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

    Gene ID: 9079, updated on 14-Nov-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
    mouse all
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    Genomic context

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    See LDB2 in Genome Data Viewer
    Location:
    4p15.32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (16501541..16898645, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (16483292..16880253, complement)
    RS_2024_09 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 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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    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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    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)

    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 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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coregulator activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    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_2024_08

    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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