U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Ldb2 LIM domain binding 2 [ Mus musculus (house mouse) ]

    Gene ID: 16826, updated on 9-Dec-2024

    Summary

    Official Symbol
    Ldb2provided by MGI
    Official Full Name
    LIM domain binding 2provided by MGI
    Primary source
    MGI:MGI:894670
    See related
    Ensembl:ENSMUSG00000039706 AllianceGenome:MGI:894670
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Ldb3; CLIM1; CLP-36
    Summary
    Enables enzyme binding activity. Involved in regulation of cell migration and regulation of kinase activity. Acts upstream of or within several processes, including epithelial structure maintenance; hair follicle development; and positive regulation of transcription by RNA polymerase II. Located in cell leading edge. Part of transcription regulator complex. Is expressed in several structures, including brain; branchial arch; eye; genitourinary system; and limb. Orthologous to human LDB2 (LIM domain binding 2). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung adult (RPKM 18.1), limb E14.5 (RPKM 9.7) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Ldb2 in Genome Data Viewer
    Location:
    5 B3; 5 24.24 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (44593292..44957466, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (44435955..44799759, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 36017 Neighboring gene predicted gene 5865 Neighboring gene predicted gene, 40297 Neighboring gene predicted gene, 36076 Neighboring gene RIKEN cDNA 4930431F12 gene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (2)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables LIM domain binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in cell leading edge IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 nucleus ISS
    Inferred from Sequence or Structural Similarity
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001077398.2NP_001070866.1  LIM domain-binding protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001070866.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site and contains an alternate exon in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK146860, BB679977, BY068608
      Consensus CDS
      CCDS80278.1
      UniProtKB/Swiss-Prot
      O55203
      Related
      ENSMUSP00000143775.2, ENSMUST00000199256.5
      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    2. NM_001286348.1NP_001273277.1  LIM domain-binding protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001273277.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 3' coding region and differs in the 3' UTR, compared to variant 1. It encodes isoform 3, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK147160, BB679977, BC079611, BY068608
      Consensus CDS
      CCDS80276.1
      UniProtKB/Swiss-Prot
      O55203
      Related
      ENSMUSP00000142442.2, ENSMUST00000199534.5
      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    3. NM_001347349.1NP_001334278.1  LIM domain-binding protein 2 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC102487, AC111033, AC129607
      Consensus CDS
      CCDS84878.1
      UniProtKB/TrEMBL
      A0A0G2JFS7
      Related
      ENSMUSP00000143289.2, ENSMUST00000199261.2
      Conserved Domains (2) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:296324
      LID; LIM interaction domain (LID)
    4. NM_001359070.1NP_001345999.1  LIM domain-binding protein 2 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses two alternate in-frame splice junctions in the 3' coding sequence compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC102487, AC111033, AC129607
      Conserved Domains (2) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:295323
      LID; LIM interaction domain (LID)
    5. NM_001359071.1NP_001346000.1  LIM domain-binding protein 2 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate 3' splice junction compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC102487, AC111033, AC129607
      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    6. NM_010698.4NP_034828.3  LIM domain-binding protein 2 isoform 1

      See identical proteins and their annotated locations for NP_034828.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK146860, BB679977, BC079611, BY068608
      Consensus CDS
      CCDS19271.1
      UniProtKB/Swiss-Prot
      O55203, O55205, Q3UHY1, Q6AXE6
      Related
      ENSMUSP00000067737.6, ENSMUST00000070748.10
      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      44593292..44957466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036164828.1XP_036020721.1  LIM domain-binding protein 2 isoform X10

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    2. XM_036164830.1XP_036020723.1  LIM domain-binding protein 2 isoform X11

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    3. XM_017320689.3XP_017176178.1  LIM domain-binding protein 2 isoform X9

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    4. XM_036164827.1XP_036020720.1  LIM domain-binding protein 2 isoform X5

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    5. XM_030254170.2XP_030110030.1  LIM domain-binding protein 2 isoform X6

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    6. XM_036164825.1XP_036020718.1  LIM domain-binding protein 2 isoform X3

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    7. XM_030254171.2XP_030110031.1  LIM domain-binding protein 2 isoform X8

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    8. XM_006503752.4XP_006503815.1  LIM domain-binding protein 2 isoform X1

      Conserved Domains (2) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:297325
      LID; LIM interaction domain (LID)
    9. XM_006503758.5XP_006503821.1  LIM domain-binding protein 2 isoform X7

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    10. XM_036164826.1XP_036020719.1  LIM domain-binding protein 2 isoform X4

      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein
    11. XM_006503754.5XP_006503817.1  LIM domain-binding protein 2 isoform X2

      See identical proteins and their annotated locations for XP_006503817.1

      UniProtKB/Swiss-Prot
      O55203
      Conserved Domains (1) summary
      pfam01803
      Location:31232
      LIM_bind; LIM-domain binding protein