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

Gene ID: 230908, updated on 29-Jan-2023

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
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Genomic context

See Tardbp in Genome Data Viewer
Location:
4; 4 E2
Exon count:
8
Annotation release Status Assembly Chr Location
109 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_000070.7Genomic Context describing neighboring genes Neighboring gene exosome component 10 Neighboring gene mannan-binding lectin serine peptidase 2 Neighboring gene spermidine synthase Neighboring gene predicted gene 572 Neighboring gene predicted gene 13203

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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
PubMed 
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
PubMed 
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
located_in cytoplasm ISO
Inferred from Sequence Orthology
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
PubMed 
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
 

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001003898.3NP_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
    A0A6P5PIS6, A0A8C6GY78, Q8BLD4, Q8BUM1
    Related
    ENSMUSP00000129342.2, ENSMUST00000165113.8
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
  2. NM_001003899.2NP_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/Swiss-Prot
    Q921F2
    UniProtKB/TrEMBL
    A0A6P5PCR5, Q8BLD4, Q8R0B4
    Related
    ENSMUSP00000101324.2, ENSMUST00000105699.8
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
  3. NM_001008545.2NP_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/Swiss-Prot
    Q921F2
    UniProtKB/TrEMBL
    A0A6P7QRW6, Q544R5, Q6VYI4, Q8BLD4, Q8R0B4
    Related
    ENSMUSP00000130963.2, ENSMUST00000172073.8
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
  4. NM_001008546.2NP_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/Swiss-Prot
    Q921F2
    UniProtKB/TrEMBL
    Q544R5, Q6VYI5, Q8BLD4, Q8R0B4
    Related
    ENSMUSP00000101327.3, ENSMUST00000105702.9
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
  5. NM_001305425.1NP_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:287
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12321
    Location:2197
    RRM1_TDP43; RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:107177
    RRM2_TDP43; RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins
  6. NM_145556.4NP_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
    Q3V0E7, Q921F2
    UniProtKB/TrEMBL
    A0A6P5PKB5, A0A8C6H011, Q544R5, Q8BLD4, Q8R0B4
    Related
    ENSMUSP00000081142.4, ENSMUST00000084125.10
    Conserved Domains (3) summary
    pfam18694
    Location:477
    TDP43_N; Transactive response DNA-binding protein N-terminal domain
    cd12321
    Location:105178
    RRM1_TDP43; RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins
    cd12322
    Location:191261
    RRM2_TDP43; RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins

RNA

  1. 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
  2. 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
  3. NR_149751.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL606969, AV376362, BB616478, BF658781, CA316311, CD548243

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    148696839..148711672 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_390742.5 RNA Sequence