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    LDB3 LIM domain binding 3 [ Homo sapiens (human) ]

    Gene ID: 11155, updated on 5-Mar-2024

    Summary

    Official Symbol
    LDB3provided by HGNC
    Official Full Name
    LIM domain binding 3provided by HGNC
    Primary source
    HGNC:HGNC:15710
    See related
    Ensembl:ENSG00000122367 MIM:605906; AllianceGenome:HGNC:15710
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MFM4; ZASP; CMD1C; CMH24; CMPD3; LVNC3; CYPHER; LDB3Z1; LDB3Z4; ORACLE; PDLIM6
    Summary
    This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]
    Annotation information
    Note: LDB3 (Gene ID: 11155) and ZASP (Gene ID: 101927655) share the ZASP alias/unofficial symbol in common. [01 Jun 2018]
    Expression
    Biased expression in heart (RPKM 95.5), prostate (RPKM 11.4) and 1 other tissue See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LDB3 in Genome Data Viewer
    Location:
    10q23.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86666788..86736072)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87550947..87620190)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88426545..88495829)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3694 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88409215-88409901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88409902-88410587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88411272-88412121 Neighboring gene ribosomal protein L7a pseudogene 8 Neighboring gene uncharacterized LOC105378409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3695 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:88433149-88433337 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88441665-88442166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88442167-88442666 Neighboring gene VISTA enhancer hs2143 Neighboring gene opsin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88459642-88460142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88460143-88460643 Neighboring gene hESC enhancers GRCh37_chr10:88470545-88471164 and GRCh37_chr10:88471165-88471784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2573 Neighboring gene bone morphogenetic protein receptor type 1A Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:88552774-88553500 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:88597221-88597813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88615649-88616230 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624164-88624816 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624817-88625468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88627361-88627948 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88631460-88632021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3697 Neighboring gene RNA polymerase II associated protein 2 pseudogene 1 Neighboring gene RNA, U1 small nuclear 19, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ35865, KIAA0613, KIAA01613

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cytoskeletal protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase C binding IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    involved_in sarcomere organization IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 and LIM domain 6
    Z-band alternatively spliced PDZ-motif protein
    cardiomyopathy, dilated 1C (autosomal dominant)
    protein cypher

    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.

    Genomic

    1. NG_008876.1 RefSeqGene

      Range
      4886..72505
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_385

    mRNA and Protein(s)

    1. NM_001080114.2NP_001073583.1  LIM domain-binding protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter but with the same N- and C-termini, when it is compared to isoform 1.
      Source sequence(s)
      AB014513, AC067750, AL601484, DA762127
      Consensus CDS
      CCDS41544.1
      UniProtKB/TrEMBL
      B4DGP4
      Related
      ENSP00000401437.3, ENST00000429277.7
      Conserved Domains (6) summary
      cd09362
      Location:500551
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09363
      Location:559612
      LIM3_Enigma_like; The third LIM domain of Enigma-like family
      cd09454
      Location:441492
      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) ...
      pfam15936
      Location:148238
      DUF4749; Domain of unknown function (DUF4749)
      cl26464
      Location:272439
      Atrophin-1; Atrophin-1 family
    2. NM_001080115.2NP_001073584.1  LIM domain-binding protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001073584.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several segments and uses a different 3' segment in its coding region, compared to variant 1. The resulting protein (isoform 3) is shorter with a distinct C-terminus when it is compared to isoform 1. Variants 3 and 7 encode isoform 3.
      Source sequence(s)
      AC067750, AF276807, BC010929, F33274
      Consensus CDS
      CCDS44450.1
      UniProtKB/TrEMBL
      A0A0S2Z501, A0A8I5KX76
      Related
      ENSP00000485389.1, ENST00000623007.3
      Conserved Domains (3) 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:194285
      DUF4749; Domain of unknown function (DUF4749)
      cl25751
      Location:77180
      DUF4045; Domain of unknown function (DUF4045)
    3. NM_001080116.1NP_001073585.1  LIM domain-binding protein 3 isoform 4

      See identical proteins and their annotated locations for NP_001073585.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences, including a different 3' segment, in its coding region, compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct C-terminus when it is compared to isoform 1. Variants 4, 11, and 12 encode isoform 4.
      Source sequence(s)
      AJ133766, BC010929, DA898241, F33274
      Consensus CDS
      CCDS41545.1
      UniProtKB/TrEMBL
      A0A0S2Z530, B4DUL3
      Related
      ENSP00000361136.3, ENST00000372066.8
      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)
    4. NM_001171610.2NP_001165081.1  LIM domain-binding protein 3 isoform 5

      See identical proteins and their annotated locations for NP_001165081.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has multiple differences in the coding region, compared to variant 1. The encoded isoform (5) is longer than isoform 1.
      Source sequence(s)
      AC067750, AK304760
      Consensus CDS
      CCDS53550.1
      UniProtKB/TrEMBL
      B4DGP4
      Related
      ENSP00000485500.1, ENST00000623056.4
      Conserved Domains (8) summary
      smart00735
      Location:189214
      ZM; ZASP-like motif
      cd09362
      Location:615666
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09363
      Location:674727
      LIM3_Enigma_like; The third LIM domain of Enigma-like family
      cd09454
      Location:556607
      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) ...
      pfam15936
      Location:263353
      DUF4749; Domain of unknown function (DUF4749)
      cl25751
      Location:77180
      DUF4045; Domain of unknown function (DUF4045)
      cl26464
      Location:387554
      Atrophin-1; Atrophin-1 family
    5. NM_001171611.2NP_001165082.1  LIM domain-binding protein 3 isoform 6

      See identical proteins and their annotated locations for NP_001165082.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 3' UTR and has multiple differences in the coding region, compared to variant 1. The encoded isoform (6) is shorter and has a distinct C-terminus, compared to isoform (1).
      Source sequence(s)
      AC067750, AF276809
      Consensus CDS
      CCDS53549.1
      UniProtKB/Swiss-Prot
      O75112
      Related
      ENSP00000361126.4, ENST00000372056.8
      Conserved Domains (4) 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:263353
      DUF4749; Domain of unknown function (DUF4749)
      cl25751
      Location:77180
      DUF4045; Domain of unknown function (DUF4045)
      cl25776
      Location:189214
      DUF4749; Domain of unknown function (DUF4749)
    6. NM_001368063.1NP_001354992.1  LIM domain-binding protein 3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS44450.1
      UniProtKB/TrEMBL
      A0A0S2Z501, A0A8I5KX76
    7. NM_001368064.1NP_001354993.1  LIM domain-binding protein 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS91289.1
      UniProtKB/TrEMBL
      B4DGP4, V5T7C5
      Related
      ENSP00000508987.1, ENST00000688001.1
    8. NM_001368065.1NP_001354994.1  LIM domain-binding protein 3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS91289.1
      UniProtKB/TrEMBL
      B4DGP4, V5T7C5
      Related
      ENSP00000510609.1, ENST00000689296.1
    9. NM_001368066.1NP_001354995.1  LIM domain-binding protein 3 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS91290.1
      UniProtKB/TrEMBL
      A0A8I5KV04
      Related
      ENSP00000509539.1, ENST00000693680.1
    10. NM_001368067.1NP_001354996.1  LIM domain-binding protein 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS41545.1
      UniProtKB/TrEMBL
      A0A0S2Z530, B4DUL3
      Related
      ENSP00000263066.7, ENST00000263066.11
      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)
    11. NM_001368068.1NP_001354997.1  LIM domain-binding protein 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC067750
      Consensus CDS
      CCDS41545.1
      UniProtKB/TrEMBL
      A0A0S2Z530, B4DUL3
      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)
    12. NM_007078.3NP_009009.1  LIM domain-binding protein 3 isoform 1

      See identical proteins and their annotated locations for NP_009009.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AB014513, AC067750, BC010929
      Consensus CDS
      CCDS7377.1
      UniProtKB/Swiss-Prot
      A2TDB7, A6NIV4, B4E3K3, O75112, Q5K6N9, Q5K6P0, Q5K6P1, Q96FH2, Q9Y4Z3, Q9Y4Z4, Q9Y4Z5
      UniProtKB/TrEMBL
      B4DGP4
      Related
      ENSP00000355296.3, ENST00000361373.9
      Conserved Domains (6) summary
      cd09362
      Location:610661
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd09363
      Location:669722
      LIM3_Enigma_like; The third LIM domain of Enigma-like family
      cd09454
      Location:551602
      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) ...
      pfam15936
      Location:194285
      DUF4749; Domain of unknown function (DUF4749)
      cl26386
      Location:352550
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      86666788..86736072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      87550947..87620190
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)