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O55203

- LDB2_MOUSE

UniProt

O55203 - LDB2_MOUSE

Protein

LIM domain-binding protein 2

Gene

Ldb2

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 2 (11 Sep 2007)
      Previous versions | rss
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    Functioni

    Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors.

    GO - Molecular functioni

    1. enzyme binding Source: UniProtKB
    2. LIM domain binding Source: UniProtKB
    3. protein binding Source: MGI
    4. transcription cofactor activity Source: InterPro
    5. transcription factor binding transcription factor activity Source: MGI

    GO - Biological processi

    1. epithelial structure maintenance Source: MGI
    2. hair follicle development Source: MGI
    3. positive regulation of cellular component biogenesis Source: MGI
    4. positive regulation of transcription from RNA polymerase II promoter Source: MGI
    5. somatic stem cell maintenance Source: MGI

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    LIM domain-binding protein 2
    Short name:
    LDB-2
    Alternative name(s):
    Carboxyl-terminal LIM domain-binding protein 1
    Short name:
    CLIM-1
    LIM domain-binding factor CLIM1
    Gene namesi
    Name:Ldb2
    Synonyms:Clim1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 5

    Organism-specific databases

    MGIiMGI:894670. Ldb2.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. nucleus Source: UniProtKB
    2. transcription factor complex Source: MGI

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 373373LIM domain-binding protein 2PRO_0000084388Add
    BLAST

    Post-translational modificationi

    Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.1 Publication

    Keywords - PTMi

    Ubl conjugation

    Proteomic databases

    PaxDbiO55203.
    PRIDEiO55203.

    PTM databases

    PhosphoSiteiO55203.

    Expressioni

    Gene expression databases

    BgeeiO55203.
    CleanExiMM_LDB2.
    GenevestigatoriO55203.

    Interactioni

    Subunit structurei

    Interacts with LHX9.2 Publications

    Protein-protein interaction databases

    BioGridi201126. 17 interactions.
    DIPiDIP-46444N.

    Structurei

    3D structure databases

    ProteinModelPortaliO55203.
    SMRiO55203. Positions 298-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni298 – 33639LIM-binding domain (LID)By similarityAdd
    BLAST

    Sequence similaritiesi

    Belongs to the LDB family.Curated

    Phylogenomic databases

    eggNOGiNOG282114.
    GeneTreeiENSGT00390000005639.
    HOGENOMiHOG000030908.
    HOVERGENiHBG000135.
    InParanoidiO55203.
    OMAiNSSPWNS.
    OrthoDBiEOG7DC24T.
    PhylomeDBiO55203.
    TreeFamiTF319923.

    Family and domain databases

    InterProiIPR029005. LIM-bd/SEUSS.
    IPR002691. LIM-dom-bd.
    [Graphical view]
    PANTHERiPTHR10378. PTHR10378. 1 hit.
    PfamiPF01803. LIM_bind. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O55203-1) [UniParc]FASTAAdd to Basket

    Also known as: CLIM-1a

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW    50
    WDAFATEFFE DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL 100
    YYILKHSKES YHNSSITVDC DQCAMVTQHG KPMFTKVCTE GRLILEFTFD 150
    DLMRIKTWHF TIRQYRELVP RSILAMHAQD PQVLDQLSKN ITRMGLTNFT 200
    LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ RMVAPPAEPT 250
    RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM 300
    VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS 350
    PWNSKPPATQ ETKSENAPPQ ASQ 373
    Length:373
    Mass (Da):42,691
    Last modified:September 11, 2007 - v2
    Checksum:i0748DBAEB5586AB4
    GO
    Isoform 2 (identifier: O55203-2) [UniParc]FASTAAdd to Basket

    Also known as: CLIM-1b

    The sequence of this isoform differs from the canonical sequence as follows:
         298-331: DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA → GLGAIPNCSLNPGRDGDLCHSTAVTPSGQFKEKH
         332-373: Missing.

    Note: Lacks LIM-binding domain.

    Show »
    Length:331
    Mass (Da):37,929
    Checksum:iA4A4131EEF631544
    GO
    Isoform 3 (identifier: O55203-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         296-297: Missing.
         298-331: DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA → GLGAIPNCSLNPGRDGDLCHSTAVTPSGQFKEKH
         332-373: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:329
    Mass (Da):37,733
    Checksum:i2F09D73318CEA63A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti272 – 2721A → G in AAB96884. (PubMed:9192866)Curated
    Sequence conflicti272 – 2721A → G in AAB96886. (PubMed:9192866)Curated
    Sequence conflicti279 – 2791A → S in AAB96884. (PubMed:9192866)Curated
    Sequence conflicti279 – 2791A → S in AAB96886. (PubMed:9192866)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei296 – 2972Missing in isoform 3. 1 PublicationVSP_027829
    Alternative sequencei298 – 33134DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2 and isoform 3. 2 PublicationsVSP_014369Add
    BLAST
    Alternative sequencei332 – 37342Missing in isoform 2 and isoform 3. 2 PublicationsVSP_014370Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U89487 mRNA. Translation: AAB96884.1.
    U89489 mRNA. Translation: AAB96886.1.
    AK147160 mRNA. Translation: BAE27725.1.
    AK146860 mRNA. Translation: BAE27488.1.
    BC079611 mRNA. Translation: AAH79611.1.
    CCDSiCCDS19271.1. [O55203-1]
    RefSeqiNP_001070866.1. NM_001077398.2. [O55203-3]
    NP_001273277.1. NM_001286348.1. [O55203-2]
    NP_034828.3. NM_010698.4. [O55203-1]
    XP_006503817.1. XM_006503754.1. [O55203-2]
    XP_006503819.1. XM_006503756.1. [O55203-3]
    UniGeneiMm.25785.

    Genome annotation databases

    EnsembliENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706. [O55203-1]
    GeneIDi16826.
    KEGGimmu:16826.
    UCSCiuc008xis.1. mouse. [O55203-3]
    uc008xit.1. mouse. [O55203-1]
    uc008xiu.1. mouse. [O55203-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U89487 mRNA. Translation: AAB96884.1 .
    U89489 mRNA. Translation: AAB96886.1 .
    AK147160 mRNA. Translation: BAE27725.1 .
    AK146860 mRNA. Translation: BAE27488.1 .
    BC079611 mRNA. Translation: AAH79611.1 .
    CCDSi CCDS19271.1. [O55203-1 ]
    RefSeqi NP_001070866.1. NM_001077398.2. [O55203-3 ]
    NP_001273277.1. NM_001286348.1. [O55203-2 ]
    NP_034828.3. NM_010698.4. [O55203-1 ]
    XP_006503817.1. XM_006503754.1. [O55203-2 ]
    XP_006503819.1. XM_006503756.1. [O55203-3 ]
    UniGenei Mm.25785.

    3D structure databases

    ProteinModelPortali O55203.
    SMRi O55203. Positions 298-325.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 201126. 17 interactions.
    DIPi DIP-46444N.

    PTM databases

    PhosphoSitei O55203.

    Proteomic databases

    PaxDbi O55203.
    PRIDEi O55203.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000070748 ; ENSMUSP00000067737 ; ENSMUSG00000039706 . [O55203-1 ]
    GeneIDi 16826.
    KEGGi mmu:16826.
    UCSCi uc008xis.1. mouse. [O55203-3 ]
    uc008xit.1. mouse. [O55203-1 ]
    uc008xiu.1. mouse. [O55203-2 ]

    Organism-specific databases

    CTDi 9079.
    MGIi MGI:894670. Ldb2.

    Phylogenomic databases

    eggNOGi NOG282114.
    GeneTreei ENSGT00390000005639.
    HOGENOMi HOG000030908.
    HOVERGENi HBG000135.
    InParanoidi O55203.
    OMAi NSSPWNS.
    OrthoDBi EOG7DC24T.
    PhylomeDBi O55203.
    TreeFami TF319923.

    Miscellaneous databases

    ChiTaRSi LDB2. mouse.
    NextBioi 290728.
    PROi O55203.
    SOURCEi Search...

    Gene expression databases

    Bgeei O55203.
    CleanExi MM_LDB2.
    Genevestigatori O55203.

    Family and domain databases

    InterProi IPR029005. LIM-bd/SEUSS.
    IPR002691. LIM-dom-bd.
    [Graphical view ]
    PANTHERi PTHR10378. PTHR10378. 1 hit.
    Pfami PF01803. LIM_bind. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins."
      Bach I., Carriere C., Ostendorff H.P., Andersen B., Rosenfeld M.G.
      Genes Dev. 11:1370-1380(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    2. "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] (ISOFORM 3).
      Strain: C57BL/6J.
      Tissue: Embryonic kidney.
    3. "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] (ISOFORM 1).
      Strain: C57BL/6.
      Tissue: Brain.
    4. "Characterization of Lhx9, a novel LIM/homeobox gene expressed by the pioneer neurons in the mouse cerebral cortex."
      Bertuzzi S., Porter F.D., Pitts A., Kumar M., Agulnick A., Wassif C., Westphal H.
      Mech. Dev. 81:193-198(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH LHX9.
    5. "Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors."
      Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M., Scheffner M., Bach I.
      Nature 416:99-103(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RLIM, UBIQUITINATION.
    6. "Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the LIM-interaction domain."
      Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J., Hirose S.
      J. Biochem. 140:105-119(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: ALTERNATIVE SPLICING.

    Entry informationi

    Entry nameiLDB2_MOUSE
    AccessioniPrimary (citable) accession number: O55203
    Secondary accession number(s): O55205, Q3UHY1, Q6AXE6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2005
    Last sequence update: September 11, 2007
    Last modified: October 1, 2014
    This is version 97 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3