK-T1 is a 55 kDa protein reacting with antibodies against the carboxy terminus of the NTRK1 protein.
DISEASE: Note=Involved in tumorigenic rearrangements with the MET or RAF genes.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/TPRID282.html";

-  MalaCards Disease Associations
  MalaCards Gene Search: TPR
Diseases sorted by gene-association score: differentiated thyroid carcinoma* (111), 8p11 myeloproliferative syndrome (10), bejel (10), familial renal papillary carcinoma (9), prostate cancer 1 (9), syphilis (8), latent syphilis (8), yaws (7), secondary syphilis (7), primary syphilis (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 40.56 RPKM in Testis
Total median expression: 794.56 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 -141.70297-0.477 Picture PostScript Text
3' UTR -541.282317-0.234 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
IPR009053 - Prefoldin
IPR015866 - Ser-tRNA-synth_1_N
IPR012929 - TPR_MLP1_2

Pfam Domains:
PF07926 - TPR/MLP1/MLP2-like protein

SCOP Domains:
46579 - Prefoldin

ModBase Predicted Comparative 3D Structure on P12270
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0015631 tubulin binding
GO:0017056 structural constituent of nuclear pore
GO:0031072 heat shock protein binding
GO:0042803 protein homodimerization activity
GO:0051019 mitogen-activated protein kinase binding
GO:0070840 dynein complex binding
GO:0005215 transporter activity
GO:0043495 protein anchor

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006404 RNA import into nucleus
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0006606 protein import into nucleus
GO:0006999 nuclear pore organization
GO:0007049 cell cycle
GO:0007094 mitotic spindle assembly checkpoint
GO:0010965 regulation of mitotic sister chromatid separation
GO:0015031 protein transport
GO:0016032 viral process
GO:0031453 positive regulation of heterochromatin assembly
GO:0031990 mRNA export from nucleus in response to heat stress
GO:0034605 cellular response to heat
GO:0035457 cellular response to interferon-alpha
GO:0042307 positive regulation of protein import into nucleus
GO:0045947 negative regulation of translational initiation
GO:0046827 positive regulation of protein export from nucleus
GO:0046832 negative regulation of RNA export from nucleus
GO:0051028 mRNA transport
GO:0051301 cell division
GO:0070849 response to epidermal growth factor
GO:0090267 positive regulation of mitotic cell cycle spindle assembly checkpoint
GO:0090316 positive regulation of intracellular protein transport
GO:1901673 regulation of mitotic spindle assembly
GO:0006611 protein export from nucleus
GO:0010793 regulation of mRNA export from nucleus
GO:0031647 regulation of protein stability
GO:0042306 regulation of protein import into nucleus
GO:0043578 nuclear matrix organization
GO:0046825 regulation of protein export from nucleus
GO:0051292 nuclear pore complex assembly

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005819 spindle
GO:0005856 cytoskeleton
GO:0005868 cytoplasmic dynein complex
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0031965 nuclear membrane
GO:0034399 nuclear periphery
GO:0042405 nuclear inclusion body
GO:0044615 nuclear pore nuclear basket
GO:0072686 mitotic spindle


-  Descriptions from all associated GenBank mRNAs
  LF205388 - JP 2014500723-A/12891: Polycomb-Associated Non-Coding RNAs.
U69668 - Human nuclear pore complex-associated protein TPR (tpr) mRNA, complete cds.
X66397 - H.sapiens tpr mRNA.
LF213699 - JP 2014500723-A/21202: Polycomb-Associated Non-Coding RNAs.
BC156389 - Synthetic construct Homo sapiens clone IMAGE:100061956, MGC:190134 translocated promoter region (to activated MET oncogene) (TPR) mRNA, encodes complete protein.
LF319940 - JP 2014500723-A/127443: Polycomb-Associated Non-Coding RNAs.
LF319939 - JP 2014500723-A/127442: Polycomb-Associated Non-Coding RNAs.
LF319936 - JP 2014500723-A/127439: Polycomb-Associated Non-Coding RNAs.
LF319935 - JP 2014500723-A/127438: Polycomb-Associated Non-Coding RNAs.
LF319934 - JP 2014500723-A/127437: Polycomb-Associated Non-Coding RNAs.
LF319933 - JP 2014500723-A/127436: Polycomb-Associated Non-Coding RNAs.
LF319932 - JP 2014500723-A/127435: Polycomb-Associated Non-Coding RNAs.
LF319931 - JP 2014500723-A/127434: Polycomb-Associated Non-Coding RNAs.
LF319930 - JP 2014500723-A/127433: Polycomb-Associated Non-Coding RNAs.
LF319929 - JP 2014500723-A/127432: Polycomb-Associated Non-Coding RNAs.
LF319928 - JP 2014500723-A/127431: Polycomb-Associated Non-Coding RNAs.
LF319927 - JP 2014500723-A/127430: Polycomb-Associated Non-Coding RNAs.
AK023111 - Homo sapiens cDNA FLJ13049 fis, clone NT2RP3001428, highly similar to NUCLEOPROTEIN TPR.
LF319926 - JP 2014500723-A/127429: Polycomb-Associated Non-Coding RNAs.
LF319925 - JP 2014500723-A/127428: Polycomb-Associated Non-Coding RNAs.
LF319924 - JP 2014500723-A/127427: Polycomb-Associated Non-Coding RNAs.
BC107788 - Homo sapiens cDNA clone IMAGE:6622169, **** WARNING: chimeric clone ****.
LF319923 - JP 2014500723-A/127426: Polycomb-Associated Non-Coding RNAs.
LF319922 - JP 2014500723-A/127425: Polycomb-Associated Non-Coding RNAs.
LF319921 - JP 2014500723-A/127424: Polycomb-Associated Non-Coding RNAs.
LF319920 - JP 2014500723-A/127423: Polycomb-Associated Non-Coding RNAs.
LF319919 - JP 2014500723-A/127422: Polycomb-Associated Non-Coding RNAs.
LF319918 - JP 2014500723-A/127421: Polycomb-Associated Non-Coding RNAs.
LF319917 - JP 2014500723-A/127420: Polycomb-Associated Non-Coding RNAs.
LF319916 - JP 2014500723-A/127419: Polycomb-Associated Non-Coding RNAs.
LF319915 - JP 2014500723-A/127418: Polycomb-Associated Non-Coding RNAs.
X63105 - H.sapiens tpr mRNA.
LF319914 - JP 2014500723-A/127417: Polycomb-Associated Non-Coding RNAs.
LF319913 - JP 2014500723-A/127416: Polycomb-Associated Non-Coding RNAs.
LF319912 - JP 2014500723-A/127415: Polycomb-Associated Non-Coding RNAs.
BC094764 - Homo sapiens translocated promoter region (to activated MET oncogene), mRNA (cDNA clone IMAGE:30528734), partial cds.
BC025177 - Homo sapiens translocated promoter region (to activated MET oncogene), mRNA (cDNA clone IMAGE:5111447), partial cds.
BC016514 - Homo sapiens translocated promoter region (to activated MET oncogene), mRNA (cDNA clone IMAGE:4339445), partial cds.
LF319911 - JP 2014500723-A/127414: Polycomb-Associated Non-Coding RNAs.
AK309473 - Homo sapiens cDNA, FLJ99514.
LF319908 - JP 2014500723-A/127411: Polycomb-Associated Non-Coding RNAs.
LF319907 - JP 2014500723-A/127410: Polycomb-Associated Non-Coding RNAs.
LF319906 - JP 2014500723-A/127409: Polycomb-Associated Non-Coding RNAs.
LF319903 - JP 2014500723-A/127406: Polycomb-Associated Non-Coding RNAs.
LF319902 - JP 2014500723-A/127405: Polycomb-Associated Non-Coding RNAs.
Y00672 - Human tpr mRNA 5'-end.
LF319899 - JP 2014500723-A/127402: Polycomb-Associated Non-Coding RNAs.
LF319897 - JP 2014500723-A/127400: Polycomb-Associated Non-Coding RNAs.
LF319896 - JP 2014500723-A/127399: Polycomb-Associated Non-Coding RNAs.
JD261416 - Sequence 242440 from Patent EP1572962.
JD139123 - Sequence 120147 from Patent EP1572962.
DL491305 - Novel nucleic acids.
JD266412 - Sequence 247436 from Patent EP1572962.
DL489942 - Novel nucleic acids.
MA440965 - JP 2018138019-A/12891: Polycomb-Associated Non-Coding RNAs.
MA449276 - JP 2018138019-A/21202: Polycomb-Associated Non-Coding RNAs.
MA555517 - JP 2018138019-A/127443: Polycomb-Associated Non-Coding RNAs.
MA555516 - JP 2018138019-A/127442: Polycomb-Associated Non-Coding RNAs.
MA555513 - JP 2018138019-A/127439: Polycomb-Associated Non-Coding RNAs.
MA555512 - JP 2018138019-A/127438: Polycomb-Associated Non-Coding RNAs.
MA555511 - JP 2018138019-A/127437: Polycomb-Associated Non-Coding RNAs.
MA555510 - JP 2018138019-A/127436: Polycomb-Associated Non-Coding RNAs.
MA555509 - JP 2018138019-A/127435: Polycomb-Associated Non-Coding RNAs.
MA555508 - JP 2018138019-A/127434: Polycomb-Associated Non-Coding RNAs.
MA555507 - JP 2018138019-A/127433: Polycomb-Associated Non-Coding RNAs.
MA555506 - JP 2018138019-A/127432: Polycomb-Associated Non-Coding RNAs.
MA555505 - JP 2018138019-A/127431: Polycomb-Associated Non-Coding RNAs.
MA555504 - JP 2018138019-A/127430: Polycomb-Associated Non-Coding RNAs.
MA555503 - JP 2018138019-A/127429: Polycomb-Associated Non-Coding RNAs.
MA555502 - JP 2018138019-A/127428: Polycomb-Associated Non-Coding RNAs.
MA555501 - JP 2018138019-A/127427: Polycomb-Associated Non-Coding RNAs.
MA555500 - JP 2018138019-A/127426: Polycomb-Associated Non-Coding RNAs.
MA555499 - JP 2018138019-A/127425: Polycomb-Associated Non-Coding RNAs.
MA555498 - JP 2018138019-A/127424: Polycomb-Associated Non-Coding RNAs.
MA555497 - JP 2018138019-A/127423: Polycomb-Associated Non-Coding RNAs.
MA555496 - JP 2018138019-A/127422: Polycomb-Associated Non-Coding RNAs.
MA555495 - JP 2018138019-A/127421: Polycomb-Associated Non-Coding RNAs.
MA555494 - JP 2018138019-A/127420: Polycomb-Associated Non-Coding RNAs.
MA555493 - JP 2018138019-A/127419: Polycomb-Associated Non-Coding RNAs.
MA555492 - JP 2018138019-A/127418: Polycomb-Associated Non-Coding RNAs.
MA555491 - JP 2018138019-A/127417: Polycomb-Associated Non-Coding RNAs.
MA555490 - JP 2018138019-A/127416: Polycomb-Associated Non-Coding RNAs.
MA555489 - JP 2018138019-A/127415: Polycomb-Associated Non-Coding RNAs.
MA555488 - JP 2018138019-A/127414: Polycomb-Associated Non-Coding RNAs.
MA555485 - JP 2018138019-A/127411: Polycomb-Associated Non-Coding RNAs.
MA555484 - JP 2018138019-A/127410: Polycomb-Associated Non-Coding RNAs.
MA555483 - JP 2018138019-A/127409: Polycomb-Associated Non-Coding RNAs.
MA555480 - JP 2018138019-A/127406: Polycomb-Associated Non-Coding RNAs.
MA555479 - JP 2018138019-A/127405: Polycomb-Associated Non-Coding RNAs.
MA555476 - JP 2018138019-A/127402: Polycomb-Associated Non-Coding RNAs.
MA555474 - JP 2018138019-A/127400: Polycomb-Associated Non-Coding RNAs.
MA555473 - JP 2018138019-A/127399: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05200 - Pathways in cancer
hsa05216 - Thyroid cancer

Reactome (by CSHL, EBI, and GO)

Protein P12270 (Reactome details) participates in the following event(s):

R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-165043 Rev multimer-bound HIV mRNA:Crm1:Ran:GTP complex associates with the NPC
R-HSA-180622 Vpr binds nucleoporins
R-HSA-180710 Rev:importin beta:B23 recruited to the nuclear pore
R-HSA-2990882 CDK1 phosphorylates NUP98
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-165047 Translocation of nuclear RNA transport complex to cytoplasm
R-HSA-180732 Translocation of Rev:importin-beta:B23 to the nucleus
R-HSA-2990880 NEK6/NEK7 phosphorylates NUP98
R-HSA-170796 NPC transports GCK1:GKRP from cytosol to nucleoplasm
R-HSA-5578744 Importin-8 imports AGO2:miRNA into the nucleus
R-HSA-6783483 tRNA:XPOT:RAN:GTP translocates from the nucleus to the cytosol
R-HSA-3000348 RANBP2 SUMOylates SP100 with SUMO2
R-HSA-3000399 RANBP2 SUMOylates SP100 with SUMO1
R-HSA-3000411 RANBP2 SUMOylates PML with SUMO2
R-HSA-4570493 RANBP2 (NUP358) SUMOylates HNRNPC with SUMO1
R-HSA-4615872 RANBP2 SUMOylates HDAC4 with SUMO1
R-HSA-4615987 RANBP2 SUMOylates HDAC4 with SUMO2,3
R-HSA-5228508 RANBP2 SUMOylates PML with SUMO1
R-HSA-5228525 RANBP2 SUMOylates TOP2A with SUMO1
R-HSA-192627 Viral mRNA Export
R-HSA-192925 Export of Spliced Viral mRNA
R-HSA-5252041 NPC transports Hikeshi:HSP70s:ATP from cytosol to nucleoplasm
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-180746 Nuclear import of Rev protein
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-177243 Interactions of Rev with host cellular proteins
R-HSA-176033 Interactions of Vpr with host cellular proteins
R-HSA-2980766 Nuclear Envelope Breakdown
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-168276 NS1 Mediated Effects on Host Pathways
R-HSA-1169408 ISG15 antiviral mechanism
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-3371453 Regulation of HSF1-mediated heat shock response
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-162587 HIV Life Cycle
R-HSA-162909 Host Interactions of HIV factors
R-HSA-68875 Mitotic Prophase
R-HSA-70171 Glycolysis
R-HSA-168253 Host Interactions with Influenza Factors
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes
R-HSA-211000 Gene Silencing by RNA
R-HSA-72306 tRNA processing
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-168273 Influenza Viral RNA Transcription and Replication
R-HSA-3371556 Cellular response to heat stress
R-HSA-8953854 Metabolism of RNA
R-HSA-162906 HIV Infection
R-HSA-68886 M Phase
R-HSA-70326 Glucose metabolism
R-HSA-168254 Influenza Infection
R-HSA-913531 Interferon Signaling
R-HSA-74160 Gene expression (Transcription)
R-HSA-2990846 SUMOylation
R-HSA-168255 Influenza Life Cycle
R-HSA-2262752 Cellular responses to stress
R-HSA-5663205 Infectious disease
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-597592 Post-translational protein modification
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-1643685 Disease
R-HSA-1640170 Cell Cycle
R-HSA-1430728 Metabolism
R-HSA-168256 Immune System
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003292, NP_003283, P12270, Q15655, Q5SWY0, TPR_HUMAN
UCSC ID: uc001grv.3
RefSeq Accession: NM_003292
Protein: P12270 (aka TPR_HUMAN)
CCDS: CCDS41446.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003292.2
exon count: 51CDS single in 3' UTR: no RNA size: 9727
ORF size: 7092CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 14108.00frame shift in genome: no % Coverage: 99.78
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: 139# 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.