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

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: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors.
Title: Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors.
LDB1-mediated transcriptional complexes are sensitive to islet stress.
Title: LDB1-mediated transcriptional complexes are sensitive to islet stress.
The transcriptional co-regulator LDB1 is required for brown adipose function.
Title: The transcriptional co-regulator LDB1 is required for brown adipose function.
Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia.
Title: Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia.
An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity.
Title: An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity.
We demonstrate that RUNX1 induction moves FLI1 from distal ETS/GATA sites to RUNX1/ETS sites and recruits the basal transcription factors CDK9, BRD4, the Mediator complex and the looping factor LDB1
Title: The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification.
Greek-island-bound transcription factor LHX2 and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans interactions in gene expression
Title: LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice.
Study identifies Pax3 interaction with members of the chromatin looping complex, including the LIM-domain binding protein 1 (Ldb1) and demonstrates that Ldb1 is recruited to a subset of Pax3-bound elements characterized by increased levels of H3K4me1 deposition. Reduced Ldb1 expression impairs Pax3-dependent myogenic specification both in vitro and in vivo.
Title: Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification.
Together our results show that Ldb1 is dispensable for mammary gland development and Neu-induced tumor progression but required for dissemination at secondary sites.
Title: The LIM domain binding protein 1, Ldb1, has distinct roles in Neu-induced mammary tumorigenesis.
Loss of Ldb1 from E8.75 using Foxg1Cre caused a disruption of midline boundary structures in the dorsal telencephalon. While this Cre line gave the expected pattern of recombination of the floxed Ldb1 locus, unexpectedly, standard Cre lines that act from embryonic day (E)10.5 (Emx1Cre) and E11.5 (NesCre) did not show efficient or complete recombination in the dorsal telencephalon by E12.5.
Title: LDB1 Is Required for the Early Development of the Dorsal Telencephalon and the Thalamus.

Submit: New GeneRIF Correction See all GeneRIFs (49)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (5) 1 citation
Endonuclease-mediated (1)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH134335 (e-PCR)
- UniSTS:217617

A116 (e-PCR), detects polymorphism
- UniSTS:226043

Homology

Homologs of the Ldb1 gene: The Ldb1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 473 organisms have orthologs with human gene Ldb1
Orthologs

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	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 homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein self-association	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype 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 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
involved_in histone H3-K4 acetylation	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 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	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	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 by RNA polymerase II	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	IMP Inferred from Mutant Phenotype more info	PubMed
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

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)

NM_001113408.3 → NP_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

P70662, Q71V68

UniProtKB/TrEMBL

A0A6P5P627, A0A8C6GZ54

Related

ENSMUSP00000139562.2, ENSMUST00000185355.7

Conserved Domains (2) summary

pfam01803
Location:70 → 271

LIM_bind; LIM-domain binding protein

pfam17916
Location:336 → 364

LID; LIM interaction domain (LID)
NM_001360336.2 → NP_001347265.1 LIM domain-binding protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC140233

Consensus CDS

CCDS29870.1

UniProtKB/TrEMBL

A0A6P7QPM8

Related

ENSMUSP00000026252.8, ENSMUST00000026252.14

Conserved Domains (2) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

pfam17916
Location:300 → 328

LID; LIM interaction domain (LID)
NM_001410966.1 → NP_001397895.1 LIM domain-binding protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC140233

UniProtKB/TrEMBL

A0A6P7QPM8
NM_001410967.1 → NP_001397896.1 LIM domain-binding protein 1 isoform 3

Status: VALIDATED

Source sequence(s)

AC140233

UniProtKB/TrEMBL

D3Z1C5
NM_010697.3 → NP_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

UniProtKB/TrEMBL

A0A6P7QPM8

Related

ENSMUSP00000053680.8, ENSMUST00000056931.14

Conserved Domains (2) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

pfam17916
Location:300 → 328

LID; LIM interaction domain (LID)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000085.7 Reference GRCm39 C57BL/6J

Range

46019963..46036584 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (2) summary

pfam01803
Location:356 → 557

LIM_bind; LIM-domain binding protein

pfam17916
Location:620 → 648

LID; LIM interaction domain (LID)
XM_030250760.2 → XP_030106620.1 LIM domain-binding protein 1 isoform X4

Related

ENSMUSP00000116909.2, ENSMUST00000152946.8

Conserved Domains (2) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

pfam17916
Location:298 → 326

LID; LIM interaction domain (LID)
XM_030250759.2 → XP_030106619.1 LIM domain-binding protein 1 isoform X3

Conserved Domains (2) summary

pfam01803
Location:34 → 235

LIM_bind; LIM-domain binding protein

pfam17916
Location:300 → 328

LID; LIM interaction domain (LID)
XM_036161453.1 → XP_036017346.1 LIM domain-binding protein 1 isoform X2

Conserved Domains (1) summary

pfam01803
Location:356 → 557

LIM_bind; LIM-domain binding protein