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

Gene ID: 24131, updated on 16-Oct-2021

Summary

Official Symbol
Ldb3provided by MGI
Official Full Name
LIM domain binding 3provided by MGI
Primary source
MGI:MGI:1344412
See related
Ensembl:ENSMUSG00000021798
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; AW742271
Expression
Biased expression in heart adult (RPKM 122.1), mammary gland adult (RPKM 32.6) and 6 other tissues See more
Orthologs
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Genomic context

See Ldb3 in Genome Data Viewer
Location:
14; 14 B
Exon count:
19
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 14 NC_000080.5 (35339885..35401867, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene bone morphogenetic protein receptor, type 1A Neighboring gene RIKEN cDNA 9230112D13 gene Neighboring gene opsin 4 (melanopsin) 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)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC118603

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables cytoskeletal protein 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
PubMed 
enables muscle alpha-actinin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables muscle alpha-actinin binding IPI
Inferred from Physical Interaction
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
PubMed 
involved_in heart development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in muscle structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoskeleton ISO
Inferred from Sequence Orthology
more info
 
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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/Swiss-Prot
    Q9JKS4
    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
    Q9JKS4
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    Q9JKS4
    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)
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