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

    Gene ID: 24131, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Biased expression in heart adult (RPKM 122.1), mammary gland adult (RPKM 32.6) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Ldb3 in Genome Data Viewer
    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_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_36380 Neighboring gene bone morphogenetic protein receptor, type 1A Neighboring gene RIKEN cDNA 9230112D13 gene Neighboring gene STARR-seq mESC enhancer starr_36382 Neighboring gene STARR-seq mESC enhancer starr_36385 Neighboring gene opsin 4 (melanopsin) Neighboring gene STARR-seq mESC enhancer starr_36389 Neighboring gene predicted gene, 52113

    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 (3) 
    • Targeted (9)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC118603

    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

    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)

    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)

    1. NM_001039071.2NP_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:544595
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:485536
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:603657
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      cd00992
      Location:581
      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:316377
      BES1_N; BES1/BZR1 plant transcription factor, N-terminal
      pfam15936
      Location:191286
      DUF4749; Domain of unknown function (DUF4749)
    2. NM_001039072.2NP_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:562613
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:503554
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:621675
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      cd00992
      Location:581
      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:334395
      BES1_N; BES1/BZR1 plant transcription factor, N-terminal
      pfam15936
      Location:148242
      DUF4749; Domain of unknown function (DUF4749)
    3. NM_001039073.2NP_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:505556
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09363
      Location:564617
      LIM3_Enigma_like; The third LIM domain of Enigma-like family
      cd09454
      Location:446497
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd00992
      Location:581
      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:277338
      BES1_N; BES1/BZR1 plant transcription factor, N-terminal
      pfam15936
      Location:148247
      DUF4749; Domain of unknown function (DUF4749)
    4. NM_001039074.2NP_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:567618
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:508559
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:626680
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      PHA03247
      Location:339489
      PHA03247; large tegument protein UL36; Provisional
      cd00992
      Location:581
      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:148254
      DUF4749; Domain of unknown function (DUF4749)
    5. NM_001039075.2NP_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:581
      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:148254
      DUF4749; Domain of unknown function (DUF4749)
    6. NM_001039076.2NP_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:581
      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:191286
      DUF4749; Domain of unknown function (DUF4749)
    7. NM_011918.4NP_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:606657
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:547598
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:665719
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      PHA03247
      Location:378528
      PHA03247; large tegument protein UL36; Provisional
      cd00992
      Location:581
      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:191293
      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

    1. NC_000080.7 Reference GRCm39 C57BL/6J

      Range
      34248656..34312276 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017316019.3XP_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:606657
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:547598
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:665719
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      PHA03247
      Location:378528
      PHA03247; large tegument protein UL36; Provisional
      cd00992
      Location:581
      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:191293
      DUF4749; Domain of unknown function (DUF4749)
    2. XM_006519018.5XP_006519081.1  LIM domain-binding protein 3 isoform X3

      Conserved Domains (6) summary
      cd09362
      Location:500551
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:441492
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:559613
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      PHA03247
      Location:243422
      PHA03247; large tegument protein UL36; Provisional
      cd00992
      Location:581
      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:148249
      DUF4749; Domain of unknown function (DUF4749)
    3. XM_006519017.5XP_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:567618
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09454
      Location:508559
      LIM1_ZASP_Cypher; The first LIM domain of ZASP/Cypher family
      cd09460
      Location:626680
      LIM3_ZASP_Cypher; The third LIM domain of ZASP/Cypher family
      PHA03247
      Location:339489
      PHA03247; large tegument protein UL36; Provisional
      cd00992
      Location:581
      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:148254
      DUF4749; Domain of unknown function (DUF4749)
    4. XM_006519019.5XP_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:581
      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:148249
      DUF4749; Domain of unknown function (DUF4749)