Human Gene LDB3 (ENST00000361373.9_9) from GENCODE V47lift37
  Description: LIM domain binding 3, transcript variant 1 (from RefSeq NM_007078.3)
Gencode Transcript: ENST00000361373.9_9
Gencode Gene: ENSG00000122367.21_18
Transcript (Including UTRs)
   Position: hg19 chr10:88,428,268-88,495,829 Size: 67,562 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr10:88,428,449-88,492,733 Size: 64,285 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:88,428,268-88,495,829)mRNA (may differ from genome)Protein (727 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: LDB3_HUMAN
DESCRIPTION: RecName: Full=LIM domain-binding protein 3; AltName: Full=Protein cypher; AltName: Full=Z-band alternatively spliced PDZ-motif protein;
FUNCTION: May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.
SUBUNIT: Interacts via its LIM domains with various PKC isoforms (By similarity). Interacts via its PDZ domain with the ACTN2 C- terminal region. Interacts with MYOZ1, MYOZ2 and MYOZ3.
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region. Cell projection, pseudopodium. Cytoplasm, cytoskeleton. Cytoplasm, myofibril, sarcomere, Z line. Note=Localized to the cytoplasm around nuclei and pseudopodia of undifferentiated cells and detected throughout the myotubes of differentiated cells. Colocalizes with ACTN2 at the Z-lines.
TISSUE SPECIFICITY: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain and placenta.
DISEASE: Defects in LDB3 are the cause of cardiomyopathy dilated type 1C (CMD1C) [MIM:601493]. Dilated cardiomyopathy is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death.
DISEASE: Defects in LDB3 are the cause of left ventricular non- compaction type 3 (LVNC3) [MIM:601493]. Left ventricular non- compaction is characterized by numerous prominent trabeculations and deep intertrabecular recesses in hypertrophied and hypokinetic segments of the left ventricle.
DISEASE: Defects in LDB3 are the cause of myopathy myofibrillar type 4 (MFM4) [MIM:609452]. A neuromuscular disorder characterized by distal and proximal muscle weakness with signs of cardiomyopathy and neuropathy.
SIMILARITY: Contains 3 LIM zinc-binding domains.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SEQUENCE CAUTION: Sequence=BAA31588.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LDB3";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LDB3
Diseases sorted by gene-association score: myopathy, myofibrillar, 4* (1376), cardiomyopathy, dilated, 1c, with or without lvnc* (1200), ldb3-related dilated cardiomyopathy* (500), dilated cardiomyopathy 1c* (400), late-onset distal myopathy, markesbery-griggs type* (400), myofibrillar myopathy* (310), familial isolated arrhythmogenic ventricular dysplasia, right dominant form* (132), familial isolated arrhythmogenic ventricular dysplasia, biventricular form* (132), familial isolated arrhythmogenic ventricular dysplasia, left dominant form* (132), dilated cardiomyopathy* (122), left ventricular noncompaction 3, with or without dilated cardiomyopathy* (100), familial isolated dilated cardiomyopathy* (59), left ventricular noncompaction* (53), muscular dystrophy, limb-girdle, type 2j (12), cardiomyopathy (12), coronary aneurysm (11), heart aneurysm (11), barth syndrome (10), dilated cardiomyopathy 1b (9), myopathy, myofibrillar, 2 (9), myopathy (8), cardiomyopathy, dilated, 1a (7), myopathy, myofibrillar, 1 (7), cardiomyopathy, dilated, 1d (6), myopathy, myofibrillar, 3 (6), muscular dystrophy, congenital, 1b (6), myopathy, spheroid body (5), anterior horn cell disease (5), arrhythmogenic right ventricular cardiomyopathy (2), inclusion body myositis (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 268.78 RPKM in Heart - Left Ventricle
Total median expression: 841.45 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.6083-0.333 Picture PostScript Text
3' UTR -986.033096-0.318 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001478 - PDZ
IPR006643 - ZASP
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain
PF00595 - PDZ domain
PF15936 - Domain of unknown function (DUF4749)

SCOP Domains:
50156 - PDZ domain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1RGW - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O75112
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005080 protein kinase C binding
GO:0005515 protein binding
GO:0008092 cytoskeletal protein binding
GO:0046872 metal ion binding
GO:0051371 muscle alpha-actinin binding

Biological Process:
GO:0045214 sarcomere organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0030018 Z disc
GO:0031143 pseudopodium
GO:0042995 cell projection
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK294696 - Homo sapiens cDNA FLJ53288 complete cds, moderately similar to LIM domain-binding protein 3.
AK304760 - Homo sapiens cDNA FLJ61577 complete cds, highly similar to LIM domain-binding protein 3.
AB014513 - Homo sapiens KIAA0613 mRNA for KIAA0613 protein.
BC111457 - Synthetic construct Homo sapiens clone IMAGE:40080656, MGC:133444 LDB3 protein (LDB3) mRNA, encodes complete protein.
AB383921 - Synthetic construct DNA, clone: pF1KSDA0613, Homo sapiens LDB3 gene for LIM domain-binding protein 3, complete cds, without stop codon, in Flexi system.
KF772970 - Homo sapiens LIM domain binding 3 transcript variant 8 (LDB3) mRNA, complete cds.
AJ133767 - Homo sapiens mRNA for ZASP protein, partial, varient 3.
AJ133768 - Homo sapiens mRNA for ZASP protein, partial, varient 2.
AK300692 - Homo sapiens cDNA FLJ53661 complete cds, highly similar to Mus musculus LIM domain binding 3 (Ldb3), transcript variant 6, mRNA.
AK297871 - Homo sapiens cDNA FLJ52572 complete cds, highly similar to LIM domain-binding protein 3.
AJ133766 - Homo sapiens mRNA for ZASP protein, partial.
BC010929 - Homo sapiens LIM domain binding 3, mRNA (cDNA clone IMAGE:4291498), complete cds.
KJ898368 - Synthetic construct Homo sapiens clone ccsbBroadEn_07762 LDB3 gene, encodes complete protein.
KR710344 - Synthetic construct Homo sapiens clone CCSBHm_00011603 LDB3 (LDB3) mRNA, encodes complete protein.
KR710345 - Synthetic construct Homo sapiens clone CCSBHm_00011604 LDB3 (LDB3) mRNA, encodes complete protein.
KR710346 - Synthetic construct Homo sapiens clone CCSBHm_00011605 LDB3 (LDB3) mRNA, encodes complete protein.
KR710347 - Synthetic construct Homo sapiens clone CCSBHm_00011607 LDB3 (LDB3) mRNA, encodes complete protein.
KU178543 - Homo sapiens LIM domain binding 3 isoform 1 (LDB3) mRNA, partial cds.
KU178544 - Homo sapiens LIM domain binding 3 isoform 2 (LDB3) mRNA, partial cds.
KU178545 - Homo sapiens LIM domain binding 3 isoform 3 (LDB3) mRNA, complete cds, alternatively spliced.
AF276807 - Homo sapiens Z-band alternatively spliced PDZ-motif protein ZASP-4 mRNA, complete cds.
AF276808 - Homo sapiens Z-band alternatively spliced PDZ-motif protein ZASP-5 mRNA, complete cds.
AF276809 - Homo sapiens Z-band alternatively spliced PDZ-motif protein ZASP-6 mRNA, complete cds.
AF086263 - Homo sapiens full length insert cDNA clone ZD42E10.
AK093184 - Homo sapiens cDNA FLJ35865 fis, clone TESTI2007692.
AX747977 - Sequence 1502 from Patent EP1308459.
JD260421 - Sequence 241445 from Patent EP1572962.
JD214791 - Sequence 195815 from Patent EP1572962.
JD039366 - Sequence 20390 from Patent EP1572962.
JD482863 - Sequence 463887 from Patent EP1572962.
JD045547 - Sequence 26571 from Patent EP1572962.
JD218150 - Sequence 199174 from Patent EP1572962.
JD192943 - Sequence 173967 from Patent EP1572962.
JD548961 - Sequence 529985 from Patent EP1572962.
JD251515 - Sequence 232539 from Patent EP1572962.
JD136799 - Sequence 117823 from Patent EP1572962.
JD241951 - Sequence 222975 from Patent EP1572962.
JD363776 - Sequence 344800 from Patent EP1572962.
JD050383 - Sequence 31407 from Patent EP1572962.
JD056772 - Sequence 37796 from Patent EP1572962.
JD203377 - Sequence 184401 from Patent EP1572962.
JD488311 - Sequence 469335 from Patent EP1572962.
JD488312 - Sequence 469336 from Patent EP1572962.
JD096601 - Sequence 77625 from Patent EP1572962.
JD549168 - Sequence 530192 from Patent EP1572962.
JD279695 - Sequence 260719 from Patent EP1572962.
JD275566 - Sequence 256590 from Patent EP1572962.
JD074625 - Sequence 55649 from Patent EP1572962.
JD163248 - Sequence 144272 from Patent EP1572962.
JD290028 - Sequence 271052 from Patent EP1572962.
JD533439 - Sequence 514463 from Patent EP1572962.
JD337279 - Sequence 318303 from Patent EP1572962.
JD525452 - Sequence 506476 from Patent EP1572962.
JD084665 - Sequence 65689 from Patent EP1572962.
JD411722 - Sequence 392746 from Patent EP1572962.
JD511041 - Sequence 492065 from Patent EP1572962.
JD107812 - Sequence 88836 from Patent EP1572962.
JD376043 - Sequence 357067 from Patent EP1572962.
JD142552 - Sequence 123576 from Patent EP1572962.
JD497749 - Sequence 478773 from Patent EP1572962.
JD542813 - Sequence 523837 from Patent EP1572962.
JD212788 - Sequence 193812 from Patent EP1572962.
JD212789 - Sequence 193813 from Patent EP1572962.
JD198182 - Sequence 179206 from Patent EP1572962.
JD413488 - Sequence 394512 from Patent EP1572962.
JD247080 - Sequence 228104 from Patent EP1572962.
JD247082 - Sequence 228106 from Patent EP1572962.
JD247081 - Sequence 228105 from Patent EP1572962.
JD286030 - Sequence 267054 from Patent EP1572962.
JD429250 - Sequence 410274 from Patent EP1572962.
JD195171 - Sequence 176195 from Patent EP1572962.
JD447125 - Sequence 428149 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2TDB7, A6NIV4, B4E3K3, ENST00000361373.1, ENST00000361373.2, ENST00000361373.3, ENST00000361373.4, ENST00000361373.5, ENST00000361373.6, ENST00000361373.7, ENST00000361373.8, KIAA0613 , LDB3 , LDB3_HUMAN, NM_007078, O75112, Q5K6N9, Q5K6P0, Q5K6P1, Q96FH2, Q9Y4Z3, Q9Y4Z4, Q9Y4Z5, uc318cao.1, uc318cao.2, ZASP
UCSC ID: ENST00000361373.9_9
RefSeq Accession: NM_007078.3
Protein: O75112 (aka LDB3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LDB3:
dcm-ov (Dilated Cardiomyopathy Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.