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

    Gene ID: 23435, updated on 22-May-2013
    Official Symbol
    TARDBPprovided by HGNC
    Official Full Name
    TAR DNA binding proteinprovided by HGNC
    Primary source
    HGNC:11571
    Locus tag
    RP4-635E18.2
    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]
    Location :
    1p36.22
    Sequence :
    Chromosome: 1; NC_000001.10 (11072679..11085549)
    See TARDBP in Epigenomics, MapViewer

    Chromosome 1 - NC_000001.10Genomic 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 Functions What's a GeneRIF?

    Amyotrophic lateral sclerosis type 10

    Summary from GeneReviews: Amyotrophic Lateral Sclerosis Overview Go to GeneReviews

    Disease Characteristics
    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving both upper motor neurons (UMN) and lower motor neurons (LMN). UMN signs include hyperreflexia, extensor plantar response, increased muscle tone, and weakness in a topographic representation. LMN signs include weakness, muscle wasting, hyporeflexia, muscle cramps, and fasciculations. Initial presentation varies. Affected individuals typically present with either asymmetric focal weakness of the extremities (stumbling or poor handgrip) or bulbar findings (dysarthria, dysphagia). Other findings may include muscle fasciculations, muscle cramps, and labile affect, but not necessarily mood. Regardless of initial symptoms, atrophy and weakness eventually affect other muscles. The mean age of onset is 56 years in individuals with no known family history and 46 years in individuals with more than one affected family member (familial ALS or FALS). Average disease duration is about three years, but it can vary significantly. Death usually results from compromise of the respiratory muscles.
    Diagnosis Testing
    The diagnosis of ALS is based on clinical features, electrodiagnostic testing, and exclusion of other health conditions with related symptoms. Molecular genetic testing, available in clinical laboratories for several genes associated with ALS, plays a prominent role in diagnosis of the genetic subtype and genetic counseling.
    Genetic Counseling
    Amyotrophic lateral sclerosis can be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Genetic counseling and risk assessment depend on accurate determination of the specific genetic diagnosis.
    References

    Summary from GeneReviews: TARDBP-Related Amyotrophic Lateral Sclerosis Go to GeneReviews

    Disease Characteristics
    TARDBP-related amyotrophic lateral sclerosis (TARDBP-related ALS) is characterized by upper motor neuron (UMN) and lower motor neuron (LMN) disease that appears indistinguishable from ALS of other known and unknown causes based on gender ratio, age of onset, symptom distribution, and severity of disease. The male to female ratio is 1.6 to 1. Mean age of onset is 54 +/- 12 years. UMN manifestations can include stiffness, spasticity, hyperreflexia, and pseudobulbar affect; LMN manifestations often include weakness accompanied by muscle atrophy, fasciculations, and cramping. Limb-onset occurs in 80% and bulbar-onset in 20%. Affected individuals typically succumb to respiratory failure when phrenic and thoracic motor neurons become severely involved.
    Diagnosis Testing
    The diagnosis of ALS is established by clinical examination, neurophysiologic testing, and neuroimaging. Molecular genetic testing for TARDBP, the only gene associated with TARDBP-related ALS, is available on a clinical basis.
    Genetic Counseling
    TARDBP-related ALS is inherited in an autosomal dominant manner. The proportion of cases caused by de novo mutations is unknown. Each child of an individual with TARDBP-related ALS has a 50% chance of inheriting the mutation. Prenatal diagnosis for TARDBP-related ALS is available.
    References
    Protein Gene Interaction Pubs
    Tat, p14 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 Protein Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description
    Q13148 Q01780 EXOSC10    HPRD  PubMed  
    Q13148 Q9UNZ2 NSFL1C    HPRD  PubMed  
    Q13148 Q15047 SETDB1    HPRD  PubMed  
    Q13148 Q9H0D6 XRN2    HPRD  PubMed  
    Q13148 Q9UKY1 ZHX1    HPRD  PubMed  
    BioGRID:117003 BioGRID:115987 AHCYL1    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:106848 APP    BioGRID  PubMed Reconstituted Complex 
    BioGRID:117003 BioGRID:122127 ARHGEF28    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:106961 ATIC    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:107140 BRCA1    BioGRID  PubMed Affinity Capture-RNA 
    BioGRID:117003 BioGRID:120937 CAND1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:114030 CUL3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:111403 EXOSC10    BioGRID  PubMed Two-hybrid 
    BioGRID:117003 BioGRID:108621 FN1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:108797 FUS    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:117003 BioGRID:115330 HDAC6    BioGRID  PubMed Affinity Capture-RNA 
    BioGRID:117003 BioGRID:109420 HNRNPA1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:109431 HNRNPK    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:115530 HNRNPR    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:109552 HSP90AA1    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:109540 HSPA4    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:200263 Hdac6    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:109863 IRAK1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:109865 IRAK2    BioGRID  PubMed Affinity Capture-MS; Reconstituted Complex 
    BioGRID:117003 BioGRID:109883 ITGA4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:128436 KHDRBS2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:115114 KIAA0101    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:35104 MFT1    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:125217 NACC1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:117003 BioGRID:121014 NSFL1C    BioGRID  PubMed Two-hybrid 
    BioGRID:117003 BioGRID:115408 NUBP2    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:203509 Nhp2l1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:113777 PABPN1    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:116625 PAXIP1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:111126 PCBP1    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:111657 PSMA3    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:111660 PSMA6    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:206136 Park2    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:34547 RPB2    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:115202 SETDB1    BioGRID  PubMed Two-hybrid 
    BioGRID:117003 BioGRID:117017 SF3B1    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:114397 SQSTM1    BioGRID  PubMed Affinity Capture-Western; Co-localization; Reconstituted Complex 
    BioGRID:117003 BioGRID:121810 SRPRB    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:112497 SUMO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:115755 SYNCRIP    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:35586 TEX1    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:35687 THO2    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:36601 THP2    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:34190 TIF1    BioGRID  PubMed Synthetic Rescue 
    BioGRID:117003 BioGRID:116466 U2AF2    BioGRID  PubMed Co-fractionation 
    BioGRID:117003 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western; Co-localization; Co-purification; Reconstituted Complex 
    BioGRID:117003 BioGRID:115791 UBD    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:119007 UBQLN1    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:117003 BioGRID:113255 VCAM1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:117003 BioGRID:113258 VCP    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:117003 BioGRID:113306 WHSC1    BioGRID  PubMed Affinity Capture-RNA 
    BioGRID:117003 BioGRID:116483 XRN2    BioGRID  PubMed Two-hybrid 
    BioGRID:117003 BioGRID:116406 ZHX1    BioGRID  PubMed Two-hybrid 

    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 
    mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
     
    sequence-specific DNA binding transcription factor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    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 
    cell death IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation by host of viral transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    NOT nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    Preferred Names
    TAR DNA-binding protein 43
    Names
    TAR DNA-binding protein 43
    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)

    mRNA and Protein(s)

    1. NM_007375.3NP_031401.1  TAR DNA-binding protein 43

      Status: REVIEWED

      Source sequence(s)
      AF311304, AL045296, AL050265, BC001487, BC059955, BI464234, BM716882, CD703666
      Consensus CDS
      CCDS122.1
      UniProtKB/Swiss-Prot
      Q13148
      UniProtKB/TrEMBL
      Q9H256
      Conserved Domains (1) summary
      cd00590
      Location:106171
      Blast Score: 173
      RRM; RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000001.10 Reference GRCh37.p10 Primary Assembly

      Range
      11072679..11085549
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000133.1 Alternate HuRef

      Range
      10224341..10237229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018912.1 Alternate CHM1_1.0

      Range
      11091467..11104345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

      Supplemental Content

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