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Q921F2

- TADBP_MOUSE

UniProt

Q921F2 - TADBP_MOUSE

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
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    • History
      Entry version 112 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    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. protein binding Source: UniProtKB
    5. 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

    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

    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

    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.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 – 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.
    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.
    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

    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:
    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

    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: October 1, 2014
    This is version 112 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