tardbpb TAR DNA binding protein b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: tardbpbprovided by ZNC
Official Full Name: TAR DNA binding protein bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-3777
See related: Ensembl:ENSDARG00000040031 AllianceGenome:ZFIN:ZDB-GENE-030131-3777
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: tardbp; wu:fb77f02; wu:fc52g10
Summary: Predicted to enable RNA binding activity. Acts upstream of or within several processes, including axon extension; neuromuscular junction development; and regulation of RNA splicing. Predicted to be located in chromatin. Predicted to be active in nucleoplasm. Is expressed in several structures, including brain; gill; head; heart; and liver. Used to study amyotrophic lateral sclerosis. 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, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 6

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	6	NC_007117.7 (45936674..45949097, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	6	NC_007117.6 (45935895..45947210, complement)

Chromosome 6 - NC_007117.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Optogenetic Phase Transition of TDP-43 in Spinal Motor Neurons of Zebrafish Larvae.
Title: Optogenetic Phase Transition of TDP-43 in Spinal Motor Neurons of Zebrafish Larvae.
TDP-43 Regulation of AChE Expression Can Mediate ALS-Like Phenotype in Zebrafish.
Title: TDP-43 Regulation of AChE Expression Can Mediate ALS-Like Phenotype in Zebrafish.
tardbp hom/hom mutants displayed gross morphological defects, early lethality, reduced locomotor function, aberrant quantal transmission, and perturbed synapse architecture at the NMJ. tardbp(+/-); tardbpl(-/-), but not hom/hom mutants, were sensitive to chronic treatments of BAY K 8644, an L-type calcium channel agonist. This result highlights the importance of partial vs. complete loss of allelic functions of TDP-43.
Title: Neuromuscular junction abnormalities in a zebrafish loss-of-function model of TDP-43.
Data indicate a method for site-directed single nucleotide editing in two disease-related genes, DNA binding protein tardbp and RNA binding protein fus.
Title: Homology Directed Knockin of Point Mutations in the Zebrafish tardbp and fus Genes in ALS Using the CRISPR/Cas9 System.
Loss of ALS-associated TDP-43 in zebrafish causes muscle degeneration, vascular dysfunction, and reduced motor neuron axon outgrowth.
Title: Loss of ALS-associated TDP-43 in zebrafish causes muscle degeneration, vascular dysfunction, and reduced motor neuron axon outgrowth.
TARDBP and FUS act in a pathogenic pathway that is independent of SOD1.
Title: FUS and TARDBP but not SOD1 interact in genetic models of amyotrophic lateral sclerosis.

Submit: New GeneRIF Correction

General gene information

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Markers

fb77f02.x1 (e-PCR)
- UniSTS:191379

fb77f02.x1 (e-PCR)
- UniSTS:191380

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 axon extension	IMP Inferred from Mutant Phenotype 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 locomotory behavior	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within regulation of RNA splicing	IMP Inferred from Mutant Phenotype 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 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)

NM_201476.1 → NP_958884.1 TAR DNA-binding protein 43

See identical proteins and their annotated locations for NP_958884.1

Status: PROVISIONAL

Source sequence(s)

BC049348

UniProtKB/TrEMBL

A0A8N7V057, Q802C7

Related

ENSDARP00000058554.5, ENSDART00000058555.7

Conserved Domains (3) summary

COG0724
Location:85 → 177

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12321
Location:111 → 187

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