Tardbp TAR DNA binding protein [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tardbpprovided by MGI
Official Full Name: TAR DNA binding proteinprovided by MGI
Primary source: MGI:MGI:2387629
See related: Ensembl:ENSMUSG00000041459 AllianceGenome:MGI:2387629
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Tdp43; TDP-43; 1190002A23Rik
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and pre-mRNA intronic binding activity. Involved in positive regulation of protein import into nucleus; regulation of circadian rhythm; and regulation of protein stability. Acts upstream of or within RNA splicing. Located in nucleus. Is expressed in several structures, including branchial arch; central nervous system; early conceptus; genitourinary system; and heart. Used to study Grn-related frontotemporal lobar degeneration with Tdp43 inclusions; amyotrophic lateral sclerosis type 10; and frontotemporal dementia. 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: Broad expression in CNS E11.5 (RPKM 74.5), limb E14.5 (RPKM 48.1) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 E2; 4 78.77 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (148696839..148711672, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (148612382..148627084, complement)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43.
Title: TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43.
Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation.
Title: Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation.
A transient protein folding response targets aggregation in the early phase of TDP-43-mediated neurodegeneration.
Title: A transient protein folding response targets aggregation in the early phase of TDP-43-mediated neurodegeneration.
Genetic ablation of Sarm1 attenuates expression and mislocalization of phosphorylated TDP-43 after mouse repetitive traumatic brain injury.
Title: Genetic ablation of Sarm1 attenuates expression and mislocalization of phosphorylated TDP-43 after mouse repetitive traumatic brain injury.
RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy.
Title: RNA-binding deficient TDP-43 drives cognitive decline in a mouse model of TDP-43 proteinopathy.
TDP-43 differentially propagates to induce antero- and retrograde degeneration in the corticospinal circuits in mouse focal ALS models.
Title: TDP-43 differentially propagates to induce antero- and retrograde degeneration in the corticospinal circuits in mouse focal ALS models.
Traumatic brain injury induces TDP-43 mislocalization and neurodegenerative effects in tissue distal to the primary injury site in a non-transgenic mouse.
Title: Traumatic brain injury induces TDP-43 mislocalization and neurodegenerative effects in tissue distal to the primary injury site in a non-transgenic mouse.
Microglial CD68 and L-ferritin upregulation in response to phosphorylated-TDP-43 pathology in the amyotrophic lateral sclerosis brain.
Title: Microglial CD68 and L-ferritin upregulation in response to phosphorylated-TDP-43 pathology in the amyotrophic lateral sclerosis brain.
Loss of TDP-43 promotes somatic CAG repeat expansion in Huntington's disease knock-in mice.
Title: Loss of TDP-43 promotes somatic CAG repeat expansion in Huntington's disease knock-in mice.
Pathologically mislocalised TDP-43 in upper motor neurons causes a die-forward spread of ALS-like pathogenic changes throughout the mouse corticomotor system.
Title: Pathologically mislocalised TDP-43 in upper motor neurons causes a die-forward spread of ALS-like pathogenic changes throughout the mouse corticomotor system.

Submit: New GeneRIF Correction See all GeneRIFs (182)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (20) 1 citation
Chemically induced (ENU) (3) 1 citation
Endonuclease-mediated (11) 1 citation

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

Tardbp (e-PCR), detects polymorphism
- UniSTS:547701

C85084 (e-PCR)
- UniSTS:179104

Tardbp (e-PCR), detects polymorphism
- UniSTS:528067

Tardbp (e-PCR), detects polymorphism
- UniSTS:528068

HSC11D022 (e-PCR)
- UniSTS:60639

Gene Ontology Provided by MGI

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	IDA Inferred from Direct Assay more info	PubMed
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 nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables pre-mRNA intronic binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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	IMP Inferred from Mutant Phenotype more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in interchromatin granule	ISO Inferred from Sequence Orthology more info
is_active_in intracellular non-membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perichromatin fibrils	ISO Inferred from Sequence Orthology 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_001003898.3 → NP_001003898.1 TAR DNA-binding protein 43 isoform 5

See identical proteins and their annotated locations for NP_001003898.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses alternate splice sites in the 3' coding region and differs in the 3' UTR compared to variant 1. It encodes isoform 5, which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK083312, AL606969, AY319514

Consensus CDS

CCDS38969.1

UniProtKB/TrEMBL

C9DT14, Q8BLD4

Related

ENSMUSP00000129342.2, ENSMUST00000165113.8

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
NM_001003899.2 → NP_001003899.1 TAR DNA-binding protein 43 isoform 3

See identical proteins and their annotated locations for NP_001003899.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses alternate splice sites in the 3' coding region and differs in the 3' UTR compared to variant 1. It encodes isoform 3, which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK004440, AK045495, AK133207, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635

Consensus CDS

CCDS38970.1

UniProtKB/TrEMBL

C9DT14, Q8R0B4

Related

ENSMUSP00000101324.2, ENSMUST00000105699.8

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
NM_001008545.2 → NP_001008545.1 TAR DNA-binding protein 43 isoform 2

See identical proteins and their annotated locations for NP_001008545.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses alternate splice sites in the 3' coding region and differs in the 3' UTR compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK004440, AK032199, AK045495, AK133207, AK146997, AY319516, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635

Consensus CDS

CCDS38968.1

UniProtKB/TrEMBL

D2KPZ5, Q6VYI4

Related

ENSMUSP00000130963.2, ENSMUST00000172073.8

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
NM_001008546.2 → NP_001008546.1 TAR DNA-binding protein 43 isoform 4

See identical proteins and their annotated locations for NP_001008546.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses alternate splice sites in the 3' coding region and differs in the 3' UTR compared to variant 1. It encodes isoform 4, which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AK004440, AK032199, AK045495, AK133207, AK146997, AY319515, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635

Consensus CDS

CCDS38967.1

UniProtKB/TrEMBL

Q6VYI5, Q8BUM1

Related

ENSMUSP00000101327.3, ENSMUST00000105702.9

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
NM_001305425.1 → NP_001292354.1 TAR DNA-binding protein 43 isoform 6

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR, uses alternate splice sites in the 5' coding region, and uses a downstream start codon compared to variant 1. It encodes isoform 6, which has a shorter N-terminus than isoform 1.

Source sequence(s)

AK004440, AK032199, AK045495, AK133207, AK146997, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635

UniProtKB/Swiss-Prot

Q921F2

UniProtKB/TrEMBL

Q544R5, Q8BLD4, Q8R0B4

Conserved Domains (3) summary

COG0724
Location:2 → 87

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

cd12321
Location:21 → 97

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

cd12322
Location:107 → 177

RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
NM_145556.4 → NP_663531.1 TAR DNA-binding protein 43 isoform 1

See identical proteins and their annotated locations for NP_663531.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK004440, AK045495, AK133207, AK146002, AK146997, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635

Consensus CDS

CCDS38971.1

UniProtKB/Swiss-Prot

Q3U591, Q3V0E7, Q921F2

UniProtKB/TrEMBL

Q544R5

Related

ENSMUSP00000081142.4, ENSMUST00000084125.10

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_027864.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate 3' splice pattern, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK045495, AL606969
NR_131120.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (8) uses an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK004440, AK045495, AK133207, AL606969, BC027105, BE335004, BE853411, BF658781, CD353594, CD548243, CF725038, CF741580, CK780683, CX202635
NR_149751.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AL606969, AV376362, BB616478, BF658781, CA316311, CD548243