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    LIMA1 LIM domain and actin binding 1 [ Homo sapiens (human) ]

    Gene ID: 51474, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LIMA1provided by HGNC
    Official Full Name
    LIM domain and actin binding 1provided by HGNC
    Primary source
    HGNC:HGNC:24636
    See related
    Ensembl:ENSG00000050405 MIM:608364; AllianceGenome:HGNC:24636
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EPLIN; LDLCQ8; SREBP3
    Summary
    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]
    Expression
    Ubiquitous expression in colon (RPKM 57.9), small intestine (RPKM 51.2) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LIMA1 in Genome Data Viewer
    Location:
    12q13.12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50175788..50283520, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50138878..50246629, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50569571..50677303, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6347 Neighboring gene cytochrome c oxidase assembly factor COX14 Neighboring gene uncharacterized LOC124902931 Neighboring gene ceramide synthase 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6349 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50561740-50562501 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:50611987-50613186 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:50615667-50616518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50628639-50629140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50629141-50629640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4450 Neighboring gene microRNA 1293 Neighboring gene RNA, U6 small nuclear 1093, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr12:50666914-50667093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4451 Neighboring gene uncharacterized LOC107984505 Neighboring gene KIAA1586 pseudogene Neighboring gene family with sequence similarity 186 member A Neighboring gene ribosomal protein L26 pseudogene 33

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. EPLIN downregulation promotes epithelial-mesenchymal transition in prostate cancer cells and correlates with clinical lymph node metastasis. Zhang S, et al. Oncogene, 2011 Dec 15. PMID 21625216, Free PMC Article
    2. Characterization of the human EPLIN (Epithelial Protein Lost in Neoplasm) gene reveals distinct promoters for the two EPLIN isoforms. Chen S, et al. Gene, 2000 May 2. PMID 10806352
    3. Epithelial Protein Lost in Neoplasm, EPLIN, the Cellular and Molecular Prospects in Cancers. Zeng J, et al. Biomolecules, 2021 Jul 16. PMID 34356662, Free PMC Article
    4. EPLIN-α and -β Isoforms Modulate Endothelial Cell Dynamics through a Spatiotemporally Differentiated Interaction with Actin. Taha M, et al. Cell Rep, 2019 Oct 22. PMID 31644899
    5. Mechanistic insights of epithelial protein lost in neoplasm in prostate cancer metastasis. Collins RJ, et al. Int J Cancer, 2018 Nov 15. PMID 30098000

    See all (191) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression and molecular insights of lima1 in cholangiocarcinoma.
      Title: Expression and molecular insights of lima1 in cholangiocarcinoma.
    2. The concerted action of SEPT9 and EPLIN modulates the adhesion and migration of human fibroblasts.
      Title: The concerted action of SEPT9 and EPLIN modulates the adhesion and migration of human fibroblasts.
    3. Nuclear-cytoplasmic translocation of SQSTM1/p62 protein enhances ESCC cell migration and invasion by stabilizing EPLIN expression.
      Title: Nuclear-cytoplasmic translocation of SQSTM1/p62 protein enhances ESCC cell migration and invasion by stabilizing EPLIN expression.
    4. MAD2 activates IGF1R/PI3K/AKT pathway and promotes cholangiocarcinoma progression by interfering USP44/LIMA1 complex.
      Title: MAD2 activates IGF1R/PI3K/AKT pathway and promotes cholangiocarcinoma progression by interfering USP44/LIMA1 complex.
    5. EPLIN-beta is a novel substrate of ornithine decarboxylase antizyme 1 and mediates cellular migration.
      Title: EPLIN-β is a novel substrate of ornithine decarboxylase antizyme 1 and mediates cellular migration.
    6. CAF-Released Exosomal miR-20a-5p Facilitates HCC Progression via the LIMA1-Mediated beta-Catenin Pathway.
      Title: CAF-Released Exosomal miR-20a-5p Facilitates HCC Progression via the LIMA1-Mediated β-Catenin Pathway.
    7. Rab40-Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration.
      Title: Rab40-Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration.
    8. Epithelial Protein Lost in Neoplasm, EPLIN, the Cellular and Molecular Prospects in Cancers.
      Title: Epithelial Protein Lost in Neoplasm, EPLIN, the Cellular and Molecular Prospects in Cancers.
    9. LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation.
      Title: LUZP1 and the tumor suppressor EPLIN modulate actin stability to restrict primary cilia formation.
    10. EPLIN-alpha and -beta Isoforms Modulate Endothelial Cell Dynamics through a Spatiotemporally Differentiated Interaction with Actin.
      Title: EPLIN-α and -β Isoforms Modulate Endothelial Cell Dynamics through a Spatiotemporally Differentiated Interaction with Actin.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 8
    MedGen: C4748092 OMIM: 618079 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat LIM domain and actin binding 1 (LIMA1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ38853, MGC131726

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables actin monomer binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cadherin binding HDA PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament bundle assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in actin filament bundle assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intestinal cholesterol absorption ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of actin filament depolymerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ruffle organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in brush border membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cleavage furrow IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in focal adhesion HDA PubMed 
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in stress fiber IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    LIM domain and actin-binding protein 1
    Names
    epithelial protein lost in neoplasm beta
    sterol regulatory element binding protein 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029859.1 RefSeqGene

      Range
      5051..112783
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001113546.2 → NP_001107018.1  LIM domain and actin-binding protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001107018.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB209512, AL136911, BC110815, BP281423
      Consensus CDS
      CCDS44877.1
      UniProtKB/TrEMBL
      Q53GG0
      Related
      ENSP00000378400.3, ENST00000394943.7
      Conserved Domains (1) summary
      cd09485
      Location:391 → 443
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    2. NM_001113547.2 → NP_001107019.1  LIM domain and actin-binding protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001107019.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs at the 5' end compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (3, also known as EPLIN-alpha) with a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF198455, AL136911, BC110815, DA738195
      Consensus CDS
      CCDS55826.1
      UniProtKB/TrEMBL
      F8VQE1
      Related
      ENSP00000448779.1, ENST00000552783.5
      Conserved Domains (1) summary
      cd09485
      Location:231 → 283
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    3. NM_001243775.2 → NP_001230704.1  LIM domain and actin-binding protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001230704.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs at the 5' end, and uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (4) with a shorter N-terminus and lacking an internal aa compared to isoform 1.
      Source sequence(s)
      AC008147, AC139016
      Consensus CDS
      CCDS58230.1
      UniProtKB/TrEMBL
      B3KTW2, F8VS07
      Related
      ENSP00000448706.1, ENST00000547825.5
      Conserved Domains (1) summary
      cd09485
      Location:88 → 140
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    4. NM_001394886.1 → NP_001381815.1  LIM domain and actin-binding protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      Consensus CDS
      CCDS44877.1
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:391 → 443
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    5. NM_001394887.1 → NP_001381816.1  LIM domain and actin-binding protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      Consensus CDS
      CCDS8802.1
      UniProtKB/Swiss-Prot
      B2RB09, Q2TAN7, Q59FE8, Q9BVF2, Q9H8J1, Q9HBN5, Q9NX96, Q9NXC3, Q9NXU6, Q9P0H8, Q9UHB5, Q9UHB6
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:390 → 442
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    6. NM_001394888.1 → NP_001381817.1  LIM domain and actin-binding protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      Consensus CDS
      CCDS8802.1
      UniProtKB/Swiss-Prot
      B2RB09, Q2TAN7, Q59FE8, Q9BVF2, Q9H8J1, Q9HBN5, Q9NX96, Q9NXC3, Q9NXU6, Q9P0H8, Q9UHB5, Q9UHB6
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:390 → 442
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    7. NM_001394889.1 → NP_001381818.1  LIM domain and actin-binding protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:390 → 442
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    8. NM_001394890.1 → NP_001381819.1  LIM domain and actin-binding protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:389 → 441
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    9. NM_001394891.1 → NP_001381820.1  LIM domain and actin-binding protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:373 → 425
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    10. NM_001394892.1 → NP_001381821.1  LIM domain and actin-binding protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      UniProtKB/TrEMBL
      Q53GG0
      Conserved Domains (1) summary
      cd09485
      Location:313 → 365
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    11. NM_001394893.1 → NP_001381822.1  LIM domain and actin-binding protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC008147, AC139016
      UniProtKB/TrEMBL
      F8VQE1
      Conserved Domains (1) summary
      cd09485
      Location:299 → 351
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    12. NM_016357.5 → NP_057441.1  LIM domain and actin-binding protein 1 isoform 2

      See identical proteins and their annotated locations for NP_057441.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at an internal coding exon compared to variant 1. This results in an isoform (2, also known as EPLIN-beta) that is 1 aa shorter than isoform 1.
      Source sequence(s)
      AL136911, BC110815, BP281423
      Consensus CDS
      CCDS8802.1
      UniProtKB/Swiss-Prot
      B2RB09, Q2TAN7, Q59FE8, Q9BVF2, Q9H8J1, Q9HBN5, Q9NX96, Q9NXC3, Q9NXU6, Q9P0H8, Q9UHB5, Q9UHB6
      UniProtKB/TrEMBL
      Q53GG0
      Related
      ENSP00000340184.4, ENST00000341247.9
      Conserved Domains (1) summary
      cd09485
      Location:390 → 442
      LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      50175788..50283520 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428969.1 → XP_047284925.1  LIM domain and actin-binding protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      50138878..50246629 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHB6.1 GenPept UniProtKB/Swiss-Prot:Q9UHB6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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