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Aliases for LIMA1 Gene

Aliases for LIMA1 Gene

  • LIM Domain And Actin Binding 1 2 3 5
  • Epithelial Protein Lost In Neoplasm Beta 2 3
  • LIM Domain And Actin-Binding Protein 1 3 4
  • SREBP3 3 4
  • EPLIN 3 4
  • Sterol Regulatory Element Binding Protein 3 3
  • Epithelial Protein Lost In Neoplasm 4
  • 1110021C24Rik 3
  • LDLCQ8 3

External Ids for LIMA1 Gene

Previous GeneCards Identifiers for LIMA1 Gene

  • GC12M048856
  • GC12M050569
  • GC12M047604

Summaries for LIMA1 Gene

Entrez Gene Summary for LIMA1 Gene

  • This gene encodes a cytoskeleton-associated protein that inhibits actin filament depolymerization and cross-links filaments in bundles. It is downregulated in some cancer cell lines. Alternatively spliced transcript variants encoding different isoforms have been described for this gene, and expression of some of the variants maybe independently regulated. [provided by RefSeq, Aug 2011]

GeneCards Summary for LIMA1 Gene

LIMA1 (LIM Domain And Actin Binding 1) is a Protein Coding gene. Diseases associated with LIMA1 include Low Density Lipoprotein Cholesterol Level Quantitative Trait Locus 8. Among its related pathways are Cytoskeletal Signaling and Stabilization and expansion of the E-cadherin adherens junction. Gene Ontology (GO) annotations related to this gene include actin filament binding and actin monomer binding.

UniProtKB/Swiss-Prot for LIMA1 Gene

  • Actin-binding protein involved in actin cytoskeleton regulation and dynamics. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments (PubMed:12566430). Plays a role in cholesterol homeostasis. Influences plasma cholesterol levels through regulation of intestinal cholesterol absorption. May act as a scaffold protein by regulating NPC1L1 transportation, an essential protein for cholesterol absorption, to the plasma membrane by recruiting MYO5B to NPC1L1, and thus facilitates cholesterol uptake (By similarity).

Gene Wiki entry for LIMA1 Gene

Additional gene information for LIMA1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIMA1 Gene

Genomics for LIMA1 Gene

GeneHancer (GH) Regulatory Elements for LIMA1 Gene

Promoters and enhancers for LIMA1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LIMA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LIMA1 gene promoter:
  • AML1a
  • Gfi-1
  • HEN1
  • Hlf
  • POU2F1
  • POU2F1a
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for LIMA1 Gene

Genomic Locations for LIMA1 Gene
chr12:50,175,780-50,283,570
(GRCh38/hg38)
Size:
107,791 bases
Orientation:
Minus strand
chr12:50,569,563-50,677,353
(GRCh37/hg19)
Size:
107,791 bases
Orientation:
Minus strand

Genomic View for LIMA1 Gene

Genes around LIMA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIMA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIMA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIMA1 Gene

Proteins for LIMA1 Gene

  • Protein details for LIMA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UHB6-LIMA1_HUMAN
    Recommended name:
    LIM domain and actin-binding protein 1
    Protein Accession:
    Q9UHB6
    Secondary Accessions:
    • B2RB09
    • Q2TAN7
    • Q59FE8
    • Q9BVF2
    • Q9H8J1
    • Q9HBN5
    • Q9NX96
    • Q9NXC3
    • Q9NXU6
    • Q9P0H8
    • Q9UHB5

    Protein attributes for LIMA1 Gene

    Size:
    759 amino acids
    Molecular mass:
    85226 Da
    Quaternary structure:
    • Interacts with NPCL1; bridges NPC1L1 with MYO5B (PubMed:29880681). Interacts with MYO5B; bridges NPC1L1 with MYO5B (PubMed:29880681). Interacts with PXN; this complex stabilizes actin dynamics (PubMed:24694988). Interacts with F-actin and G-actin (PubMed:12566430).
    SequenceCaution:
    • Sequence=AAG17267.1; Type=Frameshift; Positions=365, 662; Evidence={ECO:0000305}; Sequence=BAA91120.1; Type=Frameshift; Positions=697; Evidence={ECO:0000305}; Sequence=BAD92749.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LIMA1 Gene

    Alternative splice isoforms for LIMA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIMA1 Gene

Post-translational modifications for LIMA1 Gene

  • Phosphorylation of the C-terminal region by MAPK1/MAPK3 reduces its association with F-actin and contributes to actin filament reorganization and enhances cell motility.
  • Ubiquitination at posLast=7575, posLast=462462, and posLast=2121
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for LIMA1 Gene

Domains & Families for LIMA1 Gene

Gene Families for LIMA1 Gene

Protein Domains for LIMA1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LIMA1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55990, highly similar to LIM domain and actin-binding protein 1 (B4DN52_HUMAN)
  • Epithelial protein lost in neoplasm (LIMA1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UHB6

UniProtKB/Swiss-Prot:

LIMA1_HUMAN :
  • Contains at least 2 actin-binding domains, one on each side of the LIM domain. Both domains bind actin monomers and filaments. The C-terminal domain binds filaments more efficiently than the N-terminus.
Domain:
  • Contains at least 2 actin-binding domains, one on each side of the LIM domain. Both domains bind actin monomers and filaments. The C-terminal domain binds filaments more efficiently than the N-terminus.
genes like me logo Genes that share domains with LIMA1: view

Function for LIMA1 Gene

Molecular function for LIMA1 Gene

UniProtKB/Swiss-Prot Function:
Actin-binding protein involved in actin cytoskeleton regulation and dynamics. Increases the number and size of actin stress fibers and inhibits membrane ruffling. Inhibits actin filament depolymerization. Bundles actin filaments, delays filament nucleation and reduces formation of branched filaments (PubMed:12566430). Plays a role in cholesterol homeostasis. Influences plasma cholesterol levels through regulation of intestinal cholesterol absorption. May act as a scaffold protein by regulating NPC1L1 transportation, an essential protein for cholesterol absorption, to the plasma membrane by recruiting MYO5B to NPC1L1, and thus facilitates cholesterol uptake (By similarity).
UniProtKB/Swiss-Prot Induction:
Down-regulated in some cancer cell lines. Isoform Alpha is induced by serum. Isoform Beta is constitutively expressed.

Phenotypes From GWAS Catalog for LIMA1 Gene

Gene Ontology (GO) - Molecular Function for LIMA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IEA --
GO:0003785 actin monomer binding IDA 12566430
GO:0005515 protein binding IPI 18093941
GO:0045296 cadherin binding HDA 25468996
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LIMA1: view
genes like me logo Genes that share phenotypes with LIMA1: view

Animal Models for LIMA1 Gene

MGI Knock Outs for LIMA1:
  • Lima1 Lima1<tm1.1Blsg>
  • Lima1 Lima1<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for LIMA1 Gene

miRTarBase miRNAs that target LIMA1

Clone Products

  • Applied Biological Materials (abm): Clones for LIMA1 - Now 50% OFF >
  • * LIMA1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LIMA1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for LIMA1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LIMA1 Gene

Localization for LIMA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIMA1 Gene

Cytoplasm. Cell junction, focal adhesion. Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, stress fiber. Cell membrane. Note=Expressed in the brush border membrane of the small intestine and colocalizes with NPC1L1 and MYO5B (PubMed:29880681). Colocalizes with PXN at focal adhesions in mesangial cells (PubMed:24694988). Colocalizes with actin stress fibers in quiescent cells. PDGF stimulation induced disassembly of stress fibers and formation of peripheral and dorsal ruffles, where LIMA1 is relocalized (By similarity). {ECO:0000250 UniProtKB:Q9ERG0, ECO:0000269 PubMed:24694988, ECO:0000269 PubMed:29880681}.

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 LIMA1 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
cytosol 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (4)
  • Cytosol (4)
  • Focal adhesion sites (4)
  • Plasma membrane (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LIMA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IDA 10618726
GO:0001726 ruffle ISS --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with LIMA1: view

Pathways & Interactions for LIMA1 Gene

genes like me logo Genes that share pathways with LIMA1: view

Pathways by source for LIMA1 Gene

1 Cell Signaling Technology pathway for LIMA1 Gene

Gene Ontology (GO) - Biological Process for LIMA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0008202 steroid metabolic process IEA --
GO:0008203 cholesterol metabolic process IEA --
GO:0016477 cell migration ISS --
GO:0030299 intestinal cholesterol absorption ISS --
genes like me logo Genes that share ontologies with LIMA1: view

No data available for SIGNOR curated interactions for LIMA1 Gene

Drugs & Compounds for LIMA1 Gene

No Compound Related Data Available

Transcripts for LIMA1 Gene

Unigene Clusters for LIMA1 Gene

LIM domain and actin binding 1:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for LIMA1 - Now 50% OFF >
  • * LIMA1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LIMA1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for LIMA1

Alternative Splicing Database (ASD) splice patterns (SP) for LIMA1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c · 14d ·
SP1: - - - - - -
SP2: - - - - - -
SP3: - - -
SP4: - - -
SP5: - -
SP6: - -
SP7: - -
SP8: - - - -
SP9:
SP10: -

ExUns: 14e
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for LIMA1 Gene

GeneLoc Exon Structure for
LIMA1
ECgene alternative splicing isoforms for
LIMA1

Expression for LIMA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LIMA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LIMA1 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (35.8), Bone marrow stromal cell (9.3), and Nasal epithelium (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LIMA1 Gene



Protein tissue co-expression partners for LIMA1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LIMA1 Gene:

LIMA1

SOURCE GeneReport for Unigene cluster for LIMA1 Gene:

Hs.525419

mRNA Expression by UniProt/SwissProt for LIMA1 Gene:

Q9UHB6-LIMA1_HUMAN
Tissue specificity: Highly expressed in placenta, kidney, pancreas, prostate, ovary, spleen and heart. Also detected in lung, liver, brain, skeletal muscle, thymus, testis and intestine. Not detected in leukocytes. Isoform Beta expressed generally at very low levels. Isoform Alpha abundant in epithelial cells from mammary gland, prostate and in normal oral keratinocytes. Low levels in aortic endothelial cells and dermal fibroblasts. Not detectable in myocardium.

Evidence on tissue expression from TISSUES for LIMA1 Gene

  • Nervous system(4.8)
  • Intestine(4.4)
  • Liver(4.3)
  • Blood(4.1)
  • Kidney(2.8)
  • Skin(2.3)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with LIMA1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LIMA1 Gene

Orthologs for LIMA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LIMA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIMA1 35 34
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LIMA1 35 34
  • 86.77 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LIMA1 35 34
  • 86.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lima1 17 35 34
  • 80.43 (n)
rat
(Rattus norvegicus)
Mammalia Lima1 34
  • 80.22 (n)
oppossum
(Monodelphis domestica)
Mammalia LIMA1 35
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIMA1 35
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIMA1 35 34
  • 66.8 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIMA1 35
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lima1 34
  • 57.74 (n)
Str.6869 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.24780 34
zebrafish
(Danio rerio)
Actinopterygii im:7155904 34
  • 51.45 (n)
lima1 35
  • 38 (a)
OneToMany
LIMA1 (2 of 2) 35
  • 20 (a)
OneToMany
-- 34
Species where no ortholog for LIMA1 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for LIMA1 Gene

ENSEMBL:
Gene Tree for LIMA1 (if available)
TreeFam:
Gene Tree for LIMA1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LIMA1: view image

Paralogs for LIMA1 Gene

(1) SIMAP similar genes for LIMA1 Gene using alignment to 7 proteins:

  • LIMA1_HUMAN
  • F8VQE1_HUMAN
  • F8VRN8_HUMAN
  • F8VS07_HUMAN
  • F8VTU2_HUMAN
  • F8VVQ7_HUMAN
  • L8E8R7_HUMAN
genes like me logo Genes that share paralogs with LIMA1: view

No data available for Paralogs for LIMA1 Gene

Variants for LIMA1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for LIMA1 Gene

LIMA1_HUMAN-Q9UHB6
Genetic variations in LIMA1 influence low density lipoprotein cholesterol (LDL-C) variability and contribute to the low density lipoprotein cholesterol level quantitative trait locus 8 (LDLCQ8) [MIM:618079].

Sequence variations from dbSNP and Humsavar for LIMA1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs140372565 association, LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8, - 50,248,679(-) G/T 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1555205375 association, LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8 50,200,826(-) TTCTCCTTTT/TT coding_sequence_variant, frameshift
rs1000044839 -- 50,229,308(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000065145 -- 50,239,274(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000130837 -- 50,257,546(-) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LIMA1 Gene

Variant ID Type Subtype PubMed ID
dgv1498n100 CNV gain 25217958
esv2745869 CNV deletion 23290073
esv2745870 CNV deletion 23290073
esv2761738 CNV gain 21179565
esv3303601 CNV mobile element insertion 20981092
esv3334002 CNV insertion 20981092
esv3629477 CNV loss 21293372
nsv702 CNV deletion 18451855
nsv975487 CNV duplication 23825009

Variation tolerance for LIMA1 Gene

Residual Variation Intolerance Score: 50.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.10; 22.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LIMA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIMA1

SNP Genotyping and Copy Number Assay Products

Disorders for LIMA1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LIMA1 Gene - From: OMIM and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LIMA1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LIMA1

genes like me logo Genes that share disorders with LIMA1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIMA1 Gene

Publications for LIMA1 Gene

  1. EPLIN regulates actin dynamics by cross-linking and stabilizing filaments. (PMID: 12566430) Maul RS … Chang DD (The Journal of cell biology 2003) 2 3 4 23 58
  2. Characterization of the human EPLIN (Epithelial Protein Lost in Neoplasm) gene reveals distinct promoters for the two EPLIN isoforms. (PMID: 10806352) Chen S … Chang DD (Gene 2000) 2 3 4 23 58
  3. EPLIN, epithelial protein lost in neoplasm. (PMID: 10618726) Maul RS … Chang DD (Oncogene 1999) 2 3 4 23 58
  4. A LIMA1 variant promotes low plasma LDL cholesterol and decreases intestinal cholesterol absorption. (PMID: 29880681) Zhang YY … Song BL (Science (New York, N.Y.) 2018) 3 4 58
  5. Epithelial protein lost in neoplasm modulates platelet-derived growth factor-mediated adhesion and motility of mesangial cells. (PMID: 24694988) Tsurumi H … Igarashi T (Kidney international 2014) 3 4 58

Products for LIMA1 Gene

Sources for LIMA1 Gene

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