Ldb3 LIM domain binding 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ldb3provided by MGI
Official Full Name: LIM domain binding 3provided by MGI
Primary source: MGI:MGI:1344412
See related: Ensembl:ENSMUSG00000021798 AllianceGenome:MGI:1344412
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: ZASP; PDLIM6
Summary: Enables muscle alpha-actinin binding activity and protein kinase C binding activity. Acts upstream of or within sarcomere organization. Located in Z disc. Is expressed in several structures, including central nervous system; heart; lower urinary tract; musculature; and sensory organ. Used to study congenital myopathy; dilated cardiomyopathy 1C; and myofibrillar myopathy 1. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1C; distal myopathy; and myofibrillar myopathy 4. Orthologous to human LDB3 (LIM domain binding 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in heart adult (RPKM 122.1), mammary gland adult (RPKM 32.6) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 14 B; 14 20.83 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	14	NC_000080.7 (34248656..34312276, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	14	NC_000080.6 (34526699..34590314, complement)

Chromosome 14 - NC_000080.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Myopathy associated LDB3 mutation causes Z-disc disassembly and protein aggregation through PKCalpha and TSC2-mTOR downregulation.
Title: Myopathy associated LDB3 mutation causes Z-disc disassembly and protein aggregation through PKCα and TSC2-mTOR downregulation.
Downregulation of Cypher induces apoptosis in cardiomyocytes via Akt/p38 MAPK signaling pathway.
Title: Downregulation of Cypher induces apoptosis in cardiomyocytes via Akt/p38 MAPK signaling pathway.
beta-adrenergic regulation of CaV1.2 channels is significantly reduced in myocytes from LCyphKO mice.
Title: The AKAP Cypher/Zasp contributes to β-adrenergic/PKA stimulation of cardiac Ca(V)1.2 calcium channels.
Cypher and ENH redundantly play an essential role in sustaining Z-line structure from the earliest stages of cardiac function, and are redundantly required to maintain normal embryonic heart function and embryonic viability.
Title: Cypher and Enigma homolog protein are essential for cardiac development and embryonic survival.
results show that MFM-associated ZASP mutations in the actin-binding domain have deleterious effects on the core structure of the Z-discs in skeletal muscle.
Title: Z-disc-associated, alternatively spliced, PDZ motif-containing protein (ZASP) mutations in the actin-binding domain cause disruption of skeletal muscle actin filaments in myofibrillar myopathy.
Results indicte that Cypher/ZASP interacted with the regulatory subunit RIIalpha of PKA.
Title: Cypher/ZASP is a novel A-kinase anchoring protein.
Data demonstrated that the Z-disk proteins, ZASP, titin and vinculin preferentially bind to alpha-actinin-2.
Title: Deficiency of α-actinin-3 is associated with increased susceptibility to contraction-induced damage and skeletal muscle remodeling.
Deletion of long but not short Cypher isoforms leads to late-onset dilated cardiomyopathy.
Title: Selective deletion of long but not short Cypher isoforms leads to late-onset dilated cardiomyopathy.
mutations of a structural/cytoskeletal protein, such as ZASP, lead to cardiac functional and electric abnormalities.
Title: A ZASP missense mutation, S196L, leads to cytoskeletal and electrical abnormalities in a mouse model of cardiomyopathy.
Cypher plays a pivotal role in adult cardiac structure and function through protein-protein interactions with other Z-line proteins.
Title: Cardiac-specific ablation of Cypher leads to a severe form of dilated cardiomyopathy with premature death.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

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

Endonuclease-mediated (3)
Targeted (9) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

LDB3 (e-PCR)
- UniSTS:511832

AW742271 (e-PCR)
- UniSTS:209016

Ldb3 (e-PCR), detects polymorphism
- UniSTS:256950

Ldb3 (e-PCR), detects polymorphism
- UniSTS:256951

Ldb3 (e-PCR), detects polymorphism
- UniSTS:256952

Ldb3 (e-PCR), detects polymorphism
- UniSTS:515316

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cytoskeletal protein binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables muscle alpha-actinin binding	IBA Inferred from Biological aspect of Ancestor more info
enables muscle alpha-actinin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase C binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sarcomere organization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in pseudopodium	IEA Inferred from Electronic Annotation more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: LIM domain-binding protein 3

Names: PDZ-LIM domain protein; Z-band alternatively spliced PDZ-motif protein; cypher; oracle protein; protein cypher; protein oracle

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_001039071.2 → NP_001034160.1 LIM domain-binding protein 3 isoform b

See identical proteins and their annotated locations for NP_001034160.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment in the coding region, compared to variant 1. The resulting protein (isoform b) is shorter when compared to isoform a.

Source sequence(s)

AK052333, AK142292, BY704269

Consensus CDS

CCDS26940.1

UniProtKB/Swiss-Prot

Q9JKS4

Related

ENSMUSP00000022328.7, ENSMUST00000022328.14

Conserved Domains (6) summary

cd09362
Location:544 → 595

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:485 → 536

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:603 → 657

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam05687
Location:316 → 377

BES1_N; BES1/BZR1 plant transcription factor, N-terminal

pfam15936
Location:191 → 286

DUF4749; Domain of unknown function (DUF4749)
NM_001039072.2 → NP_001034161.1 LIM domain-binding protein 3 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform c, which is shorter but with the same N- and C-termini, when it is compared to isoform a.

Source sequence(s)

AK052333, AK142292, AK172980, BY704269

Consensus CDS

CCDS36878.1

UniProtKB/TrEMBL

E9PYJ9

Related

ENSMUSP00000066784.7, ENSMUST00000064098.14

Conserved Domains (6) summary

cd09362
Location:562 → 613

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:503 → 554

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:621 → 675

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam05687
Location:334 → 395

BES1_N; BES1/BZR1 plant transcription factor, N-terminal

pfam15936
Location:148 → 242

DUF4749; Domain of unknown function (DUF4749)
NM_001039073.2 → NP_001034162.1 LIM domain-binding protein 3 isoform d

See identical proteins and their annotated locations for NP_001034162.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform d, which is shorter but with the same N- and C-termini, when it is compared to isoform a.

Source sequence(s)

AK052333, AK142292, AK172980, BY704269

Consensus CDS

CCDS88626.1

UniProtKB/Swiss-Prot

Q9JKS4

Related

ENSMUSP00000154758.2, ENSMUST00000228044.2

Conserved Domains (6) summary

cd09362
Location:505 → 556

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09363
Location:564 → 617

LIM3_Enigma_like; The third LIM domain of Enigma-like family

cd09454
Location:446 → 497

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam05687
Location:277 → 338

BES1_N; BES1/BZR1 plant transcription factor, N-terminal

pfam15936
Location:148 → 247

DUF4749; Domain of unknown function (DUF4749)
NM_001039074.2 → NP_001034163.1 LIM domain-binding protein 3 isoform e

See identical proteins and their annotated locations for NP_001034163.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform e, which is shorter but with the same N- and C-termini, when it is compared to isoform a.

Source sequence(s)

AK052333, AK142292, AK172980

Consensus CDS

CCDS36879.1

UniProtKB/Swiss-Prot

Q9JKS4

Related

ENSMUSP00000087494.5, ENSMUST00000090040.12

Conserved Domains (6) summary

cd09362
Location:567 → 618

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:508 → 559

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:626 → 680

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:339 → 489

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:148 → 254

DUF4749; Domain of unknown function (DUF4749)
NM_001039075.2 → NP_001034164.1 LIM domain-binding protein 3 isoform f

See identical proteins and their annotated locations for NP_001034164.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) has multiple differences, including a different 3' segment, in its coding region, compared to variant 1. The resulting protein (isoform f) is shorter and has a distinct C-terminus when it is compared to isoform a.

Source sequence(s)

AK142292, AK172980, BC099596, BG794782, BY704269

Consensus CDS

CCDS88627.1

UniProtKB/Swiss-Prot

Q9JKS4

Related

ENSMUSP00000154119.2, ENSMUST00000227819.2

Conserved Domains (2) summary

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:148 → 254

DUF4749; Domain of unknown function (DUF4749)
NM_001039076.2 → NP_001034165.1 LIM domain-binding protein 3 isoform g

See identical proteins and their annotated locations for NP_001034165.1

Status: VALIDATED

Description

Transcript Variant: This variant (7) lacks several segments and uses a different 3' segment in its coding region, compared to variant 1. The resulting protein (isoform g) is shorter with a distinct C-terminus when it is compared to isoform a.

Source sequence(s)

AK142292, BC099596, BG794782, BY704269

Consensus CDS

CCDS26942.1

UniProtKB/Swiss-Prot

Q9JKS4

Related

ENSMUSP00000022330.8, ENSMUST00000022330.9

Conserved Domains (2) summary

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:191 → 286

DUF4749; Domain of unknown function (DUF4749)
NM_011918.4 → NP_036048.3 LIM domain-binding protein 3 isoform a

See identical proteins and their annotated locations for NP_036048.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest protein (isoform a).

Source sequence(s)

AK052333, AK142292, BY704269

Consensus CDS

CCDS26941.1

UniProtKB/Swiss-Prot

B2RSB0, B7ZNT6, Q6A038, Q811P2, Q811P3, Q811P4, Q811P5, Q9D130, Q9JKS3, Q9JKS4, Q9R0Z1, Q9WVH1, Q9WVH2

Related

ENSMUSP00000022327.6, ENSMUST00000022327.13

Conserved Domains (6) summary

cd09362
Location:606 → 657

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:547 → 598

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:665 → 719

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:378 → 528

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:191 → 293

DUF4749; Domain of unknown function (DUF4749)

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_000080.7 Reference GRCm39 C57BL/6J

Range

34248656..34312276 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017316019.3 → XP_017171508.1 LIM domain-binding protein 3 isoform X1

UniProtKB/Swiss-Prot

B2RSB0, B7ZNT6, Q6A038, Q811P2, Q811P3, Q811P4, Q811P5, Q9D130, Q9JKS3, Q9JKS4, Q9R0Z1, Q9WVH1, Q9WVH2

Conserved Domains (6) summary

cd09362
Location:606 → 657

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:547 → 598

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:665 → 719

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:378 → 528

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:191 → 293

DUF4749; Domain of unknown function (DUF4749)
XM_006519018.5 → XP_006519081.1 LIM domain-binding protein 3 isoform X3

Conserved Domains (6) summary

cd09362
Location:500 → 551

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:441 → 492

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:559 → 613

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:243 → 422

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:148 → 249

DUF4749; Domain of unknown function (DUF4749)
XM_006519017.5 → XP_006519080.1 LIM domain-binding protein 3 isoform X2

See identical proteins and their annotated locations for XP_006519080.1

UniProtKB/Swiss-Prot

Q9JKS4

Conserved Domains (6) summary

cd09362
Location:567 → 618

LIM2_Enigma_like; The second LIM domain of Enigma-like family

cd09454
Location:508 → 559

LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family

cd09460
Location:626 → 680

LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family

PHA03247
Location:339 → 489

PHA03247; large tegument protein UL36; Provisional

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:148 → 254

DUF4749; Domain of unknown function (DUF4749)
XM_006519019.5 → XP_006519082.1 LIM domain-binding protein 3 isoform X4

See identical proteins and their annotated locations for XP_006519082.1

Conserved Domains (2) summary

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:148 → 249

DUF4749; Domain of unknown function (DUF4749)