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Aliases for LMCD1 Gene

Aliases for LMCD1 Gene

  • LIM And Cysteine Rich Domains 1 2 3 5
  • 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. Among its related pathways are Surfactant metabolism and Metabolism of proteins. GO annotations related to this gene include transcription corepressor activity. An important paralog of this gene is TES.

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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F008456 1.7 FANTOM5 Ensembl ENCODE 13.5 -42.6 -42627 5.8 HDGF CREB3L1 ARID4B SIN3A ZNF2 YY1 SLC30A9 ZNF548 FOS ZNF263 LMCD1-AS1 RAD18 LMCD1 PIR56118 GC03M008478 GC03P008440
GH03F008442 1.3 Ensembl ENCODE 17.2 -57.1 -57135 5.1 PKNOX1 MLX ARID4B SIN3A FEZF1 ZNF2 YY1 FOS SP3 SP5 LMCD1 LMCD1-AS1 GC03P008440 GC03M008478 PIR56118
GH03F008656 1.2 Ensembl ENCODE 10.5 +157.2 157242 5.5 ARID4B FEZF1 SP5 JUNB TBX21 PPARG MEF2D RFX3 GLIS1 ETV4 LMCD1-AS1 LMCD1 CAV3 GC03P008648 PIR52972
GH03F008558 1.1 Ensembl ENCODE 11.4 +58.9 58918 4.1 HDAC1 ATF1 ARNT YBX1 RAD21 ELK1 GATA2 SCRT2 ZNF207 FOS LMCD1-AS1 LMCD1 LINC00312 PIR52959
GH03F008528 1 Ensembl ENCODE 12.2 +27.9 27894 2.8 TFAP4 JUN ARID4B CEBPG BMI1 RAD21 YY1 HNF4G NR2F6 HOMEZ LMCD1-AS1 LMCD1 PIR52959
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00001476279 93 1601 HDGF CREB3L1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF548

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

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

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,IBA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
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

Inhibitory RNA Products

Flow Cytometry 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMCD1 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 3
plasma membrane 2

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 IEA,IBA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
GO:0031012 colocalizes_with extracellular matrix IDA 20551380
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

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:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010611 regulation of cardiac muscle hypertrophy IMP 20026769
GO:0044267 cellular protein metabolic process TAS --
genes like me logo Genes that share ontologies with LMCD1: view

No data available for SIGNOR curated interactions for LMCD1 Gene

Transcripts for LMCD1 Gene

Unigene Clusters for LMCD1 Gene

LIM and cysteine-rich domains 1:
Representative Sequences:

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for LMCD1 Gene



Protein tissue co-expression partners for LMCD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LMCD1 Gene:

LMCD1

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

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 34 35
  • 99.18 (n)
dog
(Canis familiaris)
Mammalia LMCD1 34 35
  • 91.64 (n)
cow
(Bos Taurus)
Mammalia LMCD1 34 35
  • 90.82 (n)
mouse
(Mus musculus)
Mammalia Lmcd1 34 16 35
  • 87.31 (n)
rat
(Rattus norvegicus)
Mammalia Lmcd1 34
  • 87.03 (n)
oppossum
(Monodelphis domestica)
Mammalia LMCD1 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMCD1 35
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves LMCD1 34 35
  • 73.28 (n)
lizard
(Anolis carolinensis)
Reptilia LMCD1 35
  • 68 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii lmcd1 34 35
  • 60.43 (n)
zgc56533 34
fruit fly
(Drosophila melanogaster)
Insecta Tes 35
  • 13 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tes-1 35
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 26 (a)
OneToMany
Species where no ortholog for LMCD1 was found in the sources mined by GeneCards:
  • 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
rs1008003 -- 8,505,306(-) TTGCA(C/T)CCGTT intron-variant
rs10154948 -- 8,517,370(+) atatc(A/G)tatta intron-variant
rs1027327 -- 8,565,153(-) acccc(C/T)acaga intron-variant
rs10510392 -- 8,534,715(+) CCAGA(C/T)TACCA intron-variant
rs111239601 -- 8,502,076(+) AGAAG(A/G)GAACT intron-variant, upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
nsv956829 CNV deletion 24416366
nsv821980 CNV loss 20364138
nsv821979 CNV loss 20364138
nsv820839 CNV duplication 20802225
nsv519789 CNV loss 19592680
nsv1117326 CNV tandem duplication 24896259
nsv1074567 CNV deletion 25765185
nsv1011935 CNV loss 25217958
nsv1011096 CNV loss 25217958
nsv1009343 CNV gain 25217958
esv3423947 CNV duplication 20981092
esv2724875 CNV deletion 23290073
esv1238714 CNV insertion 17803354
dgv4677n100 CNV gain 25217958
dgv2653e59 CNV tandem duplication 20981092
dgv2652e59 CNV duplication 20981092

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)

Relevant External Links for LMCD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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
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. 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 22 64
  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 64
  3. LIM and cysteine-rich domains 1 regulates cardiac hypertrophy by targeting calcineurin/nuclear factor of activated T cells signaling. (PMID: 20026769) Bian Z.Y. … Li H. (Hypertension 2010) 3 4 64
  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 46 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for LMCD1 Gene

Sources for LMCD1 Gene

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