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

Summary

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

Location:: 12q13.12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (50175788..50283520, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (50138878..50246629, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (50569571..50677303, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Study proposes a role for EPLIN's ability to regulate the aggressive characteristics of prostate cancer cells partially through regulating FAK/Src signaling.
Title: Mechanistic insights of epithelial protein lost in neoplasm in prostate cancer metastasis.
this study identifies LIMA1 as a key protein regulating intestinal cholesterol absorption.
Title: A LIMA1 variant promotes low plasma LDL cholesterol and decreases intestinal cholesterol absorption.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S1908 (e-PCR)
- UniSTS:19465

D12S1620 (e-PCR), detects polymorphism
- UniSTS:26380

D8S2279 (e-PCR)
- UniSTS:473907

RH48418 (e-PCR)
- UniSTS:13926

RH47470 (e-PCR)
- UniSTS:8304

D12S1145E (e-PCR)
- UniSTS:151429

NoName (e-PCR)
- UniSTS:51627

LIMA1 (e-PCR)
- UniSTS:503999

L29953 (e-PCR)
- UniSTS:52164

RH119301 (e-PCR)
- UniSTS:133863

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 more info	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 more info	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

NG_029859.1 RefSeqGene

Range

5051..112783

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)