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Q921F2

- TADBP_MOUSE

UniProt

Q921F2 - TADBP_MOUSE

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Protein
TAR DNA-binding protein 43
Gene
Tardbp, Tdp43
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 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.

GO - Molecular functioni

  1. RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription Source: MGI
  2. double-stranded DNA binding Source: Ensembl
  3. mRNA 3'-UTR binding Source: Ensembl
  4. nucleotide binding Source: InterPro
  5. protein binding Source: UniProtKB

GO - Biological processi

  1. 3'-UTR-mediated mRNA stabilization Source: Ensembl
  2. RNA splicing Source: UniProtKB-KW
  3. mRNA processing Source: UniProtKB-KW
  4. negative regulation by host of viral transcription Source: Ensembl
  5. positive regulation of transcription from RNA polymerase II promoter Source: GOC
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: Chromosome 4

Organism-specific databases

MGIiMGI:2387629. Tardbp.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

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

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei292 – 2921Phosphoserine By 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

ArrayExpressiQ921F2.
BgeeiQ921F2.
CleanExiMM_TARDBP.
GenevestigatoriQ921F2.

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. Interacts with BRDT. Interacts with MATR3 By similarity.2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3D2WX-ray1.65A192-265[»]
ProteinModelPortaliQ921F2.
SMRiQ921F2. Positions 67-269.

Miscellaneous databases

EvolutionaryTraceiQ921F2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini104 – 20097RRM 1
Add
BLAST
Domaini191 – 26272RRM 2
Add
BLAST

Compositional bias

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

Domaini

The RRM domains can bind to both DNA and RNA.

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiNOG145464.
GeneTreeiENSGT00730000110584.
HOGENOMiHOG000254792.
HOVERGENiHBG058671.
InParanoidiQ3V0E7.
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

MSEYIRVTED ENDEPIEIPS EDDGTVLLST VTAQFPGACG LRYRNPVSQC    50
MRGVRLVEGI LHAPDAGWGN LVYVVNYPKD NKRKMDETDA SSAVKVKRAV 100
QKTSDLIVLG LPWKTTEQDL KDYFSTFGEV LMVQVKKDLK TGHSKGFGFV 150
RFTEYETQVK VMSQRHMIDG RWCDCKLPNS KQSPDEPLRS RKVFVGRCTE 200
DMTAEELQQF FCQYGEVVDV FIPKPFRAFA FVTFADDKVA QSLCGEDLII 250
KGISVHISNA EPKHNSNRQL ERSGRFGGNP GGFGNQGGFG NSRGGGAGLG 300
NNQGGNMGGG MNFGAFSINP AMMAAAQAAL QSSWGMMGML ASQQNQSGPS 350
GNNQSQGSMQ REPNQAFGSG NNSYSGSNSG APLGWGSASN AGSGSGFNGG 400
FGSSMDSKSS GWGM 414
Length:414
Mass (Da):44,548
Last modified:December 1, 2001 - v1
Checksum:i2BE6A695EC2CA106
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti8 – 81T → K in BAE32189. 1 Publication
Sequence conflicti96 – 961V → G in BAE32189. 1 Publication
Sequence conflicti298 – 2981G → C in BAE21557. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS38971.1.
RefSeqi NP_663531.1. NM_145556.4.
UniGenei Mm.22453.
Mm.378962.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3D2W X-ray 1.65 A 192-265 [» ]
ProteinModelPortali Q921F2.
SMRi Q921F2. Positions 67-269.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 231054. 10 interactions.
IntActi Q921F2. 3 interactions.
MINTi MINT-4136792.
STRINGi 10090.ENSMUSP00000081142.

PTM databases

PhosphoSitei Q921F2.

2D gel databases

REPRODUCTION-2DPAGE Q921F2.

Proteomic databases

MaxQBi Q921F2.
PaxDbi Q921F2.
PRIDEi Q921F2.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000084125 ; ENSMUSP00000081142 ; ENSMUSG00000041459 .
GeneIDi 230908.
KEGGi mmu:230908.
UCSCi uc008vvg.1. mouse.

Organism-specific databases

CTDi 23435.
MGIi MGI:2387629. Tardbp.

Phylogenomic databases

eggNOGi NOG145464.
GeneTreei ENSGT00730000110584.
HOGENOMi HOG000254792.
HOVERGENi HBG058671.
InParanoidi Q3V0E7.
OMAi KHNSSRQ.
OrthoDBi EOG7J70G1.
TreeFami TF315657.

Miscellaneous databases

EvolutionaryTracei Q921F2.
NextBioi 380280.
PROi Q921F2.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q921F2.
Bgeei Q921F2.
CleanExi MM_TARDBP.
Genevestigatori Q921F2.

Family and domain databases

Gene3Di 3.30.70.330. 2 hits.
InterProi IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view ]
Pfami PF00076. RRM_1. 2 hits.
[Graphical view ]
SMARTi SM00360. RRM. 2 hits.
[Graphical view ]
PROSITEi PS50102. RRM. 2 hits.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 111 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