Free for academic non-profit institutions. Other users need a Commercial license

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 1 3 5

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. Among its related pathways are Surfactant metabolism and Transport to the Golgi and subsequent modification. GO annotations related to this gene include transcription corepressor activity. An important paralog of this gene is PRICKLE2.

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

Enhancers for LMCD1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LMCD1 on UCSC Golden Path with GeneCards custom track

Promoters for LMCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LMCD1 on UCSC Golden Path with GeneCards custom track

Genomic Location for LMCD1 Gene

Chromosome:
3
Start:
8,501,707 bp from pter
End:
8,574,673 bp from pter
Size:
72,967 bases
Orientation:
Plus strand

Genomic View for LMCD1 Gene

Genes around LMCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 & Families for LMCD1 Gene

Gene Families 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 :
  • The LIM zinc-binding domains and the Cys-rich region mediate interaction with GATA6.
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

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 --
genes like me logo Genes that share ontologies with LMCD1: view
genes like me logo Genes that share phenotypes with LMCD1: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
nucleus 5
extracellular 4
cytosol 3
plasma membrane 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for LMCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with LMCD1: view

Pathways & Interactions for LMCD1 Gene

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

Pathways by source for LMCD1 Gene

2 Reactome pathways for LMCD1 Gene

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: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 SIGNOR curated interactions for LMCD1 Gene

Drugs & Compounds for LMCD1 Gene

No Compound Related Data Available

Transcripts for LMCD1 Gene

Unigene Clusters for LMCD1 Gene

LIM and cysteine-rich domains 1:
Representative Sequences:

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 (x7.1) and Artery - Aorta (x7.0).

Protein differential expression in normal tissues from HIPED for LMCD1 Gene

This gene is overexpressed in Spleen (13.0), Urinary Bladder (7.3), Uterus (6.6), and Bone marrow stromal cell (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with LMCD1: view

Protein tissue co-expression partners for LMCD1 Gene

- Elite partner

Primer 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
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
chimpanzee
(Pan troglodytes)
Mammalia LMCD1 35
  • 99.18 (n)
  • 99.45 (a)
LMCD1 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lmcd1 35
  • 87.03 (n)
  • 93.15 (a)
oppossum
(Monodelphis domestica)
Mammalia LMCD1 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMCD1 36
  • 82 (a)
OneToOne
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)
zgc56533 35
lmcd1 36
  • 55 (a)
OneToOne
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

(5) 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
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
rs355075 -- 8,542,003(-) aaaaa(A/G)GCTCC 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

Variation tolerance for LMCD1 Gene

Residual Variation Intolerance Score: 87.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.78; 47.25% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for LMCD1 Gene

Disorders for LMCD1 Gene

Relevant External Links for LMCD1

Genetic Association Database (GAD)
LMCD1
Human Genome Epidemiology (HuGE) Navigator
LMCD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LMCD1

No disorders were found for LMCD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LMCD1 Gene

Publications for LMCD1 Gene

  1. 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 67
  2. 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 23
  3. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. (PMID: 26638075) Gupta G.D. … Pelletier L. (Cell 2015) 3
  4. The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1 protein. (PMID: 23940030) Teixeira F.R. … Gomes M.D. (J. Biol. Chem. 2013) 3
  5. Somatic LMCD1 mutations promoted cell migration and tumor metastasis in hepatocellular carcinoma. (PMID: 21996735) Chang C.Y. … Jou Y.S. (Oncogene 2012) 3

Products for LMCD1 Gene

Sources for LMCD1 Gene

Content