TPR translocated promoter region, nuclear basket protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: TPRprovided by HGNC
Official Full Name: translocated promoter region, nuclear basket proteinprovided by HGNC
Primary source: HGNC:HGNC:12017
See related: Ensembl:ENSG00000047410 MIM:189940; AllianceGenome:HGNC:12017
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: MRT79
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 29.9), thyroid (RPKM 16.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q31.1

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (186311652..186375253, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (185666310..185729984, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (186280784..186344385, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of MKI67, TPR , and TCHH Mutations as Prognostic Biomarkers for Patients With Defective Mismatch Repair Colon Cancer Stage II/III.
Title: Identification of MKI67, TPR , and TCHH Mutations as Prognostic Biomarkers for Patients With Defective Mismatch Repair Colon Cancer Stage II/III.
Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells.
Title: Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells.
Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma.
Title: Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma.
ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR.
Title: ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR.
Cancer-related SRCAP and TPR mutations in colon cancers.
Title: Cancer-related SRCAP and TPR mutations in colon cancers.
The human nucleoporin Tpr protects cells from RNA-mediated replication stress.
Title: The human nucleoporin Tpr protects cells from RNA-mediated replication stress.
TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes.
Title: TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes.
TPR contributes to the organization of the nuclear lamina and in cooperation with lamin B1 and lamin A-C guards the interphase assembly of nuclear pore complexes.
Title: Nuclear pore protein TPR associates with lamin B1 and affects nuclear lamina organization and nuclear pore distribution.
TPR is necessary for both formation and maintenance of senescence-associated heterochromatin foci
Title: Nuclear pore density controls heterochromatin reorganization during senescence.
Fusion of TPR(2-142) protein to the MET intracellular domain strongly and selectively stabilizes the alphaG helix of the MET kinase domain.TPR has an ability to induce dimerization and activation of fusion kinases.
Title: Structural Basis of TPR-Mediated Oligomerization and Activation of Oncogenic Fusion Kinases.

Submit: New GeneRIF Correction See all GeneRIFs (30)

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

Associated conditions

Description	Tests
Intellectual developmental disorder, autosomal recessive 79 MedGen: C5830553 OMIM: 620393 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 replication requires PSIP1 (LEDGF/p75) and TPR to maintain chromatin structure amenable to integration as shown through shRNA treatment	PubMed
HIV-1 requires NUP153 and TPR for infectivity as shown by shRNA knockdown experiments utilizing HeLa-derived P4-CCR5 cells and jurkat T cells	PubMed
Knockdown of translocated promoter region (to activated MET oncogene) (TPR) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Cellular biotinylated nucleoprotein TPR is incorporated into HIV-1 Gag virus-like particles	PubMed
Tat	tat	Depletion of translocated promoter region, nuclear basket protein (TPR) by siRNA enhances HIV-1 Tat activation of HIV-1 LTR, which is not the results of increased Tat expression and release of CDK9/CCNT1 from 7SK snRNP, and activation of NF-kappaB	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-110732 (e-PCR)
- UniSTS:167993

L18426 (e-PCR)
- UniSTS:34648

G62041 (e-PCR)
- UniSTS:139135

D11S3114 (e-PCR)
- UniSTS:152207

RH80846 (e-PCR)
- UniSTS:87439

G31461 (e-PCR)
- UniSTS:73106

G19412 (e-PCR)
- UniSTS:38371

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables dynein complex binding	IDA Inferred from Direct Assay more info	PubMed
enables heat shock protein binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mitogen-activated protein kinase binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables protein-membrane adaptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables structural constituent of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of nuclear pore	IDA Inferred from Direct Assay more info	PubMed
enables tubulin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA import into nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cellular response to heat	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to interferon-alpha	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus in response to heat stress	IDA Inferred from Direct Assay more info	PubMed
involved_in mitotic spindle assembly checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of RNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of RNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in nuclear matrix organization	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in nuclear pore complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in nuclear pore organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear pore organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleocytoplasmic transport	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mitotic cell cycle spindle assembly checkpoint	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein export from nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in protein export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic sister chromatid separation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic spindle assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitotic spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of protein export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of protein stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to epidermal growth factor	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of cytoplasmic dynein complex	IDA Inferred from Direct Assay more info	PubMed
NOT located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in mitotic spindle	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear inclusion body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear periphery	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear pore	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore nuclear basket	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleoprotein TPR

Names: NPC-associated intranuclear protein; megator; nuclear pore complex-associated protein TPR; translocated promoter region (to activated MET oncogene); translocated promoter region protein; tumor potentiating region

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.

Genomic

NG_023284.1 RefSeqGene

Range

5073..68674

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003292.3 → NP_003283.2 nucleoprotein TPR

See identical proteins and their annotated locations for NP_003283.2

Status: REVIEWED

Source sequence(s)

AA688415, AL133553, AL596220, U69668, X66397

Consensus CDS

CCDS41446.1

UniProtKB/Swiss-Prot

P12270, Q15624, Q5SWY0, Q99968

Related

ENSP00000356448.3, ENST00000367478.9

Conserved Domains (5) summary

COG1196
Location:53 → 796

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR04527
Location:964 → 1050

mycoplas_twoTM; two transmembrane protein

pfam00038
Location:765 → 1087

Filament; Intermediate filament protein

pfam07851
Location:1433 → 1509

TMPIT; TMPIT-like protein

pfam07926
Location:1038 → 1166

TPR_MLP1_2; TPR/MLP1/MLP2-like protein