Reviewed, UniProtKB/Swiss-Prot Q86U70 (LDB1_HUMAN)

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

Name:	LDB1
Synonyms:	CLIM2

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-dependent Inferred from direct assay. Source: UniProtKB
Cellular component	nucleus Inferred from sequence or structural similarity. Source: UniProtKB protein complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular function	LIM domain binding Inferred from physical interaction. Source: UniProtKB protein homodimerization activity Inferred from sequence or structural similarity. Source: UniProtKB transcription corepressor activity Traceable 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

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified September 11, 2007. Version 2. Checksum: 5BB5348A36044580	FASTA	411	46,533
	10 20 30 40 50 60 MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP TYLEPGIGRH 70 80 90 100 110 120 TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED DAMLTITFCL EDGPKRYTIG 130 140 150 160 170 180 RTLIPRYFRS IFEGGATELY YVLKHPKEAF HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG 190 200 210 220 230 240 RLYLEFMFDD MMRIKTWHFS IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL 250 260 270 280 290 300 NYLRLCVILE PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPTR QQPSKRRKRK 310 320 330 340 350 360 MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF GDEDERLITR 370 380 390 400 410 LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES KSENPTSQAS Q
	Isoform 2 (b). Checksum: B086EB4D28FC8E56	FASTA	316	36,428
	10 20 30 40 50 60 MLDRDVGPTP MYPPTYLEPG IGRHTPYGNQ TDYRIFELNK RLQNWTEECD NLWWDAFTTE 70 80 90 100 110 120 FFEDDAMLTI TFCLEDGPKR YTIGRTLIPR YFRSIFEGGA TELYYVLKHP KEAFHSNFVS 130 140 150 160 170 180 LDCDQGSMVT QHGKPMFTQV CVEGRLYLEF MFDDMMRIKT WHFSIRQHRE LIPRSILAMH 190 200 210 220 230 240 AQDPQMLDQL SKNITRCGLS NSTLNYLRLC VILEPMQELM SRHKTYSLSP RDCLKTCLFQ 250 260 270 280 290 300 KWQRMVAPPA EPTRQQPSKR RKRKMSGGST MSSGGGNTNN SNSKKKSPAS TFALSSQVPV 310 SISAFFSLLG CPTTHP
	Isoform 3 (a). Checksum: 698AC67CB5BD2DE7	FASTA	375	42,809
	10 20 30 40 50 60 MLDRDVGPTP MYPPTYLEPG IGRHTPYGNQ TDYRIFELNK RLQNWTEECD NLWWDAFTTE 70 80 90 100 110 120 FFEDDAMLTI TFCLEDGPKR YTIGRTLIPR YFRSIFEGGA TELYYVLKHP KEAFHSNFVS 130 140 150 160 170 180 LDCDQGSMVT QHGKPMFTQV CVEGRLYLEF MFDDMMRIKT WHFSIRQHRE LIPRSILAMH 190 200 210 220 230 240 AQDPQMLDQL SKNITRCGLS NSTLNYLRLC VILEPMQELM SRHKTYSLSP RDCLKTCLFQ 250 260 270 280 290 300 KWQRMVAPPA EPTRQQPSKR RKRKMSGGST MSSGGGNTNN SNSKKKSPAS TFALSSQVPD 310 320 330 340 350 360 VMVVGEPTLM GGEFGDEDER LITRLENTQF DAANGIDDED SFNNSPALGA NSPWNSKPPS 370 SQESKSENPT SQASQ

References

	« Hide 'large scale' referencesShow '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. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., 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. , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., 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. , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. Science 314:268-274(2006) [PubMed: 16959974] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] GLN-299.
+	Additional computationally mapped references.

Web resources

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Cross-references

Sequence databases
EMBLGenBankDDBJ	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 , O75479, O96010, Q1EQX1, Q9UGM4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2005
Last sequence update:	September 11, 2007
Last modified:	June 16, 2009
This is version 57 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)