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    tardbpa TAR DNA binding protein a [ Danio rerio (zebrafish) ]

    Gene ID: 386630, updated on 25-Apr-2024

    Summary

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    Official Symbol
    tardbpaprovided by ZNC
    Official Full Name
    TAR DNA binding protein aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-031030-1
    See related
    Ensembl:ENSDARG00000004452 AllianceGenome:ZFIN:ZDB-GENE-031030-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    tardbp; tardbpl; wu:fb52e05; wu:fe47c11; wu:fj94b04
    Summary
    Predicted to enable RNA binding activity. Acts upstream of or within several processes, including axon extension; neuromuscular junction development; and skeletal muscle tissue development. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. Is expressed in brain and fin. Human ortholog(s) of this gene implicated in Parkinson's disease; amyotrophic lateral sclerosis; amyotrophic lateral sclerosis type 10; and motor neuron disease. Orthologous to several human genes including TARDBP (TAR DNA binding protein). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See tardbpa in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (29357753..29362846)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (29431212..29435997)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene castor zinc finger 1 Neighboring gene si:dkey-246i21.1 Neighboring gene si:ch211-129o18.4 Neighboring gene somatostatin 6 Neighboring gene phosphogluconate dehydrogenase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The Novel Small Molecule TRVA242 Stabilizes Neuromuscular Junction Defects in Multiple Animal Models of Amyotrophic Lateral Sclerosis. Bose P, et al. Neurotherapeutics, 2019 Oct. PMID 31342410, Free PMC Article
    2. Neuromuscular junction abnormalities in a zebrafish loss-of-function model of TDP-43. Bose P, et al. J Neurophysiol, 2019 Jan 1. PMID 30461368
    3. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Hruscha A, et al. Development, 2013 Dec. PMID 24257628
    4. Gain and loss of function of ALS-related mutations of TARDBP (TDP-43) cause motor deficits in vivo. Kabashi E, et al. Hum Mol Genet, 2010 Feb 15. PMID 19959528
    5. Loss of ALS-associated TDP-43 in zebrafish causes muscle degeneration, vascular dysfunction, and reduced motor neuron axon outgrowth. Schmid B, et al. Proc Natl Acad Sci U S A, 2013 Mar 26. PMID 23457265, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tardbpl splicing rescues motor neuron and axonal development.
      Title: Tardbpl splicing rescues motor neuron and axonal development in a mutant tardbp zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within axon extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within axonogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within blood vessel morphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within locomotory behavior IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within neuromuscular junction development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within skeletal muscle tissue development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    TAR DNA binding protein, like; TAR DNA-binding protein 43

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001362353.1 → NP_001349282.1  TAR DNA binding protein, like isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      CR381616, EH537260
      Conserved Domains (2) summary
      cd12321
      Location:106 → 182
      RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      cd12322
      Location:192 → 262
      RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

    2. NM_198364.2 → NP_938178.1  TAR DNA binding protein, like isoform 1

      See identical proteins and their annotated locations for NP_938178.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      CR381616
      UniProtKB/TrEMBL
      B2GP88, Q803N5
      Related
      ENSDARP00000007032.5, ENSDART00000027255.6
      Conserved Domains (2) summary
      cd12321
      Location:106 → 182
      RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      cd12322
      Location:197 → 267
      RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      29357753..29362846
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021469762.1 → XP_021325437.1  TAR DNA-binding protein 43 isoform X2

      UniProtKB/TrEMBL
      B2GP88, Q803N5
      Related
      ENSDARP00000144841.1, ENSDART00000189242.1
      Conserved Domains (2) summary
      cd12321
      Location:106 → 182
      RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      cd12322
      Location:197 → 267
      RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

    2. XM_021469761.1 → XP_021325436.1  TAR DNA-binding protein 43 isoform X1

      UniProtKB/TrEMBL
      A0A8M9PSZ1
      Related
      ENSDARP00000128116.1, ENSDART00000139223.4
      Conserved Domains (3) summary
      COG0724
      Location:179 → 363
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12321
      Location:106 → 182
      RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
      cd12322
      Location:192 → 262
      RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

    RNA

    1. XR_002456535.1 RNA Sequence

    2. XR_002456537.1 RNA Sequence

      Related
      ENSDART00000126681.5

    3. XR_002456536.1 RNA Sequence

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018395156.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      94561..99138
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.