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

    Gene ID: 23435, updated on 26-Jul-2015
    Official Symbol
    TARDBPprovided by HGNC
    Official Full Name
    TAR DNA binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:11571
    See related
    HPRD:05466; MIM:605078
    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]
    Orthologs
    See TARDBP in Epigenomics, MapViewer
    Location:
    1p36.22
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 1 NC_000001.11 (11012622..11025492)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11072462..11085549)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chromosome 1 open reading frame 127 Neighboring gene cofilin 1 (non-muscle) pseudogene 6 Neighboring gene mannan-binding lectin serine peptidase 2 Neighboring gene spermidine synthase

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    poly(A) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    3'-UTR-mediated mRNA stabilization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA splicing IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation by host of viral transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of protein phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nuclear fragmentation involved in apoptotic nuclear change IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    nuclear inner membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of insulin secretion IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to endoplasmic reticulum stress IEA
    Inferred from Electronic Annotation
    more info
     
    transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    interchromatin granule IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perichromatin fibrils IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    TAR DNA-binding protein 43
    Names
    TAR DNA-binding protein-43

    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_007375.3NP_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, BI464234, BM716882, CD703666
      Consensus CDS
      CCDS122.1
      UniProtKB/TrEMBL
      A0A024R4E2
      UniProtKB/Swiss-Prot
      Q13148
      UniProtKB/TrEMBL
      Q9H256
      Conserved Domains (4) summary
      smart00360
      Location:106175
      RRM; RNA recognition motif
      cd12321
      Location:105181
      RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      cd12322
      Location:191261
      RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      pfam14259
      Location:193252
      RRM_6; RNA recognition motif (a.k.a. RRM, RBD, or RNP domain)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p2 Primary Assembly

      Range
      11012622..11025492
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_946596.1 RNA Sequence

    2. XR_946597.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

      Range
      11060321..11073209
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)