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LDB2 LIM domain binding 2 [ Homo sapiens (human) ]

Gene ID: 9079, updated on 3-Apr-2024

Summary

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Official Symbol
LDB2provided by HGNC
Official Full Name
LIM domain binding 2provided by HGNC
Primary source
HGNC:HGNC:6533
See related
Ensembl:ENSG00000169744 MIM:603450; AllianceGenome:HGNC:6533
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LDB1; CLIM1; LDB-2
Summary
The protein encoded by this gene belongs to the LIM-domain binding family. Members of this family are characterized by a conserved nuclear localization sequence, an amino-terminal homodimerization domain and a carboxy-terminal LIM interaction domain. These proteins function as adapter molecules to allow assembly of transcriptional regulatory complexes. Genetic association studies suggest functions for this gene in rhegmatogenous retinal detachment and coronary artery disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
Expression
Broad expression in endometrium (RPKM 25.9), fat (RPKM 24.8) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
4p15.32
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (16501541..16898645, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (16483292..16880253, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (16503164..16900268, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:16362034-16363233 Neighboring gene uncharacterized LOC105374505 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:16394090-16394808 Neighboring gene zinc finger E-box binding homeobox 2 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16451182-16451689 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16451690-16452196 Neighboring gene uncharacterized LOC124900675 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_75724 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16592252-16593021 Neighboring gene uncharacterized LOC124900604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16610841-16611361 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:16694053-16695252 Neighboring gene Sharpr-MPRA regulatory region 15531 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16777326-16777893 Neighboring gene NANOG hESC enhancer GRCh37_chr4:16819631-16820182 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:16822893-16823118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16870067-16870626 Neighboring gene uncharacterized LOC107986188 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16909825-16910366 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16910367-16910908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15309 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16920031-16920848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:16943010-16943510 Neighboring gene Sharpr-MPRA regulatory region 8789 Neighboring gene NANOG hESC enhancer GRCh37_chr4:16979388-16979889 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16996053-16996798 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16996799-16997544 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16998595-16999416 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16999417-17000236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17002080-17002991 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:17004513-17005034 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:17005035-17005556 Neighboring gene NANOG hESC enhancer GRCh37_chr4:17008075-17008615 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:17028696-17029895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:17032946-17033488 Neighboring gene uncharacterized LOC105374507 Neighboring gene MT-ND5 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. LIM-domain binding protein 2 was down-regulated by miRNA-96-5p inhibited the proliferation, invasion and metastasis of lung cancer H1299 cells. Chu F, et al. Clinics (Sao Paulo), 2023. PMID 36473369, Free PMC Article
  2. [LIM-domain binding protein 2 regulated by m(6)A modification inhibits lung adenocarcinoma cell proliferation in vitro]. Zhai D, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2021 Mar 25. PMID 33849822, Free PMC Article
  3. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study. Hägg S, et al. PLoS Genet, 2009 Dec. PMID 19997623, Free PMC Article
  4. Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2. Ueki N, et al. J Hum Genet, 1999. PMID 10083735
  5. Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis. Shang MM, et al. Arterioscler Thromb Vasc Biol, 2014 Sep. PMID 24925974

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LIM-domain binding protein 2 was down-regulated by miRNA-96-5p inhibited the proliferation, invasion and metastasis of lung cancer H1299 cells.
    Title: LIM-domain binding protein 2 was down-regulated by miRNA-96-5p inhibited the proliferation, invasion and metastasis of lung cancer H1299 cells.
  2. Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
    Title: Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
  3. [LIM-domain binding protein 2 regulated by m(6)A modification inhibits lung adenocarcinoma cell proliferation in vitro].
    Title: [LIM-domain binding protein 2 regulated by m(6)A modification inhibits lung adenocarcinoma cell proliferation in vitro].
  4. The regulation of DLL4 by the LDB2 complex provides a novel mechanism of DLL4 transcriptional control that may be exploited to develop therapeutics for aberrant vascular remodeling.
    Title: LDB2 regulates the expression of DLL4 through the formation of oligomeric complexes in endothelial cells.
  5. LDB2 was the most connected gene in a transcription factor regulatory network inferred from transendothelial migration of leukocyte and atherosclerosis module genes in coronary and carotid artery disease macrophages.
    Title: Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the atherosclerosis-module.
    Title: Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Generalization of variants identified by genome-wide association studies for electrocardiographic traits in African Americans.
EBI GWAS Catalog
Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables LIM domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables LIM domain binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables enzyme binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular component biogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in epithelial structure maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in hair follicle development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cellular component biogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cell leading edge ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
part_of transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
LIM domain-binding protein 2
Names
LIM binding domain 2
LIM domain-binding factor CLIM1
LIM domain-binding factor-2
carboxyl-terminal LIM domain-binding protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001130834.3 → NP_001124306.1  LIM domain-binding protein 2 isoform b

    See identical proteins and their annotated locations for NP_001124306.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 3' coding region and differs in the 3' UTR compared to variant 1. It encodes isoform b, which is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AF064493, AK312881, DA166898, DB352456
    Consensus CDS
    CCDS47031.1
    UniProtKB/Swiss-Prot
    O43679
    Related
    ENSP00000392089.2, ENST00000441778.6
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  2. NM_001290.5 → NP_001281.1  LIM domain-binding protein 2 isoform a

    See identical proteins and their annotated locations for NP_001281.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF064492, DA166898, DB352456
    Consensus CDS
    CCDS3420.1
    UniProtKB/Swiss-Prot
    O43679, O60619, O75480
    UniProtKB/TrEMBL
    B7Z6D0
    Related
    ENSP00000306772.5, ENST00000304523.10
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:298 → 326
    LID; LIM interaction domain (LID)

  3. NM_001304434.2 → NP_001291363.1  LIM domain-binding protein 2 isoform c

    See identical proteins and their annotated locations for NP_001291363.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice donor site compared to variant 1. It encodes isoform c, which is shorter than isoform a.
    Source sequence(s)
    AC097515, AK300119, AL832772, DA521198
    Consensus CDS
    CCDS77903.1
    UniProtKB/TrEMBL
    B7Z6D0, G5E9Y7
    Related
    ENSP00000422552.1, ENST00000515064.5
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:296 → 324
    LID; LIM interaction domain (LID)

  4. NM_001304435.2 → NP_001291364.1  LIM domain-binding protein 2 isoform d

    See identical proteins and their annotated locations for NP_001291364.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region an differs in the 3' UTR compared to variant 1. It encodes isoform (d), which is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC097515, AK226029, DA521198, DB352456
    Consensus CDS
    CCDS77902.1
    UniProtKB/TrEMBL
    E9PFI4
    Related
    ENSP00000423963.1, ENST00000502640.5
    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

RNA

  1. NR_130734.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains alternate internal exons and uses an alternate 3' terminal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BX089082, DA521198

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    16501541..16898645 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008813.3 → XP_016864302.1  LIM domain-binding protein 2 isoform X6

    UniProtKB/TrEMBL
    B7Z6D0
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:295 → 323
    LID; LIM interaction domain (LID)

  2. XM_017008821.3 → XP_016864310.1  LIM domain-binding protein 2 isoform X15

  3. XM_005248197.5 → XP_005248254.1  LIM domain-binding protein 2 isoform X5

    See identical proteins and their annotated locations for XP_005248254.1

    UniProtKB/TrEMBL
    B7Z6D0
    Conserved Domains (2) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein
    pfam17916
    Location:297 → 325
    LID; LIM interaction domain (LID)

  4. XM_017008819.3 → XP_016864308.1  LIM domain-binding protein 2 isoform X13

  5. XM_017008820.3 → XP_016864309.1  LIM domain-binding protein 2 isoform X14

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  6. XM_024454278.2 → XP_024310046.1  LIM domain-binding protein 2 isoform X11

    Conserved Domains (1) summary
    pfam01803
    Location:31 → 232
    LIM_bind; LIM-domain binding protein

  7. XM_017008812.3 → XP_016864301.1  LIM domain-binding protein 2 isoform X4

  8. XM_017008816.3 → XP_016864305.1  LIM domain-binding protein 2 isoform X10

  9. XM_006713976.5 → XP_006714039.1  LIM domain-binding protein 2 isoform X2

    Conserved Domains (1) summary
    pfam01803
    Location:81 → 270
    LIM_bind; LIM-domain binding protein

  10. XM_017008815.3 → XP_016864304.1  LIM domain-binding protein 2 isoform X8

  11. XM_006713977.5 → XP_006714040.1  LIM domain-binding protein 2 isoform X3

    Conserved Domains (1) summary
    pfam01803
    Location:81 → 270
    LIM_bind; LIM-domain binding protein

  12. XM_006713983.5 → XP_006714046.1  LIM domain-binding protein 2 isoform X9

    Conserved Domains (1) summary
    pfam01803
    Location:81 → 270
    LIM_bind; LIM-domain binding protein

  13. XM_006713975.5 → XP_006714038.1  LIM domain-binding protein 2 isoform X1

    Conserved Domains (1) summary
    pfam01803
    Location:81 → 270
    LIM_bind; LIM-domain binding protein

  14. XM_006713982.5 → XP_006714045.1  LIM domain-binding protein 2 isoform X7

    Conserved Domains (1) summary
    pfam01803
    Location:81 → 270
    LIM_bind; LIM-domain binding protein

  15. XM_024454280.2 → XP_024310048.1  LIM domain-binding protein 2 isoform X17

    UniProtKB/TrEMBL
    H0YA09
    Conserved Domains (1) summary
    pfam01803
    Location:25 → 108
    LIM_bind; LIM-domain binding protein

  16. XM_017008818.2 → XP_016864307.1  LIM domain-binding protein 2 isoform X12

    UniProtKB/TrEMBL
    B7Z6D0

  17. XM_047416391.1 → XP_047272347.1  LIM domain-binding protein 2 isoform X17

  18. XM_047416390.1 → XP_047272346.1  LIM domain-binding protein 2 isoform X16

    Related
    ENSP00000425754.1, ENST00000507464.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    16483292..16880253 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351203.1 → XP_054207178.1  LIM domain-binding protein 2 isoform X6

  2. XM_054351212.1 → XP_054207187.1  LIM domain-binding protein 2 isoform X15

  3. XM_054351202.1 → XP_054207177.1  LIM domain-binding protein 2 isoform X5

  4. XM_054351210.1 → XP_054207185.1  LIM domain-binding protein 2 isoform X13

  5. XM_054351211.1 → XP_054207186.1  LIM domain-binding protein 2 isoform X14

  6. XM_054351208.1 → XP_054207183.1  LIM domain-binding protein 2 isoform X11

  7. XM_054351201.1 → XP_054207176.1  LIM domain-binding protein 2 isoform X4

  8. XM_054351207.1 → XP_054207182.1  LIM domain-binding protein 2 isoform X10

  9. XM_054351199.1 → XP_054207174.1  LIM domain-binding protein 2 isoform X2

  10. XM_054351205.1 → XP_054207180.1  LIM domain-binding protein 2 isoform X8

  11. XM_054351200.1 → XP_054207175.1  LIM domain-binding protein 2 isoform X3

  12. XM_054351206.1 → XP_054207181.1  LIM domain-binding protein 2 isoform X9

  13. XM_054351198.1 → XP_054207173.1  LIM domain-binding protein 2 isoform X1

  14. XM_054351204.1 → XP_054207179.1  LIM domain-binding protein 2 isoform X7

  15. XM_054351215.1 → XP_054207190.1  LIM domain-binding protein 2 isoform X17

  16. XM_054351209.1 → XP_054207184.1  LIM domain-binding protein 2 isoform X12

  17. XM_054351214.1 → XP_054207189.1  LIM domain-binding protein 2 isoform X17

  18. XM_054351213.1 → XP_054207188.1  LIM domain-binding protein 2 isoform X16

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43679.1 GenPept UniProtKB/Swiss-Prot:O43679

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