Reviewed,
UniProtKB/Swiss-Prot Q86U70 (LDB1_HUMAN)
Last modified
June 16, 2009.
Version 57.
History...
Clusters with 100%,
90%,
50% identity |
Documents (5) |
Third-party data |
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Names and origin
| Protein names | Recommended name: LIM domain-binding protein 1 Alternative name(s): Nuclear LIM interactor Carboxyl-terminal LIM domain-binding protein 2 Short name=CLIM-2 LIM domain-binding factor CLIM2 Short name=hLdb1 | ||||
| Gene names |
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| Organism | Homo sapiens (Human) | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Protein attributes
| Sequence length | 411 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is not processed. |
| Protein existence | Evidence at transcript level. |
General annotation (Comments)
| Function | Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. May play a role in the development of motor neurons. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state By similarity. |
| Subunit structure | Forms homodimers and heterodimers. Interacts with and activates LHX1/LIM1. Interacts with the LIM domains of ISL1 and LMO2. Can assemble in a complex with LMO2 and TAL1/SCL but doesn't interact with TAL1/SCL directly. Strongly interacts with the LIM2 domain of LMX1A and more weakly with the LIM1 domain. Homodimerization is not required for, and does not effect, LMX1A-binding. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with LHX9 By similarity. |
| Subcellular location | Nucleus Probable. |
| Tissue specificity | Expressed in a wide range of adult tissues including brain, heart, skeletal muscle, colon, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes. Ref.5 |
| Domain | The dimerization domain is located in the N-terminus By similarity. |
| Sequence similarities | Belongs to the LDB family. |
Ontologies
| Keywords | |
|---|---|
| Cellular component | Nucleus |
| Coding sequence diversity | Alternative splicing Polymorphism |
| Molecular function | Developmental protein |
| Gene Ontology (GO) | |
| Biological process | negative regulation of erythrocyte differentiation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of transcription, DNA-dependentInferred from direct assay. Source: UniProtKB |
| Cellular component | nucleus Inferred from sequence or structural similarity. Source: UniProtKB protein complexInferred from sequence or structural similarity. Source: UniProtKB |
| Molecular function | LIM domain binding Inferred from physical interaction. Source: UniProtKB protein homodimerization activityInferred from sequence or structural similarity. Source: UniProtKB transcription corepressor activityTraceable author statement. Source: ProtInc |
| Complete GO annotation... | |
Alternative products
| This entry describes 3 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q86U70-1) 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. | ||||||
| Note: No experimental confirmation available. | ||||||
| Isoform 2 (identifier: Q86U70-3) Also known as: b; The sequence of this isoform differs from the canonical sequence as follows: 1-36: Missing. 336-352: DVMVVGEPTLMGGEFGD → VSISAFFSLLGCPTTHP 353-411: Missing. | ||||||
| Note: Due to intron retention. Lacks LIM-binding domain. | ||||||
| Isoform 3 (identifier: Q86U70-2) Also known as: a; The sequence of this isoform differs from the canonical sequence as follows: 1-36: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 411 | 411 | LIM domain-binding protein 1 | PRO_0000084384 | |||||
Regions | |||||||||
| Region | 336 – 374 | 39 | LIM-binding domain (LID) By similarity | ||||||
Natural variations | |||||||||
| Alternative sequence | 1 – 36 | 36 | Missing in isoform 2 and isoform 3. | VSP_027830 | |||||
| Alternative sequence | 336 – 352 | 17 | DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2. | VSP_027831 | |||||
| Alternative sequence | 353 – 411 | 59 | Missing in isoform 2. | VSP_027832 | |||||
| Natural variant | 299 | 1 | R → Q in a colorectal cancer sample; somatic mutation. Ref.10 | VAR_036366 | |||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Cloning and chromosomal localization of two novel human genes encoding LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI." Semina E.V., Altherr M.R., Murray J.C. Mamm. Genome 9:921-924(1998) [PubMed: 9799849] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Craniofacial. |
| [2] | "Genomic structure, alternative transcripts and chromosome location of the human LIM domain binding protein gene LDB1." Drechsler M., Schumacher V., Friedrich S., Wildhardt G., Giesler S., Schroth A., Bodem J., Royer-Pokora B. Cytogenet. Cell Genet. 87:119-124(1999) [PubMed: 10640831] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
| [3] | "Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2." Ueki N., Seki N., Yano K., Ohira M., Saito T., Masuho Y., Muramatsu M. J. Hum. Genet. 44:112-115(1999) [PubMed: 10083735] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Brain. |
| [4] | "Cloning, characterization, and physical mapping of the human homologs of the mouse C-LIM gene." Phillips J.C., Goldman D.A., Wiggs J.L. Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Fetal brain. |
| [5] | "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: 16815859] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), ALTERNATIVE SPLICING, TISSUE SPECIFICITY. Tissue: Fetal brain. |
| [6] | "Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3). |
| [7] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). |
| [8] | "The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. Rogers J.Nature 429:375-381(2004) [PubMed: 15164054] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [9] | "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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3). Tissue: Muscle. |
| [10] | "The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E.Science 314:268-274(2006) [PubMed: 16959974] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] GLN-299. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |
|---|---|
| AF068652 mRNA. Translation: AAC77818.1. AJ243098 Genomic DNA. Translation: CAB45409.1. Different initiation. AB016485 mRNA. Translation: BAA31991.1. AF064491 mRNA. Translation: AAC28341.1. AB250384 mRNA. Translation: BAE95402.1. BT007054 mRNA. Translation: AAP35703.1. AK300588 mRNA. Translation: BAG62286.1. AL500527 Genomic DNA. Translation: CAH72217.1. Different initiation. BC000482 mRNA. Translation: AAH00482.1. BC009246 mRNA. Translation: AAH09246.1. | |
| IPI | IPI00428954. IPI00760574. IPI00856078. |
| RefSeq | NP_001106878.1. NP_003884.1. |
| UniGene | Hs.709666 |
3D structure databases | |
| HSSP | HSSP built from PDB template 1J2O based on UniProtKB P25801. |
| ModBase | Search... |
Protein-protein interaction databases | |
| IntAct | Q86U70. 6 interactions. |
Genome annotation databases | |
| Ensembl | ENSG00000198728. Homo sapiens. [Contig view] |
| GeneID | 8861. |
| KEGG | hsa:8861. |
Organism-specific databases | |
| GeneCards | GC10M103857. |
| HGNC | HGNC:6532. LDB1. |
| MIM | 603451. gene. |
| PharmGKB | PA30316. |
| GenAtlas | Search... |
Phylogenomic databases | |
| HOGENOM | Q86U70. |
| HOVERGEN | Q86U70. |
| OMA | Q86U70. XPALGAN. |
Gene expression databases | |
| ArrayExpress | Q86U70. |
| Bgee | Q86U70. |
| CleanEx | HS_LDB1. |
| GermOnline | ENSG00000198728. Homo sapiens. |
Family and domain databases | |
| InterPro | IPR002691. LIM_bd. [Graphical view] |
| Pfam | PF01803. LIM_bind. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other Resources | |
| NextBio | 33273. |
| SOURCE | Search... |
Entry information
| Entry name | LDB1_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q86U70 Secondary accession number(s): B4DUC4 Q9UGM4 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HPI (Human Proteome Initiative) | ||||||||
Relevant documents
| Human chromosome 10 Human chromosome 10: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with


