Tardbp TAR DNA binding protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tardbpprovided by RGD
Official Full Name: TAR DNA binding proteinprovided by RGD
Primary source: RGD:1310906
See related: Ensembl:ENSRNOG00000012455 AllianceGenome:RGD:1310906
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tdp-43
Summary: Enables RNA binding activity. Involved in positive regulation of insulin secretion and response to endoplasmic reticulum stress. Located in cytoplasm and nuclear lumen. 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, Apr 2022]
Expression: Biased expression in Thymus (RPKM 450.2), Spleen (RPKM 344.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (164330452..164348435, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (159050518..159062218, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (165432089..165442232, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TDP-43 was Involved in Radiation-induced Neuronal Damage and May Not Through the BDNF/TrkB Pathway.
Title: TDP-43 was Involved in Radiation-induced Neuronal Damage and May Not Through the BDNF/TrkB Pathway.
C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD.
Title: C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD.
Astrocytes with TDP-43 inclusions exhibit reduced noradrenergic cAMP and Ca(2+) signaling and dysregulated cell metabolism.
Title: Astrocytes with TDP-43 inclusions exhibit reduced noradrenergic cAMP and Ca(2+) signaling and dysregulated cell metabolism.
Knockdown of TDP-43 in astrocytes results in accumulation of repetitive element transcripts and dsRNA and innate immune activation.
Title: TDP-43 knockdown causes innate immune activation via protein kinase R in astrocytes.
These findings suggest that TDP-43 may regulate activity-dependent neuronal plasticity, possibly by regulating the splicing of genes that are responsible for fast synaptic transmission and membrane potential.
Title: Neuronal TDP-43 depletion affects activity-dependent plasticity.
results indicate that redundant pathways regulate TDP43 nuclear export
Title: TDP43 nuclear export and neurodegeneration in models of amyotrophic lateral sclerosis and frontotemporal dementia.
Temporal expression of mutant TDP-43 in neurons promoted serious phenotype in an animal model of Amyotrophic Lateral Sclerosis.
Title: Temporal Expression of Mutant TDP-43 Correlates with Early Amyotrophic Lateral Sclerosis Phenotype and Motor Weakness.
TDP-43 RNP granules in axons of rodent primary cortical neurons display liquid-like properties, including fusion with rapid relaxation to circular shape and shear stress-induced deformation.
Title: Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons.
Chronic traumatic encephalopathy induces increases in TDP-43 phosphorylation which contributes to defective neuronal integrity.
Title: Defective synthesis and release of astrocytic thrombospondin-1 mediates the neuronal TDP-43 proteinopathy, resulting in defects in neuronal integrity associated with chronic traumatic encephalopathy: in vitro studies.
These results suggest that residues 274-353 are responsible for the conversion of TDP-43 to amyloid-like fibrils and that templated aggregation of TDP-43 by seeding with different peptides induces various types of TDP-43 pathologies, i.e. the peptides appear to act like prion strains.
Title: Templated Aggregation of TAR DNA-binding Protein of 43 kDa (TDP-43) by Seeding with TDP-43 Peptide Fibrils.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:479044 (e-PCR)
- UniSTS:479044

Tardbp (e-PCR), detects polymorphism
- UniSTS:479044

HSC11D022 (e-PCR)
- UniSTS:60639

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables lipid binding	ISO Inferred from Sequence Orthology more info
enables mRNA 3'-UTR binding	ISO Inferred from Sequence Orthology more info
enables molecular condensate scaffold activity	ISO Inferred from Sequence Orthology more info
enables pre-mRNA intronic binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in 3'-UTR-mediated mRNA destabilization	ISO Inferred from Sequence Orthology more info
involved_in 3'-UTR-mediated mRNA stabilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in amyloid fibril formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene expression	ISO Inferred from Sequence Orthology more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation by host of viral transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in nuclear inner membrane organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
involved_in response to endoplasmic reticulum stress	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in interchromatin granule	IDA Inferred from Direct Assay more info	PubMed
is_active_in intracellular non-membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perichromatin fibrils	IDA Inferred from Direct Assay more info	PubMed

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_001011979.3 → NP_001011979.1 TAR DNA-binding protein 43 isoform 2

See identical proteins and their annotated locations for NP_001011979.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6IU83, A6IU85, I6L9G6, J9JIJ9

Related

ENSRNOP00000041889.3, ENSRNOT00000049822.4

Conserved Domains (3) summary

COG0724
Location:77 → 171

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

cd12321
Location:105 → 181

RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
NM_001399105.1 → NP_001386034.1 TAR DNA-binding protein 43 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6GLU8, A6IU84

Related

ENSRNOP00000095901.1, ENSRNOT00000103485.1

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

RNA

NR_174161.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

164330452..164348435 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006239385.5 → XP_006239447.1 TAR DNA-binding protein 43 isoform X4

See identical proteins and their annotated locations for XP_006239447.1

UniProtKB/TrEMBL

A6IU81, A6IU85

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_006239384.5 → XP_006239446.1 TAR DNA-binding protein 43 isoform X3

UniProtKB/TrEMBL

A6IU85

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_039109697.2 → XP_038965625.1 TAR DNA-binding protein 43 isoform X1

UniProtKB/TrEMBL

A0A8I6GLU8, A6IU84

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_008764236.4 → XP_008762458.1 TAR DNA-binding protein 43 isoform X6

UniProtKB/TrEMBL

A6IU85

Conserved Domains (3) summary

COG0724
Location:77 → 171

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

cd12321
Location:105 → 181

RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_006239386.5 → XP_006239448.1 TAR DNA-binding protein 43 isoform X7

Conserved Domains (2) summary

cd12321
Location:105 → 181

RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_008764234.4 → XP_008762456.1 TAR DNA-binding protein 43 isoform X2

Conserved Domains (3) summary

pfam18694
Location:4 → 77

TDP43_N; Transactive response DNA-binding protein N-terminal domain

cd12321
Location:105 → 178

RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_008764235.4 → XP_008762457.1 TAR DNA-binding protein 43 isoform X5

UniProtKB/TrEMBL

A6IU85

Conserved Domains (3) summary

COG0724
Location:77 → 171

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

cd12321
Location:105 → 181

RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

cd12322
Location:191 → 261

RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
XM_063287482.1 → XP_063143552.1 TAR DNA-binding protein 43 isoform X6
XM_063287481.1 → XP_063143551.1 TAR DNA-binding protein 43 isoform X3