Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8861
Gene name Gene Name - the full gene name approved by the HGNC.	LIM domain binding 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	LDB1
Synonyms (NCBI Gene) Gene synonyms aliases	CLIM-2, CLIM2, LDB-1, NLI
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10q24.32

Show/Hide all(201)

miRTarBase ID	miRNA	Experiments	Reference
MIRT456709	hsa-miR-3123	PAR-CLIP	23592263
MIRT456708	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT456707	hsa-miR-3919	PAR-CLIP	23592263
MIRT456706	hsa-miR-214-3p	PAR-CLIP	23592263
MIRT456705	hsa-miR-3619-5p	PAR-CLIP	23592263
MIRT456704	hsa-miR-761	PAR-CLIP	23592263
MIRT456703	hsa-miR-6773-3p	PAR-CLIP	23592263
MIRT456702	hsa-miR-215-3p	PAR-CLIP	23592263
MIRT456701	hsa-miR-1909-3p	PAR-CLIP	23592263
MIRT456700	hsa-miR-6722-3p	PAR-CLIP	23592263
MIRT456699	hsa-miR-3144-5p	PAR-CLIP	23592263
MIRT456698	hsa-miR-3191-3p	PAR-CLIP	23592263
MIRT456697	hsa-miR-4652-5p	PAR-CLIP	23592263
MIRT456696	hsa-miR-6753-3p	PAR-CLIP	23592263
MIRT456695	hsa-miR-7107-3p	PAR-CLIP	23592263
MIRT456694	hsa-miR-198	PAR-CLIP	23592263
MIRT456693	hsa-miR-6810-5p	PAR-CLIP	23592263
MIRT456692	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT456691	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT456690	hsa-miR-6873-5p	PAR-CLIP	23592263
MIRT456689	hsa-miR-9500	PAR-CLIP	23592263
MIRT456688	hsa-miR-1296-3p	PAR-CLIP	23592263
MIRT456687	hsa-miR-4481	PAR-CLIP	23592263
MIRT456686	hsa-miR-4745-5p	PAR-CLIP	23592263
MIRT456684	hsa-miR-6077	PAR-CLIP	23592263
MIRT456685	hsa-miR-3175	PAR-CLIP	23592263
MIRT456683	hsa-miR-1343-5p	PAR-CLIP	23592263
MIRT456682	hsa-miR-939-5p	PAR-CLIP	23592263
MIRT456681	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT456680	hsa-miR-491-5p	PAR-CLIP	23592263
MIRT456679	hsa-miR-520a-5p	PAR-CLIP	23592263
MIRT456678	hsa-miR-525-5p	PAR-CLIP	23592263
MIRT456677	hsa-miR-3150a-3p	PAR-CLIP	23592263
MIRT456676	hsa-miR-6763-5p	PAR-CLIP	23592263
MIRT456694	hsa-miR-198	PAR-CLIP	26701625
MIRT456694	hsa-miR-198	PAR-CLIP	26701625
MIRT456694	hsa-miR-198	PAR-CLIP	26701625
MIRT456709	hsa-miR-3123	PAR-CLIP	26701625
MIRT456709	hsa-miR-3123	PAR-CLIP	26701625
MIRT456709	hsa-miR-3123	PAR-CLIP	26701625
MIRT456699	hsa-miR-3144-5p	PAR-CLIP	26701625
MIRT456699	hsa-miR-3144-5p	PAR-CLIP	26701625
MIRT456699	hsa-miR-3144-5p	PAR-CLIP	26701625
MIRT456698	hsa-miR-3191-3p	PAR-CLIP	26701625
MIRT456698	hsa-miR-3191-3p	PAR-CLIP	26701625
MIRT456698	hsa-miR-3191-3p	PAR-CLIP	26701625
MIRT456707	hsa-miR-3919	PAR-CLIP	26701625
MIRT456707	hsa-miR-3919	PAR-CLIP	26701625
MIRT456707	hsa-miR-3919	PAR-CLIP	26701625
MIRT456697	hsa-miR-4652-5p	PAR-CLIP	26701625
MIRT456697	hsa-miR-4652-5p	PAR-CLIP	26701625
MIRT456697	hsa-miR-4652-5p	PAR-CLIP	26701625
MIRT456679	hsa-miR-520a-5p	PAR-CLIP	26701625
MIRT456679	hsa-miR-520a-5p	PAR-CLIP	26701625
MIRT456679	hsa-miR-520a-5p	PAR-CLIP	26701625
MIRT456678	hsa-miR-525-5p	PAR-CLIP	26701625
MIRT456678	hsa-miR-525-5p	PAR-CLIP	26701625
MIRT456678	hsa-miR-525-5p	PAR-CLIP	26701625
MIRT456693	hsa-miR-6810-5p	PAR-CLIP	26701625
MIRT456693	hsa-miR-6810-5p	PAR-CLIP	26701625
MIRT456693	hsa-miR-6810-5p	PAR-CLIP	26701625
MIRT456709	hsa-miR-3123	PAR-CLIP	23592263
MIRT456708	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT456707	hsa-miR-3919	PAR-CLIP	23592263
MIRT456706	hsa-miR-214-3p	PAR-CLIP	23592263
MIRT456705	hsa-miR-3619-5p	PAR-CLIP	23592263
MIRT456704	hsa-miR-761	PAR-CLIP	23592263
MIRT456703	hsa-miR-6773-3p	PAR-CLIP	23592263
MIRT456702	hsa-miR-215-3p	PAR-CLIP	23592263
MIRT456701	hsa-miR-1909-3p	PAR-CLIP	23592263
MIRT456700	hsa-miR-6722-3p	PAR-CLIP	23592263
MIRT456699	hsa-miR-3144-5p	PAR-CLIP	23592263
MIRT456698	hsa-miR-3191-3p	PAR-CLIP	23592263
MIRT456697	hsa-miR-4652-5p	PAR-CLIP	23592263
MIRT456696	hsa-miR-6753-3p	PAR-CLIP	23592263
MIRT456695	hsa-miR-7107-3p	PAR-CLIP	23592263
MIRT456694	hsa-miR-198	PAR-CLIP	23592263
MIRT456693	hsa-miR-6810-5p	PAR-CLIP	23592263
MIRT456692	hsa-miR-6758-5p	PAR-CLIP	23592263
MIRT456691	hsa-miR-6856-5p	PAR-CLIP	23592263
MIRT456690	hsa-miR-6873-5p	PAR-CLIP	23592263
MIRT456689	hsa-miR-9500	PAR-CLIP	23592263
MIRT456688	hsa-miR-1296-3p	PAR-CLIP	23592263
MIRT456687	hsa-miR-4481	PAR-CLIP	23592263
MIRT456686	hsa-miR-4745-5p	PAR-CLIP	23592263
MIRT456684	hsa-miR-6077	PAR-CLIP	23592263
MIRT456685	hsa-miR-3175	PAR-CLIP	23592263
MIRT456683	hsa-miR-1343-5p	PAR-CLIP	23592263
MIRT456682	hsa-miR-939-5p	PAR-CLIP	23592263
MIRT456681	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT456680	hsa-miR-491-5p	PAR-CLIP	23592263
MIRT456679	hsa-miR-520a-5p	PAR-CLIP	23592263
MIRT456678	hsa-miR-525-5p	PAR-CLIP	23592263
MIRT456677	hsa-miR-3150a-3p	PAR-CLIP	23592263
MIRT456676	hsa-miR-6763-5p	PAR-CLIP	23592263
MIRT1106191	hsa-miR-105	CLIP-seq
MIRT1106192	hsa-miR-1293	CLIP-seq
MIRT1106193	hsa-miR-1294	CLIP-seq
MIRT1106194	hsa-miR-1911	CLIP-seq
MIRT1106195	hsa-miR-2682	CLIP-seq
MIRT1106196	hsa-miR-3151	CLIP-seq
MIRT1106197	hsa-miR-3153	CLIP-seq
MIRT1106198	hsa-miR-3184	CLIP-seq
MIRT1106199	hsa-miR-342-5p	CLIP-seq
MIRT1106200	hsa-miR-3612	CLIP-seq
MIRT1106201	hsa-miR-3691-3p	CLIP-seq
MIRT1106202	hsa-miR-3936	CLIP-seq
MIRT1106203	hsa-miR-423-5p	CLIP-seq
MIRT1106204	hsa-miR-4257	CLIP-seq
MIRT1106205	hsa-miR-4316	CLIP-seq
MIRT1106206	hsa-miR-4330	CLIP-seq
MIRT1106207	hsa-miR-4426	CLIP-seq
MIRT1106208	hsa-miR-4436a	CLIP-seq
MIRT1106209	hsa-miR-4443	CLIP-seq
MIRT1106210	hsa-miR-4483	CLIP-seq
MIRT1106211	hsa-miR-449c	CLIP-seq
MIRT1106212	hsa-miR-4525	CLIP-seq
MIRT1106213	hsa-miR-4534	CLIP-seq
MIRT1106214	hsa-miR-4640-3p	CLIP-seq
MIRT1106215	hsa-miR-4647	CLIP-seq
MIRT1106216	hsa-miR-4651	CLIP-seq
MIRT1106217	hsa-miR-4662b	CLIP-seq
MIRT1106218	hsa-miR-4664-5p	CLIP-seq
MIRT1106219	hsa-miR-4667-5p	CLIP-seq
MIRT1106220	hsa-miR-4675	CLIP-seq
MIRT1106221	hsa-miR-4677-3p	CLIP-seq
MIRT1106222	hsa-miR-4699-5p	CLIP-seq
MIRT1106223	hsa-miR-4700-5p	CLIP-seq
MIRT1106224	hsa-miR-4701-5p	CLIP-seq
MIRT1106225	hsa-miR-4716-3p	CLIP-seq
MIRT1106226	hsa-miR-4726-3p	CLIP-seq
MIRT1106227	hsa-miR-4736	CLIP-seq
MIRT1106228	hsa-miR-4741	CLIP-seq
MIRT1106229	hsa-miR-4802-5p	CLIP-seq
MIRT1106230	hsa-miR-486-3p	CLIP-seq
MIRT1106231	hsa-miR-588	CLIP-seq
MIRT1106232	hsa-miR-608	CLIP-seq
MIRT1106233	hsa-miR-637	CLIP-seq
MIRT1106234	hsa-miR-650	CLIP-seq
MIRT1106235	hsa-miR-940	CLIP-seq
MIRT1556625	hsa-miR-214	CLIP-seq
MIRT2029370	hsa-miR-125a-5p	CLIP-seq
MIRT2029371	hsa-miR-125b	CLIP-seq
MIRT1106192	hsa-miR-1293	CLIP-seq
MIRT1106193	hsa-miR-1294	CLIP-seq
MIRT2029372	hsa-miR-145	CLIP-seq
MIRT2029373	hsa-miR-1915	CLIP-seq
MIRT1106195	hsa-miR-2682	CLIP-seq
MIRT2029374	hsa-miR-3120-5p	CLIP-seq
MIRT2029375	hsa-miR-3137	CLIP-seq
MIRT1106196	hsa-miR-3151	CLIP-seq
MIRT2029376	hsa-miR-3165	CLIP-seq
MIRT2029377	hsa-miR-3182	CLIP-seq
MIRT1106198	hsa-miR-3184	CLIP-seq
MIRT2029378	hsa-miR-3656	CLIP-seq
MIRT2029379	hsa-miR-3691-5p	CLIP-seq
MIRT2029380	hsa-miR-3918	CLIP-seq
MIRT1106203	hsa-miR-423-5p	CLIP-seq
MIRT2029381	hsa-miR-4252	CLIP-seq
MIRT2029382	hsa-miR-4283	CLIP-seq
MIRT2029383	hsa-miR-4292	CLIP-seq
MIRT2029384	hsa-miR-4308	CLIP-seq
MIRT1106205	hsa-miR-4316	CLIP-seq
MIRT2029385	hsa-miR-4319	CLIP-seq
MIRT2029386	hsa-miR-4326	CLIP-seq
MIRT1106210	hsa-miR-4483	CLIP-seq
MIRT2029387	hsa-miR-4489	CLIP-seq
MIRT1106211	hsa-miR-449c	CLIP-seq
MIRT1106216	hsa-miR-4651	CLIP-seq
MIRT1106220	hsa-miR-4675	CLIP-seq
MIRT1106221	hsa-miR-4677-3p	CLIP-seq
MIRT2029388	hsa-miR-4685-5p	CLIP-seq
MIRT2029389	hsa-miR-4690-3p	CLIP-seq
MIRT2029390	hsa-miR-4691-5p	CLIP-seq
MIRT2029391	hsa-miR-4732-3p	CLIP-seq
MIRT2029392	hsa-miR-4732-5p	CLIP-seq
MIRT1106227	hsa-miR-4736	CLIP-seq
MIRT1106228	hsa-miR-4741	CLIP-seq
MIRT2029393	hsa-miR-4755-3p	CLIP-seq
MIRT2029394	hsa-miR-4778-5p	CLIP-seq
MIRT1106230	hsa-miR-486-3p	CLIP-seq
MIRT1106232	hsa-miR-608	CLIP-seq
MIRT2029395	hsa-miR-670	CLIP-seq
MIRT2029396	hsa-miR-760	CLIP-seq
MIRT2029397	hsa-miR-767-3p	CLIP-seq
MIRT1106235	hsa-miR-940	CLIP-seq
MIRT1106192	hsa-miR-1293	CLIP-seq
MIRT2260257	hsa-miR-1298	CLIP-seq
MIRT2260258	hsa-miR-146b-3p	CLIP-seq
MIRT2260259	hsa-miR-3173-5p	CLIP-seq
MIRT2260260	hsa-miR-323-5p	CLIP-seq
MIRT1106200	hsa-miR-3612	CLIP-seq
MIRT2029383	hsa-miR-4292	CLIP-seq
MIRT1106208	hsa-miR-4436a	CLIP-seq
MIRT1106210	hsa-miR-4483	CLIP-seq
MIRT1106216	hsa-miR-4651	CLIP-seq
MIRT2029394	hsa-miR-4778-5p	CLIP-seq
MIRT1106232	hsa-miR-608	CLIP-seq
MIRT1106233	hsa-miR-637	CLIP-seq
MIRT1106234	hsa-miR-650	CLIP-seq
MIRT2260261	hsa-miR-874	CLIP-seq

Show/Hide all(51)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA	21873635
GO:0000785	Component	Chromatin	IDA	20855495
GO:0000972	Process	Transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	ISS
GO:0001102	Function	RNA polymerase II activating transcription factor binding	IBA	21873635
GO:0001102	Function	RNA polymerase II activating transcription factor binding	IPI	16314316
GO:0001702	Process	Gastrulation with mouth forming second	IEA
GO:0001942	Process	Hair follicle development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0003712	Function	Transcription coregulator activity	IEA
GO:0005515	Function	Protein binding	IPI	15231748, 21988832, 25416956, 30833792
GO:0005634	Component	Nucleus	IBA	21873635
GO:0005634	Component	Nucleus	ISS
GO:0005654	Component	Nucleoplasm	TAS
GO:0005667	Component	Transcription regulator complex	IBA	21873635
GO:0005667	Component	Transcription regulator complex	IDA	16314316
GO:0006355	Process	Regulation of transcription, DNA-templated	NAS	12792813
GO:0006366	Process	Transcription by RNA polymerase II	IEA
GO:0007275	Process	Multicellular organism development	NAS	12792813
GO:0007399	Process	Nervous system development	IBA	21873635
GO:0009948	Process	Anterior/posterior axis specification	IEA
GO:0010669	Process	Epithelial structure maintenance	IEA
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0019899	Function	Enzyme binding	IPI	23382074
GO:0021702	Process	Cerebellar Purkinje cell differentiation	IEA
GO:0022607	Process	Cellular component assembly	IEA
GO:0030182	Process	Neuron differentiation	ISS
GO:0030274	Function	LIM domain binding	IBA	21873635
GO:0030274	Function	LIM domain binding	IPI	12792813
GO:0030274	Function	LIM domain binding	ISS
GO:0030334	Process	Regulation of cell migration	ISS
GO:0031252	Component	Cell leading edge	ISS
GO:0032991	Component	Protein-containing complex	ISS
GO:0034243	Process	Regulation of transcription elongation from RNA polymerase II promoter	ISS
GO:0035019	Process	Somatic stem cell population maintenance	IEA
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0043549	Process	Regulation of kinase activity	ISS
GO:0043621	Function	Protein self-association	IEA
GO:0043973	Process	Histone H3-K4 acetylation	ISS
GO:0045647	Process	Negative regulation of erythrocyte differentiation	ISS
GO:0045785	Process	Positive regulation of cell adhesion	IEA
GO:0045892	Process	Negative regulation of transcription, DNA-templated	IDA	10767331
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA	21873635
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	20855495
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	ISS
GO:0046985	Process	Positive regulation of hemoglobin biosynthetic process	ISS
GO:0048382	Process	Mesendoderm development	IEA
GO:0051893	Process	Regulation of focal adhesion assembly	ISS
GO:0140297	Function	DNA-binding transcription factor binding	IPI	32417234
GO:1902036	Process	Regulation of hematopoietic stem cell differentiation	TAS
GO:1990907	Component	Beta-catenin-TCF complex	IDA	28296634

MIM	HGNC	e!Ensembl
603451	6532	ENSG00000198728

Protein

UniProt ID

Q86U70

Protein name

LIM domain-binding protein 1 (LDB-1) (Carboxyl-terminal LIM domain-binding protein 2) (CLIM-2) (LIM domain-binding factor CLIM2) (hLdb1) (Nuclear LIM interactor)

Protein 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. Plays a role in the development of inter

PDB

2XJY , 2XJZ , 2YPA , 6TYD , 7OB5 , 7OB8 , 8HIB , 8SSU , 9F5B

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01803	LIM_bind	69 → 225	LIM-domain binding protein	Family
PF01803	LIM_bind	215 → 271	LIM-domain binding protein	Family
PF17916	LID	336 → 364	LIM interaction domain (LID)	Domain

Tissue specificity

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. {ECO:0000269|PubMed:16815859}.

Sequence

MSVGCACPGCSSKSFKLYSPKEPPNGNAFPPFHPGTMLDRDVGPTPMYPPTYLEPGIGRH
TPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIG
RTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEG
RLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLSNSTL
NYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPTRQQPSKRRKRK
MSGGSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITR
LENTQFDAANGIDDEDSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ

Sequence length

411

Interactions

View interactions

	KEGG		Reactome
	Transcriptional misregulation in cancer		RUNX1 regulates transcription of genes involved in differentiation of HSCs

Show/Hide Causal Diseases (1)

Disease term	Disease name	dbSNP ID	References
Causal
Colorectal cancer	Colorectal Carcinoma	rs137854568, rs137854573, rs137854575, rs387906234, rs121908380, rs121908702, rs267606674, rs794729661, rs121909055, rs281865417, rs267606884, rs28934575, rs587776769, rs104893815, rs587776800 View all (467 more)

Show/Hide Unknown Diseases (2)

Disease term	Disease name	Evidence	Source
Unknown
Breast Cancer	Breast Cancer	Importantly, breast cancer patients bearing PRC2 LOF mutations displayed significantly worse prognosis compared with PRC2 wild-type patients	GWAS, CBGDA
Restless Legs Syndrome	Restless Legs Syndrome		GWAS

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text Mining
Anemia Sickle Cell	Associate	27405777
Carcinoma Squamous Cell	Associate	12771919
Colorectal Neoplasms	Associate	27713177
Congenital Abnormalities	Associate	38091987
Developmental Disabilities	Associate	38091987
Glioma	Associate	35805116
Hereditary Breast and Ovarian Cancer Syndrome	Stimulate	25079073
Hyperglycemia	Associate	35881062
Hypoxia Brain	Associate	27405777
Leukemia	Associate	26598604, 32229578, 37573405
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	37774059
Leukemia Myeloid Acute	Associate	32229578, 37573405
Leukemia T Cell	Associate	26598604
Lymphoma Large B Cell Diffuse	Associate	22517897
Neoplasm Metastasis	Inhibit	27713177
Neoplasms	Associate	12771919, 27713177, 35805116
Pancreatic Neoplasms	Associate	35881062
Precancerous Conditions	Associate	37573405
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	37573405
Squamous Cell Carcinoma of Head and Neck	Associate	12771919

LDB1 (LIM domain binding 1)