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    Ldb2 LIM domain binding 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289664, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Ldb2provided by RGD
    Official Full Name
    LIM domain binding 2provided by RGD
    Primary source
    RGD:1307921
    See related
    EnsemblRapid:ENSRNOG00000003205 AllianceGenome:RGD:1307921
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable enzyme binding activity and transcription coregulator activity. Predicted to be involved in several processes, including regulation of cell migration; regulation of kinase activity; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including epithelial structure maintenance; hair follicle development; and somatic stem cell population maintenance. Predicted to be located in cell leading edge; nuclear lumen; and plasma membrane. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human LDB2 (LIM domain binding 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 122.3), Uterus (RPKM 89.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ldb2 in Genome Data Viewer
    Location:
    14q21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (70489243..70810573)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (66277044..66598071)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (70780605..71112857)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene KDEL endoplasmic reticulum protein retention receptor 1, pseudogene 1 Neighboring gene uncharacterized LOC120096620 Neighboring gene uncharacterized LOC134481760 Neighboring gene uncharacterized LOC108352764 Neighboring gene uncharacterized LOC134481761 Neighboring gene Rac family small GTPase 1 like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The Ldb1 and Ldb2 transcriptional cofactors interact with the Ste20-like kinase SLK and regulate cell migration. Storbeck CJ, et al. Mol Biol Cell, 2009 Oct. PMID 19675209, Free PMC Article
    2. A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins. Bach I, et al. Genes Dev, 1997 Jun 1. PMID 9192866
    3. Selection system for genes encoding nuclear-targeted proteins. Ueki N, et al. Nat Biotechnol, 1998 Dec. PMID 9853615
    4. Co-factors of LIM domains (Clims/Ldb/Nli) regulate corneal homeostasis and maintenance of hair follicle stem cells. Xu X, et al. Dev Biol, 2007 Dec 15. PMID 17991461, Free PMC Article
    5. Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors. Ostendorff HP, et al. Nature, 2002 Mar 7. PMID 11882901

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within epithelial structure maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hair follicle development ISO
    Inferred from Sequence Orthology
    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
    		  
    acts_upstream_of_or_within positive regulation of cellular component biogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within somatic stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cell leading edge ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    LIM domain-binding protein 2

    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_001106009.1 → NP_001099479.1  LIM domain-binding protein 2

      See identical proteins and their annotated locations for NP_001099479.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473963
      UniProtKB/TrEMBL
      A6IJM3
      Conserved Domains (2) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:298 → 326
      LID; LIM interaction domain (LID)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      70489243..70810573
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017599112.3 → XP_017454601.1  LIM domain-binding protein 2 isoform X8

      UniProtKB/TrEMBL
      B5DF10, E9PTQ0
      Related
      ENSRNOP00000055594.5, ENSRNOT00000058803.5
      Conserved Domains (1) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein

    2. XM_063272933.1 → XP_063129003.1  LIM domain-binding protein 2 isoform X7

    3. XM_017599113.3 → XP_017454602.1  LIM domain-binding protein 2 isoform X11

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

    4. XM_063272934.1 → XP_063129004.1  LIM domain-binding protein 2 isoform X9

    5. XM_008770200.4 → XP_008768422.1  LIM domain-binding protein 2 isoform X2

      See identical proteins and their annotated locations for XP_008768422.1

      UniProtKB/TrEMBL
      A0A8J8XZV4
      Conserved Domains (2) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:296 → 324
      LID; LIM interaction domain (LID)

    6. XM_008770203.4 → XP_008768425.1  LIM domain-binding protein 2 isoform X10

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

    7. XM_008770199.4 → XP_008768421.1  LIM domain-binding protein 2 isoform X1

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

    8. XM_008770201.4 → XP_008768423.1  LIM domain-binding protein 2 isoform X3

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

    9. XM_017599109.3 → XP_017454598.1  LIM domain-binding protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A0G2K287
      Conserved Domains (1) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein

    10. XM_063272932.1 → XP_063129002.1  LIM domain-binding protein 2 isoform X4

      UniProtKB/TrEMBL
      A0A0G2K287

    11. XM_017599111.3 → XP_017454600.1  LIM domain-binding protein 2 isoform X6

      UniProtKB/TrEMBL
      A0A0G2K287
      Related
      ENSRNOP00000072146.3, ENSRNOT00000083871.3
      Conserved Domains (1) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein

    12. XM_008770202.4 → XP_008768424.1  LIM domain-binding protein 2 isoform X5

      Conserved Domains (1) summary
      pfam01803
      Location:31 → 232
      LIM_bind; LIM-domain binding protein
    Nucleotide Protein Strain
    Heading Accession and Version

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