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

Gene ID: 51474, updated on 12-Aug-2018
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; Vega:OTTHUMG00000169852
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
See LIMA1 in Genome Data Viewer
Location:
12q13.12
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (50175780..50283570, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50569563..50677353, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene cytochrome c oxidase assembly factor COX14 Neighboring gene ceramide synthase 5 Neighboring gene microRNA 1293 Neighboring gene RNA, U6 small nuclear 1093, pseudogene Neighboring gene uncharacterized LOC107984505 Neighboring gene KIAA1586 pseudogene Neighboring gene family with sequence similarity 186 member A Neighboring gene ribosomal protein L26 pseudogene 33

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

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

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

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ38853, MGC131726

Gene Ontology Provided by GOA

Function Evidence Code Pubs
actin filament binding IDA
Inferred from Direct Assay
more info
PubMed 
actin monomer binding IDA
Inferred from Direct Assay
more info
PubMed 
cadherin binding HDA PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin filament bundle assembly IDA
Inferred from Direct Assay
more info
PubMed 
intestinal cholesterol absorption ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of actin filament depolymerization IDA
Inferred from Direct Assay
more info
PubMed 
ruffle organization IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
cleavage furrow IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
focal adhesion HDA PubMed 
focal adhesion IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
stress fiber IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
LIM domain and actin-binding protein 1
Names
1110021C24Rik
epithelial protein lost in neoplasm beta
sterol regulatory element binding protein 3

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
    5001..112791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001113546.1NP_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)
    AA772616, AB209512, AL136911, BC110815, BP216703, BP281423
    Consensus CDS
    CCDS44877.1
    UniProtKB/Swiss-Prot
    Q9UHB6
    Related
    ENSP00000378400.3, OTTHUMP00000242284, ENST00000394943.7, OTTHUMT00000406234
    Conserved Domains (1) summary
    cd09485
    Location:391443
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)
  2. NM_001113547.1NP_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)
    AA772616, AF198455, AL136911, BC110815, DA738195
    Consensus CDS
    CCDS55826.1
    UniProtKB/Swiss-Prot
    Q9UHB6
    Related
    ENSP00000448779.1, OTTHUMP00000242286, ENST00000552783.5, OTTHUMT00000406236
    Conserved Domains (1) summary
    cd09485
    Location:231283
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)
  3. NM_001243775.1NP_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)
    AA772616, AF157325, AK023649, AL136911, BC110815
    Consensus CDS
    CCDS58230.1
    UniProtKB/Swiss-Prot
    Q9UHB6
    Related
    ENSP00000448706.1, OTTHUMP00000242379, ENST00000547825.5, OTTHUMT00000406410
    Conserved Domains (1) summary
    cd09485
    Location:88140
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)
  4. NM_016357.4NP_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)
    AA772616, AL136911, BC110815, BP216703, BP281423
    Consensus CDS
    CCDS8802.1
    UniProtKB/Swiss-Prot
    Q9UHB6
    Related
    ENSP00000340184.4, OTTHUMP00000242285, ENST00000341247.8, OTTHUMT00000406235
    Conserved Domains (1) summary
    cd09485
    Location:390442
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    50175780..50283570 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019430.1XP_016874919.1  LIM domain and actin-binding protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q9UHB6
    Conserved Domains (1) summary
    cd09485
    Location:88140
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)
  2. XM_011538455.2XP_011536757.1  LIM domain and actin-binding protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011536757.1

    UniProtKB/Swiss-Prot
    Q9UHB6
    Conserved Domains (1) summary
    cd09485
    Location:391443
    LIM_Eplin_alpha_beta; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)
  3. XM_017019429.1XP_016874918.1  LIM domain and actin-binding protein 1 isoform X2

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