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

Summary

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: mouse all
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Genomic context

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_000012.12 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?

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.
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.
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.
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.
LMO3 reprograms visceral adipocyte metabolism during obesity.
Title: LMO3 reprograms visceral adipocyte metabolism during obesity.
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.
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.
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.
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.
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

A002A33 (e-PCR)
- UniSTS:11021

G19860 (e-PCR)
- UniSTS:11022

GDB:214810 (e-PCR)
- UniSTS:156184

BCD1517 (e-PCR)
- UniSTS:5161

G62377 (e-PCR)
- UniSTS:139348

D12S383E (e-PCR)
- UniSTS:148573

RH1605 (e-PCR)
- UniSTS:64949

SHGC-30138 (e-PCR)
- UniSTS:65740

RH91802 (e-PCR)
- UniSTS:88788

RH66254 (e-PCR)
- UniSTS:15328

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 glucocorticoid receptor 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

NG_029785.2 RefSeqGene

Range

7053..64843

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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)
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
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

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
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
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

16548372..16610174 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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
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)
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)
XM_047429156.1 → XP_047285112.1 LIM domain only protein 3 isoform X4
XM_047429154.1 → XP_047285110.1 LIM domain only protein 3 isoform X2
XM_047429155.1 → XP_047285111.1 LIM domain only protein 3 isoform X3

UniProtKB/TrEMBL

F5H655