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

Gene ID: 9079, updated on 21-Apr-2019

Summary

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
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

Genomic context

See LDB2 in Genome Data Viewer
Location:
4p15.32
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (16501534..16898809, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (16503164..16900424, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene fibroblast growth factor binding protein 1 pseudogene Neighboring gene uncharacterized LOC105374505 Neighboring gene zinc finger E-box binding homeobox 2 pseudogene 1 Neighboring gene uncharacterized LOC107986188 Neighboring gene uncharacterized LOC105374507 Neighboring gene MT-ND5 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Ectoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Ectoderm Differentiation, organism-specific biosystemModel depicting ectoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
LIM domain binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enzyme binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coregulator activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
epithelial structure maintenance IEA
Inferred from Electronic Annotation
more info
 
hair follicle development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cellular component biogenesis IEA
Inferred from Electronic Annotation
more info
 
regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell leading edge ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

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)

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_001130834.2NP_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)
    AC097515, AF064493, AK312881, DA166898, DA521198, DB352456
    Consensus CDS
    CCDS47031.1
    UniProtKB/Swiss-Prot
    O43679
    Related
    ENSP00000392089.2, ENST00000441778.6
    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  2. NM_001290.5NP_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
    Related
    ENSP00000306772.5, ENST00000304523.10
    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  3. NM_001304434.1NP_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, DB352456
    Consensus CDS
    CCDS77903.1
    UniProtKB/TrEMBL
    B7Z6D0, G5E9Y7
    Related
    ENSP00000422552.1, ENST00000515064.5
    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  4. NM_001304435.1NP_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:31232
    LIM_bind; LIM-domain binding protein

RNA

  1. NR_130734.1 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    16501534..16898809 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

  2. XM_017008816.2XP_016864305.1  LIM domain-binding protein 2 isoform X14

  3. XM_017008814.2XP_016864303.1  LIM domain-binding protein 2 isoform X10

  4. XM_017008815.2XP_016864304.1  LIM domain-binding protein 2 isoform X12

  5. XM_006713980.4XP_006714043.1  LIM domain-binding protein 2 isoform X8

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  6. XM_006713981.4XP_006714044.1  LIM domain-binding protein 2 isoform X9

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  7. XM_006713975.4XP_006714038.1  LIM domain-binding protein 2 isoform X1

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  8. XM_006713982.4XP_006714045.1  LIM domain-binding protein 2 isoform X11

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  9. XM_017008813.2XP_016864302.1  LIM domain-binding protein 2 isoform X6

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  10. XM_017008821.2XP_016864310.1  LIM domain-binding protein 2 isoform X21

  11. XM_017008819.2XP_016864308.1  LIM domain-binding protein 2 isoform X19

  12. XM_005248201.3XP_005248258.1  LIM domain-binding protein 2 isoform X16

    See identical proteins and their annotated locations for XP_005248258.1

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  13. XM_017008817.2XP_016864306.1  LIM domain-binding protein 2 isoform X16

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  14. XM_017008820.2XP_016864309.1  LIM domain-binding protein 2 isoform X20

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  15. XM_006713976.4XP_006714039.1  LIM domain-binding protein 2 isoform X2

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  16. XM_006713977.4XP_006714040.1  LIM domain-binding protein 2 isoform X3

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  17. XM_006713983.4XP_006714046.1  LIM domain-binding protein 2 isoform X13

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  18. XM_006713978.4XP_006714041.1  LIM domain-binding protein 2 isoform X7

    See identical proteins and their annotated locations for XP_006714041.1

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
  19. XM_005248197.4XP_005248254.1  LIM domain-binding protein 2 isoform X5

    See identical proteins and their annotated locations for XP_005248254.1

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  20. XM_005248202.3XP_005248259.1  LIM domain-binding protein 2 isoform X18

    See identical proteins and their annotated locations for XP_005248259.1

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  21. XM_024454278.1XP_024310046.1  LIM domain-binding protein 2 isoform X15

    Conserved Domains (1) summary
    pfam01803
    Location:31232
    LIM_bind; LIM-domain binding protein
  22. XM_011513905.2XP_011512207.1  LIM domain-binding protein 2 isoform X22

    Conserved Domains (1) summary
    pfam01803
    Location:5157
    LIM_bind; LIM-domain binding protein
  23. XM_024454279.1XP_024310047.1  LIM domain-binding protein 2 isoform X23

    Conserved Domains (1) summary
    pfam01803
    Location:25108
    LIM_bind; LIM-domain binding protein
  24. XM_017008822.1XP_016864311.1  LIM domain-binding protein 2 isoform X23

    Conserved Domains (1) summary
    pfam01803
    Location:25108
    LIM_bind; LIM-domain binding protein
  25. XM_024454280.1XP_024310048.1  LIM domain-binding protein 2 isoform X23

    Related
    ENSP00000425754.1, ENST00000507464.5
    Conserved Domains (1) summary
    pfam01803
    Location:25108
    LIM_bind; LIM-domain binding protein
  26. XM_017008818.1XP_016864307.1  LIM domain-binding protein 2 isoform X17

  27. XM_006713979.4XP_006714042.1  LIM domain-binding protein 2 isoform X7

    See identical proteins and their annotated locations for XP_006714042.1

    Conserved Domains (1) summary
    pfam01803
    Location:81270
    LIM_bind; LIM-domain binding protein
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