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Protein

TAR DNA-binding protein 43

Gene

Tardbp

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3' UTR.By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
TAR DNA-binding protein 43
Short name:
TDP-43
Gene namesi
Name:Tardbp
Synonyms:Tdp43
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:2387629. Tardbp.

Subcellular locationi

  • Nucleus By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000819731 – 414TAR DNA-binding protein 43Add BLAST414

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki102Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki181Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei183PhosphoserineCombined sources1
Modified residuei292PhosphoserineBy similarity1
Modified residuei293Omega-N-methylarginineCombined sources1

Post-translational modificationi

Hyperphosphorylated.By similarity
Ubiquitinated.By similarity

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ921F2.
MaxQBiQ921F2.
PaxDbiQ921F2.
PRIDEiQ921F2.
TopDownProteomicsiQ921F2.

2D gel databases

REPRODUCTION-2DPAGEQ921F2.

PTM databases

iPTMnetiQ921F2.
PhosphoSitePlusiQ921F2.
SwissPalmiQ921F2.

Expressioni

Gene expression databases

BgeeiENSMUSG00000041459.
CleanExiMM_TARDBP.
ExpressionAtlasiQ921F2. baseline and differential.
GenevisibleiQ921F2. MM.

Interactioni

Subunit structurei

Homodimer. Interacts with BRDT (PubMed:22570411). Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimun of six contiguous repeats. Interacts with ATNX2; the interaction is RNA-dependent. Interacts with MATR3. Interacts with UBQLN2. Interacts with HNRNPA2B1 (By similarity).By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

BioGridi231054. 11 interactors.
IntActiQ921F2. 4 interactors.
MINTiMINT-4136792.
STRINGi10090.ENSMUSP00000081142.

Structurei

Secondary structure

1414
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi192 – 197Combined sources6
Helixi204 – 211Combined sources8
Turni212 – 214Combined sources3
Beta strandi217 – 221Combined sources5
Beta strandi228 – 235Combined sources8
Helixi237 – 243Combined sources7
Beta strandi247 – 250Combined sources4
Beta strandi253 – 259Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3D2WX-ray1.65A192-265[»]
ProteinModelPortaliQ921F2.
SMRiQ921F2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ921F2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini104 – 200RRM 1PROSITE-ProRule annotationAdd BLAST97
Domaini191 – 262RRM 2PROSITE-ProRule annotationAdd BLAST72

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni216 – 414Interaction with UBQLN2By similarityAdd BLAST199

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi274 – 413Gly-richAdd BLAST140

Domaini

The RRM domains can bind to both DNA and RNA.

Sequence similaritiesi

Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410IFJS. Eukaryota.
ENOG410ZYQJ. LUCA.
GeneTreeiENSGT00850000132362.
HOGENOMiHOG000254792.
HOVERGENiHBG058671.
InParanoidiQ921F2.
OMAiKHNSSRQ.
OrthoDBiEOG091G0BJZ.
TreeFamiTF315657.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q921F2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEYIRVTED ENDEPIEIPS EDDGTVLLST VTAQFPGACG LRYRNPVSQC
60 70 80 90 100
MRGVRLVEGI LHAPDAGWGN LVYVVNYPKD NKRKMDETDA SSAVKVKRAV
110 120 130 140 150
QKTSDLIVLG LPWKTTEQDL KDYFSTFGEV LMVQVKKDLK TGHSKGFGFV
160 170 180 190 200
RFTEYETQVK VMSQRHMIDG RWCDCKLPNS KQSPDEPLRS RKVFVGRCTE
210 220 230 240 250
DMTAEELQQF FCQYGEVVDV FIPKPFRAFA FVTFADDKVA QSLCGEDLII
260 270 280 290 300
KGISVHISNA EPKHNSNRQL ERSGRFGGNP GGFGNQGGFG NSRGGGAGLG
310 320 330 340 350
NNQGGNMGGG MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS
360 370 380 390 400
GNNQSQGSMQ REPNQAFGSG NNSYSGSNSG APLGWGSASN AGSGSGFNGG
410
FGSSMDSKSS GWGM
Length:414
Mass (Da):44,548
Last modified:December 1, 2001 - v1
Checksum:i2BE6A695EC2CA106
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti8T → K in BAE32189 (PubMed:16141072).Curated1
Sequence conflicti96V → G in BAE32189 (PubMed:16141072).Curated1
Sequence conflicti298G → C in BAE21557 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK133207 mRNA. Translation: BAE21557.1.
AK153803 mRNA. Translation: BAE32189.1.
BC012873 mRNA. Translation: AAH12873.1.
BC025544 mRNA. Translation: AAH25544.1.
BC027772 mRNA. Translation: AAH27772.1.
BC031126 mRNA. Translation: AAH31126.1.
BC033475 mRNA. Translation: AAH33475.1.
CCDSiCCDS38971.1.
RefSeqiNP_001003899.1. NM_001003899.2.
NP_001008545.1. NM_001008545.2.
NP_001008546.1. NM_001008546.2.
NP_001292354.1. NM_001305425.1.
NP_663531.1. NM_145556.4.
UniGeneiMm.22453.
Mm.378962.

Genome annotation databases

EnsembliENSMUST00000084125; ENSMUSP00000081142; ENSMUSG00000041459.
GeneIDi230908.
KEGGimmu:230908.
UCSCiuc008vvg.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK133207 mRNA. Translation: BAE21557.1.
AK153803 mRNA. Translation: BAE32189.1.
BC012873 mRNA. Translation: AAH12873.1.
BC025544 mRNA. Translation: AAH25544.1.
BC027772 mRNA. Translation: AAH27772.1.
BC031126 mRNA. Translation: AAH31126.1.
BC033475 mRNA. Translation: AAH33475.1.
CCDSiCCDS38971.1.
RefSeqiNP_001003899.1. NM_001003899.2.
NP_001008545.1. NM_001008545.2.
NP_001008546.1. NM_001008546.2.
NP_001292354.1. NM_001305425.1.
NP_663531.1. NM_145556.4.
UniGeneiMm.22453.
Mm.378962.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3D2WX-ray1.65A192-265[»]
ProteinModelPortaliQ921F2.
SMRiQ921F2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi231054. 11 interactors.
IntActiQ921F2. 4 interactors.
MINTiMINT-4136792.
STRINGi10090.ENSMUSP00000081142.

PTM databases

iPTMnetiQ921F2.
PhosphoSitePlusiQ921F2.
SwissPalmiQ921F2.

2D gel databases

REPRODUCTION-2DPAGEQ921F2.

Proteomic databases

EPDiQ921F2.
MaxQBiQ921F2.
PaxDbiQ921F2.
PRIDEiQ921F2.
TopDownProteomicsiQ921F2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000084125; ENSMUSP00000081142; ENSMUSG00000041459.
GeneIDi230908.
KEGGimmu:230908.
UCSCiuc008vvg.1. mouse.

Organism-specific databases

CTDi23435.
MGIiMGI:2387629. Tardbp.

Phylogenomic databases

eggNOGiENOG410IFJS. Eukaryota.
ENOG410ZYQJ. LUCA.
GeneTreeiENSGT00850000132362.
HOGENOMiHOG000254792.
HOVERGENiHBG058671.
InParanoidiQ921F2.
OMAiKHNSSRQ.
OrthoDBiEOG091G0BJZ.
TreeFamiTF315657.

Miscellaneous databases

ChiTaRSiTardbp. mouse.
EvolutionaryTraceiQ921F2.
PROiQ921F2.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000041459.
CleanExiMM_TARDBP.
ExpressionAtlasiQ921F2. baseline and differential.
GenevisibleiQ921F2. MM.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTADBP_MOUSE
AccessioniPrimary (citable) accession number: Q921F2
Secondary accession number(s): Q3U591, Q3V0E7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: December 1, 2001
Last modified: November 2, 2016
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.