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

    Gene ID: 23435, updated on 16-Apr-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TARDBP in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11012654..11030528)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (10553914..10571805)
    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 H3K4me1 hESC enhancer GRCh37_chr1:11008047-11008548 Neighboring gene chromosome 1 open reading frame 127 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:11018518-11019287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11020057-11020826 Neighboring gene Sharpr-MPRA regulatory region 3012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 257 Neighboring gene cofilin 1 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 258 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11072454-11073421 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11073783-11074029 Neighboring gene MBL associated serine protease 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11105801-11106633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 163 Neighboring gene spermidine synthase Neighboring gene exosome component 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11152350-11152530 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11159092-11159654 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11159655-11160215 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

    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
     
    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
    part_of 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

    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
      A4GUK4, A4GUK5, A4GUK6, B2R629, B4DJ45, E2PU12, Q13148, Q53H27, Q6FI92, Q96DJ0
      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: GCF_000001405.40-RS_2023_10

    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..10571805
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008485970.1 RNA Sequence

    2. XR_008485971.1 RNA Sequence

    3. XR_008485972.1 RNA Sequence

    4. XR_008485973.1 RNA Sequence

    5. XR_008485976.1 RNA Sequence

    6. XR_008485978.1 RNA Sequence

    7. XR_008485979.1 RNA Sequence

    8. XR_008485980.1 RNA Sequence

    9. XR_008485974.1 RNA Sequence

    10. XR_008485975.1 RNA Sequence

    11. XR_008485977.1 RNA Sequence