Format

Send to:

Choose Destination

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

Gene ID: 11155, updated on 1-Jun-2020

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
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

Genomic context

See LDB3 in Genome Data Viewer
Location:
10q23.2
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (86666788..86736072)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88426542..88495829)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L7a pseudogene 8 Neighboring gene uncharacterized LOC105378409 Neighboring gene VISTA enhancer hs2143 Neighboring gene opsin 4 Neighboring gene bone morphogenetic protein receptor type 1A 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

Homology

Clone Names

  • FLJ35865, KIAA0613, KIAA01613

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoskeletal protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
muscle alpha-actinin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase C binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heart development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
muscle structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sarcomere organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Z disc IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Z disc IDA
Inferred from Direct Assay
more info
PubMed 
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
pseudopodium IEA
Inferred from Electronic Annotation
more info
 
stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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/Swiss-Prot
    O75112
    Related
    ENSP00000263066.6, ENST00000263066.10
    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/Swiss-Prot
    O75112
    UniProtKB/TrEMBL
    A0A0S2Z501
    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/Swiss-Prot
    O75112
    UniProtKB/TrEMBL
    A0A0S2Z530
    Related
    ENSP00000361136.3, ENST00000372066.7
    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:148238
    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/Swiss-Prot
    O75112
    Related
    ENSP00000401437.2, ENST00000429277.6
    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
  7. NM_001368064.1NP_001354993.1  LIM domain-binding protein 3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC067750
  8. NM_001368065.1NP_001354994.1  LIM domain-binding protein 3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC067750
  9. NM_001368066.1NP_001354995.1  LIM domain-binding protein 3 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC067750
  10. NM_001368067.1NP_001354996.1  LIM domain-binding protein 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC067750
  11. NM_001368068.1NP_001354997.1  LIM domain-binding protein 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC067750
  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
    O75112
    Related
    ENSP00000355296.3, ENST00000361373.8
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

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