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Q921F2

- TADBP_MOUSE

UniProt

Q921F2 - TADBP_MOUSE

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Protein

TAR DNA-binding protein 43

Gene

Tardbp

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).By similarity

GO - Molecular functioni

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

GO - Biological processi

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

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

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 .
CCDSi CCDS38971.1.
RefSeqi NP_663531.1. NM_145556.4.
UniGenei Mm.22453.
Mm.378962.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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 Q921F2.
OMAi KHNSSRQ.
OrthoDBi EOG7J70G1.
TreeFami TF315657.

Miscellaneous databases

ChiTaRSi Tardbp. mouse.
EvolutionaryTracei Q921F2.
NextBioi 380280.
PROi Q921F2.
SOURCEi Search...

Gene expression databases

Bgeei Q921F2.
CleanExi MM_TARDBP.
ExpressionAtlasi Q921F2. baseline and differential.
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: November 26, 2014
This is version 114 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