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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 (By similarity).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
ProteomesiUP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:2387629. Tardbp.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 414414TAR DNA-binding protein 43PRO_0000081973Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei292 – 2921PhosphoserineBy similarity

Post-translational modificationi

Hyperphosphorylated.By similarity
Ubiquitinated.By similarity

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ921F2.
PaxDbiQ921F2.
PRIDEiQ921F2.

2D gel databases

REPRODUCTION-2DPAGEQ921F2.

PTM databases

PhosphoSiteiQ921F2.

Expressioni

Gene expression databases

BgeeiQ921F2.
CleanExiMM_TARDBP.
ExpressionAtlasiQ921F2. baseline and differential.
GenevisibleiQ921F2. MM.

Interactioni

Subunit structurei

Homodimer. 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 (By similarity). Interacts with BRDT. Interacts with MATR3 (By similarity). Interacts with ATNX2; the interaction is RNA-dependent (By similarity). Interacts with UBQLN2 (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi231054. 10 interactions.
IntActiQ921F2. 3 interactions.
MINTiMINT-4136792.
STRINGi10090.ENSMUSP00000081142.

Structurei

Secondary structure

1
414
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi192 – 1976Combined sources
Helixi204 – 2118Combined sources
Turni212 – 2143Combined sources
Beta strandi217 – 2215Combined sources
Beta strandi228 – 2358Combined sources
Helixi237 – 2437Combined sources
Beta strandi247 – 2504Combined sources
Beta strandi253 – 2597Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3D2WX-ray1.65A192-265[»]
ProteinModelPortaliQ921F2.
SMRiQ921F2. Positions 67-269.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ921F2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini104 – 20097RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini191 – 26272RRM 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni216 – 414199Interaction with UBQLN2By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi274 – 413140Gly-richAdd
BLAST

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

eggNOGiNOG145464.
GeneTreeiENSGT00730000110584.
HOGENOMiHOG000254792.
HOVERGENiHBG058671.
InParanoidiQ921F2.
OMAiKHNSSRQ.
OrthoDBiEOG7J70G1.
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]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti8 – 81T → K in BAE32189 (PubMed:16141072).Curated
Sequence conflicti96 – 961V → G in BAE32189 (PubMed:16141072).Curated
Sequence conflicti298 – 2981G → C in BAE21557 (PubMed:16141072).Curated

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_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_663531.1. NM_145556.4.
UniGeneiMm.22453.
Mm.378962.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3D2WX-ray1.65A192-265[»]
ProteinModelPortaliQ921F2.
SMRiQ921F2. Positions 67-269.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi231054. 10 interactions.
IntActiQ921F2. 3 interactions.
MINTiMINT-4136792.
STRINGi10090.ENSMUSP00000081142.

PTM databases

PhosphoSiteiQ921F2.

2D gel databases

REPRODUCTION-2DPAGEQ921F2.

Proteomic databases

MaxQBiQ921F2.
PaxDbiQ921F2.
PRIDEiQ921F2.

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

eggNOGiNOG145464.
GeneTreeiENSGT00730000110584.
HOGENOMiHOG000254792.
HOVERGENiHBG058671.
InParanoidiQ921F2.
OMAiKHNSSRQ.
OrthoDBiEOG7J70G1.
TreeFamiTF315657.

Miscellaneous databases

ChiTaRSiTardbp. mouse.
EvolutionaryTraceiQ921F2.
NextBioi380280.
PROiQ921F2.
SOURCEiSearch...

Gene expression databases

BgeeiQ921F2.
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]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Testis and Thymus.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary gland.
  3. Lubec G., Klug S.
    Submitted (MAR-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 276-293, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Hippocampus.
  4. "The testis-specific double bromodomain-containing protein BRDT forms a complex with multiple spliceosome components and is required for mRNA splicing and 3'-UTR truncation in round spermatids."
    Berkovits B.D., Wang L., Guarnieri P., Wolgemuth D.J.
    Nucleic Acids Res. 40:7162-7175(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH BRDT.
  5. "Structural insights into TDP-43 in nucleic-acid binding and domain interactions."
    Kuo P.H., Doudeva L.G., Wang Y.T., Shen C.K., Yuan H.S.
    Nucleic Acids Res. 37:1799-1808(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 192-265 IN COMPLEX WITH SINGLE-STRANDED DNA, SUBUNIT.

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: June 24, 2015
This is version 119 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

External Data

Dasty 3

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 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.