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    Ldb1 LIM domain binding 1 [ Mus musculus (house mouse) ]

    Gene ID: 16825, updated on 23-Jun-2021

    Summary

    Official Symbol
    Ldb1provided by MGI
    Official Full Name
    LIM domain binding 1provided by MGI
    Primary source
    MGI:MGI:894762
    See related
    Ensembl:ENSMUSG00000025223
    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
    CLI; NLI; CLIM2
    Expression
    Ubiquitous expression in thymus adult (RPKM 131.0), CNS E14 (RPKM 82.2) and 27 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Ldb1 in Genome Data Viewer
    Location:
    19 C3; 19 38.75 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (46019963..46036584, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (46031525..46048145, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (46107084..46119701, complement)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene armadillo-like helical domain containing 3 Neighboring gene ribosomal protein L21 pseudogene Neighboring gene RIKEN cDNA 4930505N22 gene Neighboring gene HPS6, biogenesis of lysosomal organelles complex 2 subunit 3 Neighboring gene ES cell cis-regulatory motif 2c Neighboring gene peroxisome proliferative activated receptor, gamma, coactivator-related 1

    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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    contributes_to DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables LIM domain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables LIM domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables LIM domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables LIM domain binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein self-association IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within anterior/posterior axis specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within cellular component assembly IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within cerebellar Purkinje cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cerebellum development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within epithelial structure maintenance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within gastrulation with mouth forming second IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within hair follicle development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in head development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in histone H3-K4 acetylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mesendoderm development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of erythrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within neuron differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of cell adhesion IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of hemoglobin biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in primitive erythrocyte differentiation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of focal adhesion assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription elongation from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within somatic stem cell population maintenance IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of beta-catenin-TCF complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cell leading edge IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    LIM domain-binding protein 1
    Names
    LIM domain-binding factor CLIM2
    carboxyl-terminal LIM domain-binding protein 2
    nuclear LIM interactor

    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_001113408.2NP_001106879.1  LIM domain-binding protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001106879.1

      Status: VALIDATED

      Source sequence(s)
      AC140233, U70375
      Consensus CDS
      CCDS50455.1
      UniProtKB/Swiss-Prot
      P70662
      Related
      ENSMUSP00000139562.2, ENSMUST00000185355.7
      Conserved Domains (2) summary
      pfam01803
      Location:70271
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:336364
      LID; LIM interaction domain (LID)
    2. NM_001360336.1NP_001347265.1  LIM domain-binding protein 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC140233, U69270
      Consensus CDS
      CCDS29870.1
      Related
      ENSMUSP00000026252.8, ENSMUST00000026252.14
      Conserved Domains (2) summary
      pfam01803
      Location:34235
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:300328
      LID; LIM interaction domain (LID)
    3. NM_010697.2NP_034827.1  LIM domain-binding protein 1 isoform 2

      See identical proteins and their annotated locations for NP_034827.1

      Status: VALIDATED

      Source sequence(s)
      AC140233, U69270
      Consensus CDS
      CCDS29870.1
      UniProtKB/Swiss-Prot
      P70662
      Related
      ENSMUSP00000053680.8, ENSMUST00000056931.14
      Conserved Domains (2) summary
      pfam01803
      Location:34235
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:300328
      LID; LIM interaction domain (LID)

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000085.7 Reference GRCm39 C57BL/6J

      Range
      46019963..46036584 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006526723.4XP_006526786.3  LIM domain-binding protein 1 isoform X1

      Conserved Domains (2) summary
      pfam01803
      Location:356557
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:620648
      LID; LIM interaction domain (LID)
    2. XM_030250760.2XP_030106620.1  LIM domain-binding protein 1 isoform X4

      Related
      ENSMUSP00000116909.2, ENSMUST00000152946.8
      Conserved Domains (2) summary
      pfam01803
      Location:34235
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:298326
      LID; LIM interaction domain (LID)
    3. XM_030250759.2XP_030106619.1  LIM domain-binding protein 1 isoform X3

      Conserved Domains (2) summary
      pfam01803
      Location:34235
      LIM_bind; LIM-domain binding protein
      pfam17916
      Location:300328
      LID; LIM interaction domain (LID)
    4. XM_036161453.1XP_036017346.1  LIM domain-binding protein 1 isoform X2

      Conserved Domains (1) summary
      pfam01803
      Location:356557
      LIM_bind; LIM-domain binding protein
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