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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
  • SREBP3 3 4
  • EPLIN 3 4
  • Sterol Regulatory Element Binding Protein 3 3
  • LIM Domain And Actin-Binding Protein 1 3
  • Epithelial Protein Lost In Neoplasm 4
  • 1110021C24Rik 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. 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. An important paralog of this gene is LIMD2.

UniProtKB/Swiss-Prot for LIMA1 Gene

  • Binds to actin monomers and filaments. 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.

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
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
GH12J050217 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.2 +62.4 62405 8 HNRNPUL1 PKNOX1 CLOCK SMAD1 ARNT NEUROD1 SIN3A FEZF1 ZNF2 IRF4 ENSG00000257256 LIMA1 SMARCD1 CERS5 SPATS2 ATF1 LOC101927267 PRPF40B ENSG00000257531 GC12M050135
GH12J050279 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 661.3 +1.5 1488 5.3 HDGF ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF766 ZNF207 ZNF143 LIMA1 LARP4 GC12P050283 CERS5 SMARCD1 ATF1 BCDIN3D FAM186A DIP2B GC12M050258
GH12J050200 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 660.4 +81.1 81083 4.6 USF1 JUN ZIC2 RAD21 BRCA1 RFX5 CTBP1 GATA3 POLR2A SCRT2 LIMA1 CERS5 RNU6-1093P COX14 LARP4 FAM186A ATF1 PIR58326 ENSG00000257298 GC12M050135
GH12J050399 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 64.6 -118.3 -118313 4 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF548 SP3 ZNF610 ZNF585B NBN GC12M050402 LARP4 SMARCD1 LIMA1 BCDIN3D PRPF40B ATF1 ENSG00000257298 ENSG00000257964 LOC100422296
GH12J050056 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 50.5 +226.0 226006 1.3 ZNF493 ZNF133 ARID4B SIN3A GLI4 ZNF2 GLIS2 ZNF213 ZNF416 ZNF207 ASIC1 KMT2D SMARCD1 LMBR1L LIMA1 ATF1 BCDIN3D LOC101927267 CERS5 SPATS2
- 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:
  • SREBP-1b
  • SREBP-1a
  • SREBP-1c
  • Hlf
  • HEN1
  • Gfi-1
  • AML1a
  • POU2F1
  • POU2F1a

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:
    No Data Available
    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

  • Ubiquitination at isoforms=3, 4, 5, 2462, posLast=7575, 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

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

Protein Domains for LIMA1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LIMA1 Gene

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:
Binds to actin monomers and filaments. 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.
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 IDA 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<tm1b(KOMP)Wtsi>

Animal Model Products

miRNA for LIMA1 Gene

miRTarBase miRNAs that target LIMA1

Clone Products

  • 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. Note=This cytoskeletal protein co-localizes with actin stress fibers and focal adhesion plaques.

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
cytoskeleton 5
plasma membrane 3
nucleus 3
cytosol 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:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane IDA --
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:0030835 negative regulation of actin filament depolymerization IEA,IDA 12566430
GO:0031529 ruffle organization IDA 12566430
GO:0051017 actin filament bundle assembly IDA,IEA 12566430
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:

Clone Products

  • 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 34 33
  • 99.44 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LIMA1 34 33
  • 86.77 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LIMA1 34 33
  • 86.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lima1 16 34 33
  • 80.43 (n)
rat
(Rattus norvegicus)
Mammalia Lima1 33
  • 80.22 (n)
oppossum
(Monodelphis domestica)
Mammalia LIMA1 34
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIMA1 34
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIMA1 34 33
  • 66.8 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIMA1 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lima1 33
  • 57.74 (n)
Str.6869 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.24780 33
zebrafish
(Danio rerio)
Actinopterygii im:7155904 33
  • 51.45 (n)
lima1 34
  • 38 (a)
OneToMany
LIMA1 (2 of 2) 34
  • 20 (a)
OneToMany
-- 33
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

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

Variants for LIMA1 Gene

Sequence variations from dbSNP and Humsavar for LIMA1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
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
rs1000182514 -- 50,211,197(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000188748 -- 50,203,340(-) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIMA1 Gene

Disorders for LIMA1 Gene

Additional Disease Information for LIMA1

No disorders were found for LIMA1 Gene.

No data available for MalaCards , 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 22 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 22 58
  3. EPLIN, epithelial protein lost in neoplasm. (PMID: 10618726) Maul RS … Chang DD (Oncogene 1999) 2 3 4 22 58
  4. The actin-binding and bundling protein, EPLIN, is required for cytokinesis. (PMID: 19221476) Chircop M … Khanna KK (Cell cycle (Georgetown, Tex.) 2009) 3 22 58
  5. Eplin-alpha expression in human breast cancer, the impact on cellular migration and clinical outcome. (PMID: 18796137) Jiang WG … Mansel RE (Molecular cancer 2008) 3 22 58

Products for LIMA1 Gene

Sources for LIMA1 Gene

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