TARDBP TAR DNA binding protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: TARDBPprovided by HGNC
Official Full Name: TAR DNA binding proteinprovided by HGNC
Primary source: HGNC:HGNC:11571
See related: Ensembl:ENSG00000120948 MIM:605078; AllianceGenome:HGNC:11571
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: ALS10; TDP-43
Summary: HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. The protein encoded by this gene is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in lymph node (RPKM 32.8), appendix (RPKM 30.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.22

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (11012654..11030528)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (10553914..10571805)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (11072711..11085549)

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 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?

TARDBP drives T-cell acute lymphoblastic leukemia progression by binding MDM2 mRNA, involving beta-catenin pathway.
Title: TARDBP drives T-cell acute lymphoblastic leukemia progression by binding MDM2 mRNA, involving β-catenin pathway.
DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43.
Title: DNAJA2 and Hero11 mediate similar conformational extension and aggregation suppression of TDP-43.
Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor.
Title: Electrostatics Choreographs the Aggregation Dynamics of Full-Length TDP-43 via a Monomeric Amyloid Precursor.
HIV-1 Vpu induces neurotoxicity by promoting Caspase 3-dependent cleavage of TDP-43.
Title: HIV-1 Vpu induces neurotoxicity by promoting Caspase 3-dependent cleavage of TDP-43.
The TDP-43/TP63 Positive Feedback Circuit Promotes Esophageal Squamous Cell Carcinoma Progression.
Title: The TDP-43/TP63 Positive Feedback Circuit Promotes Esophageal Squamous Cell Carcinoma Progression.
TDP-43 Is Associated with Subiculum and Cornu Ammonis 1 Hippocampal Subfield Atrophy in Primary Age-Related Tauopathy.
Title: TDP-43 Is Associated with Subiculum and Cornu Ammonis 1 Hippocampal Subfield Atrophy in Primary Age-Related Tauopathy.
TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
Title: TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic splicing inhibition.
TDP-43 dysfunction leads to bioenergetic failure and lipid metabolic rewiring in human cells.
Title: TDP-43 dysfunction leads to bioenergetic failure and lipid metabolic rewiring in human cells.
NMR assignments for the C-terminal domain of human TDP-43.
Title: NMR assignments for the C-terminal domain of human TDP-43.
Annexin A11 aggregation in FTLD-TDP type C and related neurodegenerative disease proteinopathies.
Title: Annexin A11 aggregation in FTLD-TDP type C and related neurodegenerative disease proteinopathies.

Submit: New GeneRIF Correction See all GeneRIFs (846)

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
Amyotrophic lateral sclerosis type 10 MedGen: C2677565 OMIM: 612069 GeneReviews: Amyotrophic Lateral Sclerosis Overview, TARDBP-Related Amyotrophic Lateral Sclerosis-Frontotemporal Dementia	Compare labs
TARDBP-related frontotemporal dementia MedGen: C3150169 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-09-25) ClinGen Genome Curation Page Haploinsufficency No evidence available (Last evaluated 2018-09-25) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Common variants near TARDBP and EGR2 are associated with susceptibility to Ewing sarcoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify TAR DNA binding protein (TARDBP; TDP-43), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify TAR DNA binding protein (TARDBP; TDP-43), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify TAR DNA binding protein (TARDBP; TDP-43), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify TAR DNA binding protein (TARDBP; TDP-43), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Tat	tat	TAR DNA binding protein (TARDBP, TDP43) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS	PubMed
	tat	TDP-43 is a cellular protein that binds specifically to pyrimidine-rich motifs in HIV-1 double-stranded TAR DNA and represses transcription from the HIV-1 LTR promoter in both the presence and absence of HIV-1 Tat	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

RH10991 (e-PCR)
- UniSTS:91464

WI-8757 (e-PCR)
- UniSTS:51582

D1S1845E (e-PCR)
- UniSTS:150926

SHGC-74204 (e-PCR)
- UniSTS:21915

HSC11D022 (e-PCR)
- UniSTS:60639

RH27226 (e-PCR)
- UniSTS:88053

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	EXP Inferred from Experiment more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables lipid binding	EXP Inferred from Experiment more info	PubMed
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables molecular condensate scaffold activity	IDA Inferred from Direct Assay more info	PubMed
enables pre-mRNA intronic binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in 3'-UTR-mediated mRNA destabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in 3'-UTR-mediated mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in amyloid fibril formation	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation by host of viral transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear inner membrane organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of insulin secretion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein import into nucleus	IEA Inferred from Electronic Annotation more info
involved_in regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to endoplasmic reticulum stress	IEA Inferred from Electronic Annotation more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic stress granule	IEA Inferred from Electronic Annotation more info
located_in interchromatin granule	IEA Inferred from Electronic Annotation more info
is_active_in intracellular non-membrane-bounded organelle	EXP Inferred from Experiment more info	PubMed
is_active_in intracellular non-membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perichromatin fibrils	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: TAR DNA-binding protein 43

Names: TAR DNA-binding protein-43

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_008734.1 RefSeqGene

Range

5001..17871

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_659

mRNA and Protein(s)

NM_007375.4 → NP_031401.1 TAR DNA-binding protein 43

See identical proteins and their annotated locations for NP_031401.1

Status: REVIEWED

Source sequence(s)

AF311304, AL045296, AL050265, BC001487, BC059955, BM716882, CD703666

Consensus CDS

CCDS122.1

UniProtKB/Swiss-Prot

A4GUK4, A4GUK5, A4GUK6, B2R629, B4DJ45, E2PU12, Q13148, Q53H27, Q6FI92, Q96DJ0

Related

ENSP00000240185.4, ENST00000240185.8

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins