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

Gene ID: 51474, updated on 2-Nov-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
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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.

Chemical Information
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