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

Gene ID: 16825, updated on 12-May-2024

Summary

Official Symbol
Ldb1provided by MGI
Official Full Name
LIM domain binding 1provided by MGI
Primary source
MGI:MGI:894762
See related
Ensembl:ENSMUSG00000025223 AllianceGenome:MGI:894762
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
NLI; CLIM2
Summary
Enables several functions, including LIM domain binding activity; protein homodimerization activity; and protein self-association. Contributes to DNA binding activity. Involved in several processes, including histone H3-K4 acetylation; negative regulation of erythrocyte differentiation; and regulation of cellular macromolecule biosynthetic process. Acts upstream of or within several processes, including cerebellar Purkinje cell differentiation; epithelial structure maintenance; and hair follicle development. Located in cell leading edge and nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including branchial arch; central nervous system; embryo mesenchyme; eye; and genitourinary system. Used to study nail-patella syndrome. Orthologous to human LDB1 (LIM domain binding 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 131.0), CNS E14 (RPKM 82.2) and 27 other tissues See more
Orthologs
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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
RS_2024_02 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)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene armadillo-like helical domain containing 3 Neighboring gene STARR-seq mESC enhancer starr_46288 Neighboring gene ribosomal protein L21 pseudogene Neighboring gene STARR-seq mESC enhancer starr_46291 Neighboring gene RIKEN cDNA 4930505N22 gene Neighboring gene STARR-positive B cell enhancer ABC_E4287 Neighboring gene HPS6, biogenesis of lysosomal organelles complex 2 subunit 3 Neighboring gene STARR-seq mESC enhancer starr_46294 Neighboring gene STARR-positive B cell enhancer ABC_E5707 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:46114769-46114954 Neighboring gene STARR-positive B cell enhancer ABC_E1527 Neighboring gene STARR-positive B cell enhancer ABC_E7666 Neighboring gene peroxisome proliferative activated receptor, gamma, coactivator-related 1 Neighboring gene nucleolar and coiled-body phosphoprotein 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)
  • Endonuclease-mediated (1) 
  • Targeted (5)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 IPI
Inferred from Physical Interaction
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
 
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 homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 cell adhesion IGI
Inferred from Genetic Interaction
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 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
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
 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in 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
 
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 positive regulation of transcription elongation by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 
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 
part_of 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
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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
 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator complex IMP
Inferred from Mutant Phenotype
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)

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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_001113408.3NP_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
    Consensus CDS
    CCDS50455.1
    UniProtKB/Swiss-Prot
    O55204, P70662, Q1EQX2, Q71V68
    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_001360336.2NP_001347265.1  LIM domain-binding protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC140233
    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_001410966.1NP_001397895.1  LIM domain-binding protein 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC140233
  4. NM_001410967.1NP_001397896.1  LIM domain-binding protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC140233
    UniProtKB/TrEMBL
    D3Z1C5
    Related
    ENSMUSP00000116909.2, ENSMUST00000152946.8
  5. NM_010697.3NP_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
    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: 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_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_036161453.1XP_036017346.1  LIM domain-binding protein 1 isoform X2

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