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Aliases for LIMCH1 Gene

Aliases for LIMCH1 Gene

  • LIM And Calponin Homology Domains 1 2 3 5
  • LIM And Calponin Homology Domains-Containing Protein 1 3
  • KIAA1102 4
  • LIMCH1A 3
  • LMO7B 3

External Ids for LIMCH1 Gene

Previous GeneCards Identifiers for LIMCH1 Gene

  • GC04P041057
  • GC04P040684

Summaries for LIMCH1 Gene

GeneCards Summary for LIMCH1 Gene

LIMCH1 (LIM And Calponin Homology Domains 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include actin binding. An important paralog of this gene is LMO7.

Gene Wiki entry for LIMCH1 Gene

Additional gene information for LIMCH1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMCH1 Gene

Genomics for LIMCH1 Gene

GeneHancer (GH) Regulatory Elements for LIMCH1 Gene

Promoters and enhancers for LIMCH1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J041358 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 666.4 +2.6 2611 7.4 ZSCAN4 SIN3A MZF1 RAD21 RFX5 YY1 ETS1 ZNF335 GLIS2 EGR1 LIMCH1 RPL12P20
GH04J041537 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 664.9 +179.3 179291 2.7 PKNOX1 ESRRA ZNF10 OSR2 ZNF664 PRDM6 SCRT2 KLF9 PRDM10 ZNF600 LIMCH1 LOC105374423 GC04P041460
GH04J041611 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 650.1 +253.3 253265 2.9 SCRT1 ZNF768 CEBPB ZNF384 ZIC2 RAD21 ZNF664 ZNF217 CTBP1 GATA3 LIMCH1 LOC105374423 LOC105374421
GH04J041317 Enhancer 1 ENCODE dbSUPER 23.6 -40.0 -39984 4.1 PKNOX1 FOXA2 SIN3A RAD21 YY1 TCF12 ZSCAN5C ATF7 FOS ELK4 LIMCH1 UCHL1 GC04M041303 ENSG00000207481
GH04J041346 Enhancer 1 ENCODE dbSUPER 20.8 -12.8 -12751 1 PKNOX1 ARNT ZSCAN4 ZNF133 INSM2 FEZF1 GLI4 ZNF2 ZNF121 ZNF416 LIMCH1 SLC30A9 ENSG00000249122 LOC105374426 DCAF4L1 UCHL1 ENSG00000207481 GC04M041303
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIMCH1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIMCH1 gene promoter:
  • E2F
  • c-Ets-1
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Nkx2-5
  • Pax-4a
  • PPAR-gamma1

Genomic Locations for LIMCH1 Gene

Genomic Locations for LIMCH1 Gene
chr4:41,359,607-41,700,044
(GRCh38/hg38)
Size:
340,438 bases
Orientation:
Plus strand
chr4:41,361,624-41,702,061
(GRCh37/hg19)
Size:
340,438 bases
Orientation:
Plus strand

Genomic View for LIMCH1 Gene

Genes around LIMCH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMCH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMCH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMCH1 Gene

Proteins for LIMCH1 Gene

  • Protein details for LIMCH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPQ0-LIMC1_HUMAN
    Recommended name:
    LIM and calponin homology domains-containing protein 1
    Protein Accession:
    Q9UPQ0
    Secondary Accessions:
    • A8MXC3
    • E9PHM7
    • Q503B5
    • Q5CZB1
    • Q5CZB6
    • Q5H9S8
    • Q68E07
    • Q6PJ44
    • Q7Z3G5
    • Q8N3S9
    • Q8N6M2

    Protein attributes for LIMCH1 Gene

    Size:
    1083 amino acids
    Molecular mass:
    121867 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA83054.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for LIMCH1 Gene

neXtProt entry for LIMCH1 Gene

Post-translational modifications for LIMCH1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for LIMCH1
  • Boster Bio Antibodies for LIMCH1

No data available for DME Specific Peptides for LIMCH1 Gene

Domains & Families for LIMCH1 Gene

Gene Families for LIMCH1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for LIMCH1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UPQ0

UniProtKB/Swiss-Prot:

LIMC1_HUMAN :
  • Belongs to the LIMCH1 family.
Family:
  • Belongs to the LIMCH1 family.
genes like me logo Genes that share domains with LIMCH1: view

Function for LIMCH1 Gene

Phenotypes From GWAS Catalog for LIMCH1 Gene

Gene Ontology (GO) - Molecular Function for LIMCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0005515 protein binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMCH1: view
genes like me logo Genes that share phenotypes with LIMCH1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMCH1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LIMCH1 Gene

Localization for LIMCH1 Gene

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 LIMCH1 gene
Compartment Confidence
cytosol 4
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LIMCH1 Gene

Pathways & Interactions for LIMCH1 Gene

SuperPathways for LIMCH1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LIMCH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031032 actomyosin structure organization IEA --
genes like me logo Genes that share ontologies with LIMCH1: view

No data available for Pathways by source and SIGNOR curated interactions for LIMCH1 Gene

Drugs & Compounds for LIMCH1 Gene

No Compound Related Data Available

Transcripts for LIMCH1 Gene

Unigene Clusters for LIMCH1 Gene

LIM and calponin homology domains 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LIMCH1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIMCH1 Gene

No ASD Table

Relevant External Links for LIMCH1 Gene

GeneLoc Exon Structure for
LIMCH1
ECgene alternative splicing isoforms for
LIMCH1

Expression for LIMCH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIMCH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIMCH1 Gene

This gene is overexpressed in Muscle - Skeletal (x4.4).

Protein differential expression in normal tissues from HIPED for LIMCH1 Gene

This gene is overexpressed in Thyroid (16.4), Plasma (7.1), and Fetal Brain (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIMCH1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LIMCH1 Gene:

LIMCH1

SOURCE GeneReport for Unigene cluster for LIMCH1 Gene:

Hs.335163

Evidence on tissue expression from TISSUES for LIMCH1 Gene

  • Nervous system(4.9)
  • Muscle(4.4)
  • Liver(4.2)
  • Spleen(2.4)
  • Heart(2.3)
  • Lung(2.2)
  • Gall bladder(2.1)
  • Eye(2)
genes like me logo Genes that share expression patterns with LIMCH1: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMCH1 Gene

Orthologs for LIMCH1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LIMCH1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIMCH1 34 33
  • 99.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LIMCH1 34 33
  • 90.52 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LIMCH1 34 33
  • 87.32 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Limch1 16 34 33
  • 86.08 (n)
rat
(Rattus norvegicus)
Mammalia Limch1 33
  • 85.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LIMCH1 34
  • 76 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LIMCH1 34
  • 47 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIMCH1 34 33
  • 70.94 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIMCH1 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia limch1 33
  • 63.19 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13843 33
zebrafish
(Danio rerio)
Actinopterygii limch1b 34 33
  • 58.64 (n)
OneToMany
limch1a 34
  • 18 (a)
OneToMany
wufk03g12 33
fruit fly
(Drosophila melanogaster)
Insecta CG43427 34
  • 6 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lim-8 34
  • 10 (a)
OneToMany
Species where no ortholog for LIMCH1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)

Evolution for LIMCH1 Gene

ENSEMBL:
Gene Tree for LIMCH1 (if available)
TreeFam:
Gene Tree for LIMCH1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIMCH1: view image

Paralogs for LIMCH1 Gene

Paralogs for LIMCH1 Gene

(3) SIMAP similar genes for LIMCH1 Gene using alignment to 10 proteins:

  • LIMC1_HUMAN
  • D6R8Y0_HUMAN
  • D6RD46_HUMAN
  • D6RGH8_HUMAN
  • D6RJ93_HUMAN
  • E7EPK0_HUMAN
  • E9PDJ9_HUMAN
  • G5EA03_HUMAN
  • H0Y8P3_HUMAN
  • Q6NVB9_HUMAN
genes like me logo Genes that share paralogs with LIMCH1: view

Variants for LIMCH1 Gene

Sequence variations from dbSNP and Humsavar for LIMCH1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000005109 -- 41,571,370(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000019996 -- 41,526,935(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000023 -- 41,552,486(+) G/A/C genic_upstream_transcript_variant, intron_variant
rs1000024 -- 41,552,449(+) C/G/T genic_upstream_transcript_variant, intron_variant
rs1000028708 -- 41,386,663(+) G/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LIMCH1 Gene

Variant ID Type Subtype PubMed ID
esv1310867 CNV deletion 17803354
esv2002334 CNV deletion 18987734
esv2017028 CNV deletion 18987734
esv2430788 CNV deletion 19546169
esv2482453 CNV deletion 19546169
esv2667299 CNV deletion 23128226
esv2727482 CNV deletion 23290073
esv2727483 CNV deletion 23290073
esv2727484 CNV deletion 23290073
esv2727486 CNV deletion 23290073
esv2727487 CNV deletion 23290073
esv2727488 CNV deletion 23290073
esv27465 CNV loss 19812545
esv275061 CNV loss 21479260
esv275374 CNV loss 21479260
esv3049983 CNV deletion 24192839
esv3112 CNV loss 18987735
esv3333046 CNV insertion 20981092
esv3559600 CNV deletion 23714750
esv3569399 CNV loss 25503493
esv3569400 CNV loss 25503493
esv3600332 CNV loss 21293372
esv3600333 CNV gain 21293372
esv3600335 CNV loss 21293372
nsv1139236 CNV deletion 24896259
nsv1149893 CNV deletion 26484159
nsv290711 CNV deletion 16902084
nsv293326 CNV deletion 16902084
nsv4309 CNV insertion 18451855
nsv441871 CNV loss 18776908
nsv441872 CNV loss 18776908
nsv471807 CNV loss 16327809
nsv476037 CNV novel sequence insertion 20440878
nsv477274 CNV novel sequence insertion 20440878
nsv524341 CNV loss 19592680
nsv829916 CNV loss 17160897

Variation tolerance for LIMCH1 Gene

Residual Variation Intolerance Score: 46.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.13; 96.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIMCH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMCH1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIMCH1 Gene

Disorders for LIMCH1 Gene

Additional Disease Information for LIMCH1

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

No disorders were found for LIMCH1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LIMCH1 Gene

Publications for LIMCH1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. LIMCH1 regulates nonmuscle myosin-II activity and suppresses cell migration. (PMID: 28228547) Lin YH … Pai LM (Molecular biology of the cell 2017) 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. (PMID: 29117863) Choudhury NR … Michlewski G (BMC biology 2017) 3 58

Products for LIMCH1 Gene

Sources for LIMCH1 Gene

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