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

Summary

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Official Symbol: Ldb1provided by MGI
Official Full Name: LIM domain binding 1provided by MGI
Primary source: MGI:894762
See related: Ensembl:ENSMUSG00000025223; Vega:OTTMUSG00000033442
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: NLI; CLIM2

Genomic context

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Location :: 19 C3; 19 38.75 cM

Sequence :: Chromosome: 19; NC_000085.6 (46032594..46045211, complement)

See Ldb1 in Epigenomics, MapViewer

Chromosome 19 - NC_000085.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

Isl1 and the Ldb co-regulators of transcription are essential early determinants of mouse limb development
Title: Isl1 and Ldb co-regulators of transcription are essential early determinants of mouse limb development.
Data suggest that Ldb1 is critical transcriptional coregulator during pancreatic islet alpha-, beta-, and delta-cell development through Isl1-dependent and potentially Isl1-independent control mechanisms.
Title: Islet α-, β-, and δ-cell development is controlled by the Ldb1 coregulator, acting primarily with the islet-1 transcription factor.
Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions.
Title: Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions.
Studied the solution structure of Lmo2(LIM2) /Ldb1(LID) complex. Results show modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions/ conformational changes in both proteins.
Title: Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex.
Taken together, these data show that Ldb1 forms a regulatory complex to maintain Car1 expression in erythroid cells.
Title: Ldb1 regulates carbonic anhydrase 1 during erythroid differentiation.
Findings establish Ldb1 as a critical effector of GATA1-mediated loop formation and indicate that chromatin looping causally underlies gene regulation.
Title: Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor.
controls transcriptional program required for stem cells maintenance by restricting their differentiation
Title: Nuclear adaptor Ldb1 regulates a transcriptional program essential for the maintenance of hematopoietic stem cells.
knockout mice demonstrated a significantly enhanced growth of liver cancer (HCC) by means of tumor size and number, advocating for an essential role of Ldb1 in HCC development
Title: Liver-specific Ldb1 deletion results in enhanced liver cancer development.
a role for Ldb1 in erythropoiesis in vivo and establish a critical function for Ldb1-nucleated complexes in regulating the erythroid/megakaryocyte transcriptional program.
Title: A requirement for Lim domain binding protein 1 in erythropoiesis.
Ldb1 stabilizes its erythroid complex partners on beta-globin chromatin, even though it is not one of the DNA-binding components. In addition, Ldb1 is necessary for enrichment of key transcriptional components in the locus.
Title: Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation.

Submit: New GeneRIF Correction See all (20)

Alleles

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

Targeted (Floxed/Frt) (2) 1 citation
Targeted (knock-out) (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
BioGRID:201125	BioGRID:198081	Alx4	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:222938	Csdc2	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:199838	Gata1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:201125	BioGRID:200391	Hoxd1	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:222577	Isl2	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201154	Lhx1	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201155	Lhx2	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201157	Lhx4	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201158	Lhx5	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201161	Lhx9	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:224887	Lmo1	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201179	Lmo2	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:224886	Lmo3	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201180	Lmo4	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:225780	Lmx1a	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:201183	Lmx1b	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:202187	Pitx2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:201125	BioGRID:215174	Pygo1	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:211844	Ssbp2	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:215389	Ssbp3	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:218387	Ssbp4	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:203962	Tal1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:201125	BioGRID:231054	Tardbp	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:232803	Tgif2lx1	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:204623	Ywhaz	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western
BioGRID:201125	BioGRID:234724	Zfp446	BioGRID	PubMed	Two-hybrid
BioGRID:201125	BioGRID:212620	Zfp593	BioGRID	PubMed	Two-hybrid

Pathways from BioSystems

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PodNet: protein-protein interactions in the podocyte, organism-specific biosystem (from WikiPathways)
PodNet: protein-protein interactions in the podocyte, organism-specific biosystemPodNet is a manually curated network of protein-protein interactions occurring in the podocyte.
Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
Transcriptional misregulation in cancer, organism-specific biosystem
Transcriptional misregulation in cancer
Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
Transcriptional misregulation in cancer, conserved biosystem
Transcriptional misregulation in cancer
XPodNet - protein-protein interactions in the podocyte expanded by STRING, organism-specific biosystem (from WikiPathways)
XPodNet - protein-protein interactions in the podocyte expanded by STRING, organism-specific biosystemXPodNet is a larger version of PodNet. Interactions from STRING database have been added to PodNet to build XPodNet. Hence, not all interactions found in XPodNet do necessarily have to be curated.

General gene information

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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 C.elegans.
Map Viewer (Human, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
contributes_to DNA binding	IDA Inferred from Direct Assay more info	PubMed
LIM domain binding	IDA Inferred from Direct Assay more info	PubMed
LIM domain binding	IPI Inferred from Physical Interaction more info	PubMed
LIM domain binding	ISO Inferred from Sequence Orthology more info
RNA polymerase II activating transcription factor binding	ISO Inferred from Sequence Orthology more info
chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enhancer sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
protein self-association	IPI Inferred from Physical Interaction more info	PubMed
transcription cofactor activity	IEA Inferred from Electronic Annotation more info
transcription factor binding transcription factor activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
Wnt receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
anterior/posterior axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
cellular component assembly	IGI Inferred from Genetic Interaction more info	PubMed
cerebellar Purkinje cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
cerebellum development	IMP Inferred from Mutant Phenotype more info	PubMed
epithelial structure maintenance	IGI Inferred from Genetic Interaction more info	PubMed
gastrulation with mouth forming second	IMP Inferred from Mutant Phenotype more info	PubMed
hair follicle development	IGI Inferred from Genetic Interaction more info	PubMed
head development	IGI Inferred from Genetic Interaction more info	PubMed
histone H3-K4 acetylation	IMP Inferred from Mutant Phenotype more info
multicellular organismal development	IEA Inferred from Electronic Annotation more info
negative regulation of erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of transcription, DNA-dependent	ISO Inferred from Sequence Orthology more info
positive regulation of cell adhesion	IGI Inferred from Genetic Interaction more info	PubMed
positive regulation of hemoglobin biosynthetic process	IMP Inferred from Mutant Phenotype more info
positive regulation of transcription from RNA polymerase II promoter	IGI Inferred from Genetic Interaction more info	PubMed
positive regulation of transcription from RNA polymerase II promoter	IMP Inferred from Mutant Phenotype more info
positive regulation of transcription from RNA polymerase II promoter	ISO Inferred from Sequence Orthology more info
primitive erythrocyte differentiation	TAS Traceable Author Statement more info
regulation of DNA-dependent transcription, elongation	IMP Inferred from Mutant Phenotype more info
somatic stem cell maintenance	IGI Inferred from Genetic Interaction more info	PubMed
transcription from RNA polymerase II promoter	IDA Inferred from Direct Assay more info	PubMed
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	IMP Inferred from Mutant Phenotype more info

Component	Evidence Code	Pubs
nuclear chromatin	ISO Inferred from Sequence Orthology more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
nucleus	ISO Inferred from Sequence Orthology more info
protein complex	IDA Inferred from Direct Assay more info	PubMed
protein complex	IPI Inferred from Physical Interaction more info	PubMed
transcription factor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM domain-binding protein 1

Names: LIM domain-binding protein 1; LDB-1; mLdb1; CLIM-2; nuclear LIM interactor; LIM domain-binding factor CLIM2; carboxyl-terminal 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)

NM_001113408.1 → NP_001106879.1 LIM domain-binding protein 1 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AF030333, CK790183, U69270

Consensus CDS

CCDS50455.1

UniProtKB/Swiss-Prot

P70662

Related

ENSMUSP00000118546, OTTMUSP00000045212, ENSMUST00000156585, OTTMUST00000084014

Conserved Domains (1) summary

pfam01803
Location:69 – 272
Blast Score: 595

LIM_bind; LIM-domain binding protein
NM_010697.1 → NP_034827.1 LIM domain-binding protein 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) has a different 5'-terminal exon and 5' UTR, compared to variant 1. This variant encodes a protein (isoform 3) that lacks 36 aa at the N-terminus, compared to isoform 1.

Source sequence(s)

U69270

Consensus CDS

CCDS29870.1

UniProtKB/Swiss-Prot

P70662

Related

ENSMUSP00000053680, OTTMUSP00000045210, ENSMUST00000056931, OTTMUST00000084010

Conserved Domains (1) summary

pfam01803
Location:33 – 236
Blast Score: 591

LIM_bind; LIM-domain binding protein

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 103

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

Reference GRCm38.p1 C57BL/6J

Genomic

NC_000085.6 Reference GRCm38.p1 C57BL/6J

Range

46032594..46045211, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Mm_Celera

Genomic

AC_000041.1 Alternate Mm_Celera

Range

46795488..46808103, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein	Strain
Heading	Accession and Version	Protein	Strain
genomic	AAHY01143962.1 (3759..16374)	None
genomic	AC108484.25 (69412..76443)	None	129/Sv
genomic	AC140233.3 (59815..66842)	None
genomic	AF024524.1	AAC40064.1	129/Sv
genomic	CH466534.1	EDL41974.1	mixed
mRNA	AB221569.1	None
mRNA	AB250383.1	BAE95401.1
mRNA	AF030333.1	AAB94131.1
mRNA	AK048463.1	None	C57BL/6J
mRNA	AK193238.1	None
mRNA	AK210031.1	None
mRNA	BC013624.1	AAH13624.1	FVB/N
mRNA	CK790183.1	None
mRNA	U69270.1	AAC52887.1
mRNA	U70375.1	AAC52933.1	Swiss Webster
mRNA	U89488.1	AAB96885.1