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

Gene ID: 386630, updated on 28-Oct-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 chromatin. 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 human TARDBP (TAR DNA binding protein). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs
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Genomic context

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See tardbpa in Genome Data Viewer
Location:
chromosome: 23
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (29357784..29362538)
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 uncharacterized LOC137489134 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 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 (17) 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
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
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

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
    Related
    ENSDARP00000110177.2, ENSDART00000126681.5
    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: GCF_000002035.6-RS_2024_08

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
    29357784..29362538
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021469762.2 → XP_021325437.1  TAR DNA binding protein, like 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_021469761.2 → XP_021325436.1  TAR DNA binding protein, like 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_011008371.1 RNA Sequence

  2. XR_011008372.1 RNA Sequence

  3. XR_011008373.1 RNA Sequence

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018395156.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    94430..99138
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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