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

Gene ID: 23435, updated on 29-Jan-2023

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
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Genomic context

See TARDBP in Genome Data Viewer
Location:
1p36.22
Exon count:
10
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11012654..11030528)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (10553914..10566770)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11072711..11085549)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chromosome 1 open reading frame 127 Neighboring gene Sharpr-MPRA regulatory region 3012 Neighboring gene cofilin 1 pseudogene 6 Neighboring gene MBL associated serine protease 2 Neighboring gene spermidine synthase Neighboring gene exosome component 10 Neighboring gene EXOSC10 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
EBI GWAS Catalog

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding EXP
Inferred from Experiment
more info
PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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
PubMed 
involved_in regulation of protein stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasmic stress 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
 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
TAR DNA-binding protein 43
Names
TAR DNA-binding protein-43

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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

  1. NG_008734.1 RefSeqGene

    Range
    5001..17871
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_659

mRNA and Protein(s)

  1. NM_007375.4NP_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
    Q13148, Q96DJ0
    UniProtKB/TrEMBL
    A0A024R4E2, Q9H256
    Related
    ENSP00000240185.4, ENST00000240185.8
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    11012654..11030528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007058560.1 RNA Sequence

  2. XR_007058562.1 RNA Sequence

  3. XR_007058563.1 RNA Sequence

  4. XR_007058564.1 RNA Sequence

  5. XR_007058558.1 RNA Sequence

  6. XR_007058559.1 RNA Sequence

  7. XR_007058561.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    10553914..10566770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)