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

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 branchial arch; eye; genitourinary system; limb; and nervous system. 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: human all
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Genomic context

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_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CLP36 promotes p53 deficient sarcoma progression through suppression of atrophin-1 interacting protein-4 (AIP-4)-dependent degradation of YAP1.
Title: CLP36 promotes p53 deficient sarcoma progression through suppression of atrophin-1 interacting protein-4 (AIP-4)-dependent degradation of YAP1.
Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
Title: Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
Animals lacking both Ldb1 and Ldb2 uncover the requirement for Ldb2 during corticospinal motor neuron differentiation
Title: Compensatory Actions of Ldb Adaptor Proteins During Corticospinal Motor Neuron Differentiation.
Results show that CLP36 is accumulated in Atg7-deficient cardiomyocytes, and suggest that autophagy may protect cardiomyocytes from the ischemia-reperfusion injury through the clearance of CLP36.
Title: Autophagy protects cardiomyocytes from the myocardial ischaemia-reperfusion injury through the clearance of CLP36.
An intricate regulatory network exists that is mediated by Ldb1 and Ldb2, and promotes retinal progenitor cells proliferation and multipotency; it also controls specification of mammalian retina cells.
Title: The stage-dependent roles of Ldb1 and functional redundancy with Ldb2 in mammalian retinogenesis.
CLIM interacts with estrogen receptor alpha at the H19 locus, potentially explaining the higher expression of H19 in female than male corneas.
Title: Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function.
In Ldlr(-/-)Apob(100/100) mice, loss of Ldb2 increased atherosclerotic lesion size approximately 2-fold and decreased plaque stability.
Title: Lim domain binding 2: a key driver of transendothelial migration of leukocytes and atherosclerosis.
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 show an inhibitory function of CLP-36 in GPVI immunoreceptor tyrosine-based activation motif signaling and as a key regulator of arterial thrombosis.
Title: CLP36 is a negative regulator of glycoprotein VI signaling in platelets.
The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the atherosclerosis-module.
Title: Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI035351 (e-PCR)
- UniSTS:165396

D5Mit232 (e-PCR), detects polymorphism
- UniSTS:130366

RH125308 (e-PCR)
- UniSTS:162130

D5Mit391 (e-PCR), detects polymorphism
- UniSTS:130542

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

Process	Evidence Code	Pubs
acts_upstream_of cellular component biogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within epithelial structure maintenance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hair follicle development	IGI Inferred from Genetic Interaction 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
acts_upstream_of_or_within positive regulation of cellular component biogenesis	IGI Inferred from Genetic Interaction 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
involved_in regulation of cell migration	IMP Inferred from Mutant Phenotype 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

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

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Preferred Names: LIM domain-binding protein 2

Names: LIM domain-binding factor CLIM1; carboxyl-terminal LIM domain-binding protein 1

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_001077398.2 → NP_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:31 → 232

LIM_bind; LIM-domain binding protein
NM_001286348.1 → NP_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:31 → 232

LIM_bind; LIM-domain binding protein
NM_001347349.1 → NP_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:31 → 232

LIM_bind; LIM-domain binding protein

pfam17916
Location:296 → 324

LID; LIM interaction domain (LID)
NM_001359070.1 → NP_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:31 → 232

LIM_bind; LIM-domain binding protein

pfam17916
Location:295 → 323

LID; LIM interaction domain (LID)
NM_001359071.1 → NP_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:31 → 232

LIM_bind; LIM-domain binding protein
NM_010698.4 → NP_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:31 → 232

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

NC_000071.7 Reference GRCm39 C57BL/6J

Range

44593292..44957466 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_036164830.1 → XP_036020723.1 LIM domain-binding protein 2 isoform X11

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_017320689.3 → XP_017176178.1 LIM domain-binding protein 2 isoform X9

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_036164827.1 → XP_036020720.1 LIM domain-binding protein 2 isoform X5

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_030254170.2 → XP_030110030.1 LIM domain-binding protein 2 isoform X6

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_036164825.1 → XP_036020718.1 LIM domain-binding protein 2 isoform X3

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_030254171.2 → XP_030110031.1 LIM domain-binding protein 2 isoform X8

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_006503752.4 → XP_006503815.1 LIM domain-binding protein 2 isoform X1

Conserved Domains (2) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein

pfam17916
Location:297 → 325

LID; LIM interaction domain (LID)
XM_006503758.5 → XP_006503821.1 LIM domain-binding protein 2 isoform X7

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_036164826.1 → XP_036020719.1 LIM domain-binding protein 2 isoform X4

Conserved Domains (1) summary

pfam01803
Location:31 → 232

LIM_bind; LIM-domain binding protein
XM_006503754.5 → XP_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:31 → 232

LIM_bind; LIM-domain binding protein