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Aliases for LMCD1 Gene

Aliases for LMCD1 Gene

  • LIM And Cysteine-Rich Domains 1 2 3
  • Dyxin 2 3 4
  • LIM And Cysteine-Rich Domains Protein 1 3

External Ids for LMCD1 Gene

Previous GeneCards Identifiers for LMCD1 Gene

  • GC03P008472

Summaries for LMCD1 Gene

Entrez Gene Summary for LMCD1 Gene

  • This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

GeneCards Summary for LMCD1 Gene

LMCD1 (LIM And Cysteine-Rich Domains 1) is a Protein Coding gene. GO annotations related to this gene include transcription corepressor activity. An important paralog of this gene is PRICKLE3.

UniProtKB/Swiss-Prot for LMCD1 Gene

  • Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMCD1 Gene

Genomics for LMCD1 Gene

Regulatory Elements for LMCD1 Gene

Genomic Location for LMCD1 Gene

Start:
8,501,707 bp from pter
End:
8,568,125 bp from pter
Size:
66,419 bases
Orientation:
Plus strand

Genomic View for LMCD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LMCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMCD1 Gene

Proteins for LMCD1 Gene

  • Protein details for LMCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZU5-LMCD1_HUMAN
    Recommended name:
    LIM and cysteine-rich domains protein 1
    Protein Accession:
    Q9NZU5
    Secondary Accessions:
    • B4DG80

    Protein attributes for LMCD1 Gene

    Size:
    365 amino acids
    Molecular mass:
    40833 Da
    Quaternary structure:
    • Interacts with GATA1 and GATA4 (By similarity). Interacts with beta-dystroglycan. Interacts with GATA6.

    Alternative splice isoforms for LMCD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMCD1 Gene

Proteomics data for LMCD1 Gene at MOPED

Post-translational modifications for LMCD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LMCD1 Gene

Domains for LMCD1 Gene

Protein Domains for LMCD1 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9NZU5

UniProtKB/Swiss-Prot:

LMCD1_HUMAN :
  • Q9NZU5
Domain:
  • The LIM zinc-binding domains and the Cys-rich region mediate interaction with GATA6.
  • Contains 2 LIM zinc-binding domains.
  • Contains 1 PET domain.
genes like me logo Genes that share domains with LMCD1: view

No data available for Gene Families for LMCD1 Gene

Function for LMCD1 Gene

Molecular function for LMCD1 Gene

GENATLAS Biochemistry: LIM and cysteine-rich domains 1
UniProtKB/Swiss-Prot Function: Transcriptional cofactor that restricts GATA6 function by inhibiting DNA-binding, resulting in repression of GATA6 transcriptional activation of downstream target genes. Represses GATA6-mediated trans activation of lung- and cardiac tissue-specific promoters. Inhibits DNA-binding by GATA4 and GATA1 to the cTNC promoter (By similarity). Plays a critical role in the development of cardiac hypertrophy via activation of calcineurin/nuclear factor of activated T-cells signaling pathway.

Gene Ontology (GO) - Molecular Function for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with LMCD1: view

Phenotypes for LMCD1 Gene

GenomeRNAi human phenotypes for LMCD1:
genes like me logo Genes that share phenotypes with LMCD1: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LMCD1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for LMCD1 Gene

Localization for LMCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMCD1 Gene

Cytoplasm. Nucleus. Note=May shuttle between the cytoplasm and the nucleus. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LMCD1 Gene COMPARTMENTS Subcellular localization image for LMCD1 gene
Compartment Confidence
extracellular 4
cytosol 3
nucleus 3
cytoskeleton 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 20551380
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IEA --
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
genes like me logo Genes that share ontologies with LMCD1: view

Pathways for LMCD1 Gene

SuperPathways for LMCD1 Gene

No Data Available

Interacting Proteins for LMCD1 Gene

Gene Ontology (GO) - Biological Process for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006351 transcription, DNA-templated IEA --
GO:0010611 regulation of cardiac muscle hypertrophy IMP 20026769
GO:0070886 positive regulation of calcineurin-NFAT signaling cascade IMP 20026769
genes like me logo Genes that share ontologies with LMCD1: view

No data available for Pathways by source for LMCD1 Gene

Transcripts for LMCD1 Gene

Unigene Clusters for LMCD1 Gene

LIM and cysteine-rich domains 1:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LMCD1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LMCD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8
SP1: - - -
SP2:
SP3: -
SP4: - - -
SP5:

Relevant External Links for LMCD1 Gene

GeneLoc Exon Structure for
LMCD1
ECgene alternative splicing isoforms for
LMCD1

Expression for LMCD1 Gene

mRNA expression in normal human tissues for LMCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMCD1 Gene

This gene is overexpressed in Muscle - Skeletal (7.1) and Artery - Aorta (7.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for LMCD1 Gene

SOURCE GeneReport for Unigene cluster for LMCD1 Gene Hs.475353

mRNA Expression by UniProt/SwissProt for LMCD1 Gene

Q9NZU5-LMCD1_HUMAN
Tissue specificity: Expressed in the heart (at protein level). Expressed in many tissues with highest abundance in skeletal muscle.
genes like me logo Genes that share expressions with LMCD1: view

In Situ Assay Products

Orthologs for LMCD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LMCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LMCD1 35
  • 99.18 (n)
  • 99.45 (a)
LMCD1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LMCD1 35
  • 90.82 (n)
  • 94.21 (a)
LMCD1 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LMCD1 35
  • 91.64 (n)
  • 93.94 (a)
LMCD1 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lmcd1 35
  • 87.31 (n)
  • 92.88 (a)
Lmcd1 16
Lmcd1 36
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LMCD1 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMCD1 36
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lmcd1 35
  • 87.03 (n)
  • 93.15 (a)
chicken
(Gallus gallus)
Aves LMCD1 35
  • 73.28 (n)
  • 72.35 (a)
LMCD1 36
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LMCD1 36
  • 68 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii lmcd1 35
  • 60.43 (n)
  • 57.36 (a)
lmcd1 36
  • 55 (a)
OneToOne
zgc56533 35
fruit fly
(Drosophila melanogaster)
Insecta Tes 36
  • 13 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tes-1 36
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 26 (a)
OneToMany
Species with no ortholog for LMCD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for LMCD1 Gene

ENSEMBL:
Gene Tree for LMCD1 (if available)
TreeFam:
Gene Tree for LMCD1 (if available)

Paralogs for LMCD1 Gene

Paralogs for LMCD1 Gene

Selected SIMAP similar genes for LMCD1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with LMCD1: view

Variants for LMCD1 Gene

Sequence variations from dbSNP and Humsavar for LMCD1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs8363 -- 8,565,621(+) GTCTG(C/T)GGCCC reference, missense
rs11314 -- 8,567,620(+) AGCCA(G/T)AATCC utr-variant-3-prime
rs165177 -- 8,561,557(-) CCGGC(A/G)TCAGT intron-variant
rs165178 -- 8,558,038(-) GCCCT(C/G)AGCTG intron-variant
rs171408 -- 8,567,234(-) TCAGA(C/T)GGAAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LMCD1 Gene

Variant ID Type Subtype PubMed ID
esv1238714 CNV Insertion 17803354
nsv519789 CNV Loss 19592680
esv2724875 CNV Deletion 23290073
esv259668 OTHER Complex 20981092
esv259915 OTHER Complex 20981092
nsv820839 CNV Duplication 20802225
nsv821979 CNV Loss 20364138
nsv821980 CNV Loss 20364138

Relevant External Links for LMCD1 Gene

HapMap Linkage Disequilibrium report
LMCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMCD1 Gene

Disorders for LMCD1 Gene

Relevant External Links for LMCD1

Genetic Association Database (GAD)
LMCD1
Human Genome Epidemiology (HuGE) Navigator
LMCD1
genes like me logo Genes that share disorders with LMCD1: view

No data available for UniProtKB/Swiss-Prot for LMCD1 Gene

Publications for LMCD1 Gene

  1. LMCD1/Dyxin is a novel transcriptional cofactor that restricts GATA6 function by inhibiting DNA binding. (PMID: 16199866) Rath N. … Morrisey E.E. (Mol. Cell. Biol. 2005) 3 4 23
  2. Identification of a novel LIM domain gene, LMCD1, and chromosomal localization in human and mouse. (PMID: 10662546) Bespalova I.N. … Burmeister M. (Genomics 2000) 2 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 48
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for LMCD1 Gene

Sources for LMCD1 Gene

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