Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TARDBP Gene

Aliases for TARDBP Gene

  • TAR DNA Binding Protein 2 3
  • TDP-43 3 4
  • ALS10 3 6
  • TDP43 4 6
  • TAR DNA-Binding Protein 43 3
  • TAR DNA-Binding Protein-43 3

External Ids for TARDBP Gene

Summaries for TARDBP Gene

Entrez Gene Summary for TARDBP Gene

  • 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]

GeneCards Summary for TARDBP Gene

TARDBP (TAR DNA Binding Protein) is a Protein Coding gene. Diseases associated with TARDBP include amyotrophic lateral sclerosis 10, with or without ftd and ftdals1. Among its related pathways are Neuroscience. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and identical protein binding. An important paralog of this gene is DAZAP1.

UniProtKB/Swiss-Prot for TARDBP Gene

  • DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3 UTR.

Gene Wiki entry for TARDBP Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TARDBP Gene

Genomics for TARDBP Gene

Genomic Location for TARDBP Gene

Start:
11,012,344 bp from pter
End:
11,026,420 bp from pter
Size:
14,077 bases
Orientation:
Plus strand

Genomic View for TARDBP Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TARDBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TARDBP Gene

Regulatory Elements for TARDBP Gene

Proteins for TARDBP Gene

  • Protein details for TARDBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13148-TADBP_HUMAN
    Recommended name:
    TAR DNA-binding protein 43
    Protein Accession:
    Q13148
    Secondary Accessions:
    • A4GUK4
    • A4GUK5
    • A4GUK6
    • B2R629
    • B4DJ45
    • E2PU12
    • Q53H27
    • Q6FI92
    • Q96DJ0

    Protein attributes for TARDBP Gene

    Size:
    414 amino acids
    Molecular mass:
    44740 Da
    Quaternary structure:
    • Homodimer. Interacts with BRDT (By similarity). Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimun of six contiguous repeats. Interacts with ATNX2; the interaction is RNA-dependent. Interacts with MATR3.
    SequenceCaution:
    • Sequence=ABO32290.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=ABO32292.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TARDBP Gene

    Alternative splice isoforms for TARDBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TARDBP Gene

Proteomics data for TARDBP Gene at MOPED

Post-translational modifications for TARDBP Gene

  • Cleaved to generate C-terminal fragments in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU
  • Hyperphosphorylated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU
  • Ubiquitinated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys95, Lys102, Lys114, Lys160, and Lys181

No data available for DME Specific Peptides for TARDBP Gene

Domains for TARDBP Gene

Gene Families for TARDBP Gene

HGNC:
  • RBM :RNA binding motif (RRM) containing

Protein Domains for TARDBP Gene

Graphical View of Domain Structure for InterPro Entry

Q13148

UniProtKB/Swiss-Prot:

TADBP_HUMAN
Domain:
  • The RRM domains can bind to both DNA and RNA.:
    • Q13148
  • Contains 2 RRM (RNA recognition motif) domains.:
    • Q13148
genes like me logo Genes that share domains with TARDBP: view

Function for TARDBP Gene

Molecular function for TARDBP Gene

UniProtKB/Swiss-Prot Function: DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3 UTR.

Gene Ontology (GO) - Molecular Function for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0001205 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IEA --
GO:0003676 nucleic acid binding --
GO:0003690 double-stranded DNA binding IDA 7745706
GO:0003700 sequence-specific DNA binding transcription factor activity TAS 7745706
genes like me logo Genes that share ontologies with TARDBP: view
genes like me logo Genes that share phenotypes with TARDBP: view

Animal Models for TARDBP Gene

MGI Knock Outs for TARDBP:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for TARDBP Gene

Localization for TARDBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for TARDBP Gene

Nucleus. Note=In patients with frontotemporal lobar degeneration and amyotrophic lateral sclerosis, it is absent from the nucleus of affected neurons but it is the primary component of cytoplasmic ubiquitin-positive inclusion bodies.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TARDBP Gene COMPARTMENTS Subcellular localization image for TARDBP gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
endoplasmic reticulum 1
mitochondrion 1
vacuole 1

Gene Ontology (GO) - Cellular Components for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005726 perichromatin fibrils --
GO:0005737 cytoplasm --
GO:0016607 nuclear speck --
genes like me logo Genes that share ontologies with TARDBP: view

Pathways for TARDBP Gene

SuperPathways for TARDBP Gene

Superpath Contained pathways
1 Neuroscience
genes like me logo Genes that share pathways with TARDBP: view

Pathways by source for TARDBP Gene

1 Cell Signaling Technology pathway for TARDBP Gene

Gene Ontology (GO) - Biological Process for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001933 negative regulation of protein phosphorylation IMP 18305152
GO:0006366 transcription from RNA polymerase II promoter TAS 7745706
GO:0006397 mRNA processing IEA --
GO:0008219 cell death --
GO:0008380 RNA splicing IDA 11285240
genes like me logo Genes that share ontologies with TARDBP: view

Compounds for TARDBP Gene

(1) Novoseek inferred chemical compound relationships for TARDBP Gene

Compound -log(P) Hits PubMed IDs
superoxide 16.9 3
genes like me logo Genes that share compounds with TARDBP: view

Transcripts for TARDBP Gene

Unigene Clusters for TARDBP Gene

TAR DNA binding protein:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TARDBP Gene

No ASD Table

Relevant External Links for TARDBP Gene

GeneLoc Exon Structure for
TARDBP
ECgene alternative splicing isoforms for
TARDBP

Expression for TARDBP Gene

mRNA expression in normal human tissues for TARDBP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for TARDBP Gene

SOURCE GeneReport for Unigene cluster for TARDBP Gene Hs.300624

mRNA Expression by UniProt/SwissProt for TARDBP Gene

Q13148-TADBP_HUMAN
Tissue specificity: Ubiquitously expressed. In particular, expression is high in pancreas, placenta, lung, genital tract and spleen
genes like me logo Genes that share expressions with TARDBP: view

No data available for mRNA differential expression in normal tissues for TARDBP Gene

Orthologs for TARDBP Gene

This gene was present in the common ancestor of animals.

Orthologs for TARDBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TARDBP 35
  • 99.52 (n)
  • 100 (a)
TARDBP 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TARDBP 35
  • 92.75 (n)
  • 97.58 (a)
TARDBP 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TARDBP 35
  • 89.94 (n)
  • 97.83 (a)
TARDBP 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tardbp 35
  • 90.34 (n)
  • 96.14 (a)
Tardbp 16
Tardbp 36
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TARDBP 36
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TARDBP 36
  • 98 (a)
OneToOne
chicken
(Gallus gallus)
Aves TARDBP 35
  • 82.45 (n)
  • 95.17 (a)
TARDBP 36
  • 95 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia tardbp-prov 35
tropical clawed frog
(Silurana tropicalis)
Amphibia MGC75857 35
tardbp 35
  • 76.49 (n)
  • 86.63 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3538 35
zebrafish
(Danio rerio)
Actinopterygii tardbp 35
  • 70.56 (n)
  • 78.44 (a)
tardbp 36
  • 75 (a)
OneToMany
tardbpl 36
  • 76 (a)
OneToMany
wufb77f02 35
fruit fly
(Drosophila melanogaster)
Insecta CG7804 36
  • 47 (a)
OneToMany
TBPH 36
  • 38 (a)
OneToMany
TBPH 37
  • 56 (a)
CG7804 37
  • 54 (a)
worm
(Caenorhabditis elegans)
Secernentea tdp-1 36
  • 30 (a)
OneToOne
F44G4.4 37
  • 38 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3080 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10473 36
  • 44 (a)
OneToOne
Species with no ortholog for TARDBP:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TARDBP Gene

ENSEMBL:
Gene Tree for TARDBP (if available)
TreeFam:
Gene Tree for TARDBP (if available)

Paralogs for TARDBP Gene

Paralogs for TARDBP Gene

genes like me logo Genes that share paralogs with TARDBP: view

Variants for TARDBP Gene

Sequence variations from dbSNP and Humsavar for TARDBP Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs11093 -- 11,023,881(-) GAACT(C/T)TGCTT utr-variant-3-prime
rs968545 -- 11,012,522(-) AATTC(A/G)AGCCT upstream-variant-2KB
rs1064824 -- 11,023,231(+) CTTCA(C/T)TGAAA utr-variant-3-prime
rs1138362 -- 11,021,885(+) GCGCT(A/G)GGATT intron-variant
rs1138363 -- 11,021,891(+) ggatt(A/G)caggc intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TARDBP Gene

Variant ID Type Subtype PubMed ID
nsv832425 CNV Loss 17160897

Relevant External Links for TARDBP Gene

HapMap Linkage Disequilibrium report
TARDBP
Human Gene Mutation Database (HGMD)
TARDBP
Locus Specific Mutation Databases (LSDB)
TARDBP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TARDBP Gene

Disorders for TARDBP Gene

(1) OMIM Diseases for TARDBP Gene (605078)

UniProtKB/Swiss-Prot

TADBP_HUMAN
  • Amyotrophic lateral sclerosis 10 (ALS10) [MIM:612069]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. {ECO:0000269 PubMed:18288693, ECO:0000269 PubMed:18309045, ECO:0000269 PubMed:18372902, ECO:0000269 PubMed:18396105, ECO:0000269 PubMed:18438952, ECO:0000269 PubMed:19224587, ECO:0000269 PubMed:19695877, ECO:0000269 PubMed:21220647, ECO:0000269 PubMed:21418058, ECO:0000269 PubMed:22456481}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(13) Novoseek inferred disease relationships for TARDBP Gene

Disease -log(P) Hits PubMed IDs
frontotemporal dementia 96.1 87
amyotrophic lateral sclerosis 92.3 89
motor neuron disease 85.1 12
inclusion body myopathy 80.4 2
neurodegeneration 75.6 16

Relevant External Links for TARDBP

GeneTests
TARDBP
GeneReviews
TARDBP
Genetic Association Database (GAD)
TARDBP
Human Genome Epidemiology (HuGE) Navigator
TARDBP
genes like me logo Genes that share disorders with TARDBP: view

Publications for TARDBP Gene

  1. Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs. (PMID: 7745706) Ou S.-H.I. … Gaynor R.B. (J. Virol. 1995) 2 3 4 23
  2. High frequency of TARDBP gene mutations in Italian patients with amyotrophic lateral sclerosis. (PMID: 19224587) Corrado L. … D'Alfonso S. (Hum. Mutat. 2009) 3 4 23 48
  3. TARDBP (TDP-43) sequence analysis in patients with familial and sporadic ALS: identification of two novel mutations. (PMID: 19236453) Del Bo R. … Comi G.P. (Eur. J. Neurol. 2009) 3 23 48
  4. TDP-43 is not a common cause of sporadic amyotrophic lateral sclerosis. (PMID: 18545701) Guerreiro R.J. … Traynor B.J. (PLoS ONE 2008) 3 23 48
  5. TDP-43 mutation in familial amyotrophic lateral sclerosis. (PMID: 18438952) Yokoseki A. … Onodera O. (Ann. Neurol. 2008) 3 4 23

Products for TARDBP Gene

Sources for TARDBP Gene

Back to Top

Content