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LMO3 LIM domain only 3 [ Homo sapiens (human) ]

Gene ID: 55885, updated on 7-Apr-2025

Summary

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Official Symbol
LMO3provided by HGNC
Official Full Name
LIM domain only 3provided by HGNC
Primary source
HGNC:HGNC:6643
See related
Ensembl:ENSG00000048540 MIM:180386; AllianceGenome:HGNC:6643
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
RBTN3; RHOM3; RBTNL2; Rhom-3
Summary
The protein encoded by this gene belongs to the rhombotin family of cysteine-rich LIM domain oncogenes. This gene is predominantly expressed in the brain. Related family members, LMO1 and LMO2 on chromosome 11, have been reported to be involved in chromosomal translocations in T-cell leukemia. Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]
Expression
Biased expression in brain (RPKM 41.7), lung (RPKM 13.9) and 7 other tissues See more
Orthologs
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Genomic context

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See LMO3 in Genome Data Viewer
Location:
12p12.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (16548372..16610174, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (16425771..16487621, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (16701306..16761148, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene microsomal glutathione S-transferase 1 Neighboring gene SPT16 homolog, facilitates chromatin remodeling subunit pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:16602892-16603466 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:16603467-16604039 Neighboring gene VISTA enhancer hs607 Neighboring gene NANOG hESC enhancer GRCh37_chr12:16703865-16704366 Neighboring gene VISTA enhancer hs336 Neighboring gene GOT2 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:16757530-16758030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:16762919-16763418 Neighboring gene VISTA enhancer hs661 Neighboring gene uncharacterized LOC105369677 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:17135721-17136920 Neighboring gene S-phase kinase associated protein 1 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism. Ohara Y, et al. Carcinogenesis, 2024 Jul 8. PMID 38366633, Free PMC Article
  2. MiR-101 reverses the hypomethylation of the LMO3 promoter in glioma cells. Liu X, et al. Oncotarget, 2015 Apr 10. PMID 25829251, Free PMC Article
  3. LMO3 promotes gastric cancer cell invasion and proliferation through Akt-mTOR and Akt-GSK3β signaling. Qiu YS, et al. Int J Mol Med, 2018 May. PMID 29436606, Free PMC Article
  4. Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway. Kang Y, et al. J Mol Histol, 2022 Apr. PMID 35165791
  5. LMO3 reprograms visceral adipocyte metabolism during obesity. Wagner G, et al. J Mol Med (Berl), 2021 Aug. PMID 34018016, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism.
    Title: LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism.
  2. Circ_0007385 promotes the proliferation and inhibits the apoptosis of non-small cell lung cancer cells via miR-337-3p-dependent regulation of LMO3.
    Title: Circ_0007385 promotes the proliferation and inhibits the apoptosis of non-small cell lung cancer cells via miR-337-3p-dependent regulation of LMO3.
  3. Hyperglycemia affects neuronal differentiation and Nestin, FOXO1, and LMO3 mRNA expression of human Wharton's jelly mesenchymal stem cells of children from diabetic mothers.
    Title: Hyperglycemia affects neuronal differentiation and Nestin, FOXO1, and LMO3 mRNA expression of human Wharton's jelly mesenchymal stem cells of children from diabetic mothers.
  4. Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway.
    Title: Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway.
  5. LMO3 reprograms visceral adipocyte metabolism during obesity.
    Title: LMO3 reprograms visceral adipocyte metabolism during obesity.
  6. MicroRNA-381 inhibits lung adenocarcinoma cell biological progression by directly targeting LMO3 through regulation of the PI3K/Akt signaling pathway and epithelial-to-mesenchymal transition.
    Title: MicroRNA-381 inhibits lung adenocarcinoma cell biological progression by directly targeting LMO3 through regulation of the PI3K/Akt signaling pathway and epithelial-to-mesenchymal transition.
  7. our results suggest that LMO3-BORCS5 fusion oncogene plays an essential role in tumorigenesis
    Title: Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression.
  8. These results suggest that LMO3 promotes hepatocellular carcinoma (HCC) cell invasion and anoikis inhibition by interacting with LATS1 and suppressing Hippo signaling. LMO3 may serve as a potential therapeutic target for HCC in future
    Title: LMO3 promotes hepatocellular carcinoma invasion, metastasis and anoikis inhibition by directly interacting with LATS1 and suppressing Hippo signaling.
  9. These results suggested that LMO3 promotes Gastric Cancer cell invasion and proliferation mainly through Akt/mTOR and Akt/GSK3beta signaling.
    Title: LMO3 promotes gastric cancer cell invasion and proliferation through Akt-mTOR and Akt-GSK3β signaling.
  10. SH3BP5, LMO3, and SNAP25 were expressed in diffuse large B-cell lymphoma cells and associated with clinical features.
    Title: Expressions of SH3BP5, LMO3, and SNAP25 in diffuse large B-cell lymphoma cells and their association with clinical features.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC26081

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in negative regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of peroxisome proliferator activated receptor signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
LIM domain only protein 3
Names
LIM domain only 3 (rhombotin-like 2)
dopamine associated transcription factor-1
neuronal-specific transcription factor DAT1
rhombotin-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_029785.2 RefSeqGene

    Range
    7053..64843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001001395.2 → NP_001001395.1  LIM domain only protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001001395.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' non-coding exon compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AF258348, AK294474, AL050152, BQ029059, DA780743
    Consensus CDS
    CCDS8678.1
    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000346689.1, ENST00000354662.5
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  2. NM_001243609.1 → NP_001230538.1  LIM domain only protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001230538.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs at the 5' end compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AB044746, AF258348, AL050152, BQ029059, DA780743
    Consensus CDS
    CCDS8678.1
    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000412479.2, ENST00000441439.6
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  3. NM_001243610.1 → NP_001230539.1  LIM domain only protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001230539.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs at the 5' end compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AL050152, BC050085, BQ029059
    Consensus CDS
    CCDS8678.1
    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000413703.1, ENST00000447609.5
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  4. NM_001243611.1 → NP_001230540.1  LIM domain only protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001230540.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame upstream start codon, and an isoform (2) with a longer N-terminus compared to isoform 1.
    Source sequence(s)
    AB044745, AL050152, BC026311, BQ029059, DC324870
    Consensus CDS
    CCDS58211.1
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000261169.6, ENST00000261169.10
    Conserved Domains (2) summary
    cd09388
    Location:24 → 78
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:88 → 142
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  5. NM_001243612.1 → NP_001230541.1  LIM domain only protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001230541.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame upstream start codon, and an isoform (3) with a longer N-terminus compared to isoform 1.
    Source sequence(s)
    AK294474, AL050152, BQ029059
    Consensus CDS
    CCDS58212.1
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000446463.1, ENST00000541295.5
    Conserved Domains (2) summary
    cd09388
    Location:31 → 85
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:95 → 149
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  6. NM_001243613.1 → NP_001230542.1  LIM domain only protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001230542.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs at the 5' end, and contains an additional in-frame coding exon compared to variant 1. This results in a longer isoform (4) with an internal protein segment not found in isoform 1.
    Source sequence(s)
    AK294909, AL050152, BQ029059
    Consensus CDS
    CCDS58210.1
    UniProtKB/Swiss-Prot
    Q8TAP4
    Related
    ENSP00000442786.1, ENST00000540445.5
    Conserved Domains (2) summary
    cd09389
    Location:99 → 153
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cl02475
    Location:13 → 49
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

  7. NM_018640.5 → NP_061110.2  LIM domain only protein 3 isoform 1

    See identical proteins and their annotated locations for NP_061110.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (1). Variants 1-4 encode the same isoform.
    Source sequence(s)
    AL050152, BC026311, BQ029059
    Consensus CDS
    CCDS8678.1
    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000440099.1, ENST00000537304.6
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

RNA

  1. NR_045012.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs at the 5' end and contains an additional internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF258348, AK294909, AK308826, AL050152, BQ029059, DA780743

  2. NR_045013.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs at the 5' end and uses an alternate donor splice site at an internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF258348, AL050152, BC017777, BQ029059, DA780743
    Related
    ENST00000396205.6

  3. NR_045014.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) differs at the 5' end and uses an alternate donor splice site at an internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF258348, AL050152, BC017777, BQ029059, DA780743

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
    16548372..16610174 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719111.3 → XP_006719174.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006719174.1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  2. XM_047429153.1 → XP_047285109.1  LIM domain only protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Related
    ENSP00000439275.1, ENST00000534946.5

  3. XM_006719110.5 → XP_006719173.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006719173.1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  4. XM_011520762.2 → XP_011519064.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011519064.1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631
    Conserved Domains (2) summary
    cd09388
    Location:13 → 67
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77 → 131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

  5. XM_047429156.1 → XP_047285112.1  LIM domain only protein 3 isoform X4

  6. XM_047429154.1 → XP_047285110.1  LIM domain only protein 3 isoform X2

  7. XM_047429155.1 → XP_047285111.1  LIM domain only protein 3 isoform X3

    UniProtKB/TrEMBL
    F5H655

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    16425771..16487621 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372560.1 → XP_054228535.1  LIM domain only protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631

  2. XM_054372559.1 → XP_054228534.1  LIM domain only protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631

  3. XM_054372558.1 → XP_054228533.1  LIM domain only protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
    UniProtKB/TrEMBL
    B2R631

  4. XM_054372562.1 → XP_054228537.1  LIM domain only protein 3 isoform X4

  5. XM_054372561.1 → XP_054228536.1  LIM domain only protein 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TAP4.1 GenPept UniProtKB/Swiss-Prot:Q8TAP4

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