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O55203

- LDB2_MOUSE

UniProt

O55203 - LDB2_MOUSE

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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

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. transcription cofactor activity Source: InterPro
  4. 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
Complete GO annotation...

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
Complete GO annotation...

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

MaxQBiO55203.
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

        10         20         30         40         50
MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW
60 70 80 90 100
WDAFATEFFE DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL
110 120 130 140 150
YYILKHSKES YHNSSITVDC DQCAMVTQHG KPMFTKVCTE GRLILEFTFD
160 170 180 190 200
DLMRIKTWHF TIRQYRELVP RSILAMHAQD PQVLDQLSKN ITRMGLTNFT
210 220 230 240 250
LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ RMVAPPAEPT
260 270 280 290 300
RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM
310 320 330 340 350
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS
360 370
PWNSKPPATQ ETKSENAPPQ ASQ
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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

MaxQBi O55203.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 99 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