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O55203 (LDB2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Ldb2
Synonyms:Clim1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subunit structure

Interacts with LHX9. Ref.4 Ref.5

Subcellular location

Nucleus Probable.

Post-translational modification

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome. Ref.5

Sequence similarities

Belongs to the LDB family.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O55203-1)

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.
Isoform 2 (identifier: O55203-2)

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.
Isoform 3 (identifier: O55203-3)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 373373LIM domain-binding protein 2
PRO_0000084388

Regions

Region298 – 33639LIM-binding domain (LID) By similarity

Natural variations

Alternative sequence296 – 2972Missing in isoform 3.
VSP_027829
Alternative sequence298 – 33134DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2 and isoform 3.
VSP_014369
Alternative sequence332 – 37342Missing in isoform 2 and isoform 3.
VSP_014370

Experimental info

Sequence conflict2721A → G in AAB96884. Ref.1
Sequence conflict2721A → G in AAB96886. Ref.1
Sequence conflict2791A → S in AAB96884. Ref.1
Sequence conflict2791A → S in AAB96886. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (CLIM-1a) [UniParc].

Last modified September 11, 2007. Version 2.
Checksum: 0748DBAEB5586AB4

FASTA37342,691
        10         20         30         40         50         60 
MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE 

        70         80         90        100        110        120 
DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC 

       130        140        150        160        170        180 
DQCAMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD 

       190        200        210        220        230        240 
PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ 

       250        260        270        280        290        300 
RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM 

       310        320        330        340        350        360 
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ 

       370 
ETKSENAPPQ ASQ 

« Hide

Isoform 2 (CLIM-1b) [UniParc].

Checksum: A4A4131EEF631544
Show »

FASTA33137,929
Isoform 3 [UniParc].

Checksum: 2F09D73318CEA63A
Show »

FASTA32937,733

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001070866.1. NM_001077398.2.
NP_001273277.1. NM_001286348.1.
NP_034828.3. NM_010698.4.
XP_006503817.1. XM_006503754.1.
XP_006503819.1. XM_006503756.1.
UniGeneMm.25785.

3D structure databases

ProteinModelPortalO55203.
SMRO55203. Positions 298-325.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid201126. 17 interactions.
DIPDIP-46444N.

PTM databases

PhosphoSiteO55203.

Proteomic databases

PaxDbO55203.
PRIDEO55203.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706. [O55203-1]
GeneID16826.
KEGGmmu:16826.
UCSCuc008xis.1. mouse. [O55203-3]
uc008xit.1. mouse. [O55203-1]
uc008xiu.1. mouse. [O55203-2]

Organism-specific databases

CTD9079.
MGIMGI:894670. Ldb2.

Phylogenomic databases

eggNOGNOG282114.
GeneTreeENSGT00390000005639.
HOGENOMHOG000030908.
HOVERGENHBG000135.
InParanoidO55203.
OMANSSPWNS.
OrthoDBEOG7DC24T.
PhylomeDBO55203.
TreeFamTF319923.

Gene expression databases

BgeeO55203.
CleanExMM_LDB2.
GenevestigatorO55203.

Family and domain databases

InterProIPR002691. LIM-dom-bd.
[Graphical view]
PANTHERPTHR10378. PTHR10378. 1 hit.
ProtoNetSearch...

Other

ChiTaRSLDB2. mouse.
NextBio290728.
PROO55203.
SOURCESearch...

Entry information

Entry nameLDB2_MOUSE
AccessionPrimary (citable) accession number: O55203
Secondary accession number(s): O55205, Q3UHY1, Q6AXE6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: September 11, 2007
Last modified: April 16, 2014
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot