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

Gene ID: 23435, updated on 14-Oct-2018

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; Vega:OTTHUMG00000002120
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

Genomic context

See TARDBP in Genome Data Viewer
Location:
1p36.22
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (11012622..11030528)
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 pseudogene 6 Neighboring gene mannan binding lectin serine peptidase 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat'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

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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
distal enhancer DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
single-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
3'-UTR-mediated mRNA stabilization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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 by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
interchromatin granule IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2, Q9H256
    Related
    ENSP00000240185.3, OTTHUMP00000002171, ENST00000240185.7, OTTHUMT00000006063
    Conserved Domains (2) summary
    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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    11012622..11030528
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000863.2XP_016856352.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Conserved Domains (2) summary
    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
  2. XM_017000864.2XP_016856353.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Conserved Domains (2) summary
    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
  3. XM_017000865.2XP_016856354.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Conserved Domains (2) summary
    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
  4. XM_017000867.2XP_016856356.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Conserved Domains (2) summary
    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
  5. XM_017000866.2XP_016856355.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Conserved Domains (2) summary
    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
  6. XM_017000868.2XP_016856357.1  TAR DNA-binding protein 43 isoform X1

    UniProtKB/Swiss-Prot
    Q13148
    UniProtKB/TrEMBL
    A0A024R4E2
    Related
    ENSP00000491203.1, ENST00000639083.1
    Conserved Domains (2) summary
    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
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