LMO1 LIM domain only 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LMO1provided by HGNC
Official Full Name: LIM domain only 1provided by HGNC
Primary source: HGNC:HGNC:6641
See related: Ensembl:ENSG00000166407 MIM:186921; AllianceGenome:HGNC:6641
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: TTG1; RBTN1; RHOM1
Summary: This locus encodes a transcriptional regulator that contains two cysteine-rich LIM domains but lacks a DNA-binding domain. LIM domains may play a role in protein interactions; thus the encoded protein may regulate transcription by competitively binding to specific DNA-binding transcription factors. Alterations at this locus have been associated with acute lymphoblastic T-cell leukemia. Chromosomal rearrangements have been observed between this locus and at least two loci, the delta subunit of the T-cell antigen receptor gene and the LIM domain binding 1 gene. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2012]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.4

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (8224309..8268787, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (8305646..8350087, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (8245856..8290334, complement)

Chromosome 11 - NC_000011.10 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?

Circ_0021087 acts as a miR-184 sponge and represses gastric cancer progression by adsorbing miR-184 and elevating FOSB expression.
Title: Circ_0021087 acts as a miR-184 sponge and represses gastric cancer progression by adsorbing miR-184 and elevating FOSB expression.
LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies.
Title: LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies.
ASCL1 and LMO1 directly regulate the expression of CRC genes, indicating that ASCL1 is a member and LMO1 is a coregulator of the ADRN neuroblastoma core regulatory circuitry.
Title: ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry.
Target genes of the LMO1-regulated microRNAs and their relevant pathways may be a potential therapeutic targe
Title: Indirect Down-regulation of Tumor-suppressive let-7 Family MicroRNAs by LMO1 in Neuroblastoma.
IKZF1 rs10235796 C allele, IKZF1 rs6964969A>G, CDKN2A rs3731246 G>C, and CDKN2A rs3731246 C allele were signi fi cantly associated with Acute Lymphoblastic Leukemia in Yemenis of Arab-Asian descent. Borderline association found in IKZF1 rs4132601 T>G variant. No associations found with LMO1 rs442264; rs3794012; rs4237770
Title: Contributions of IKZF1, DDC, CDKN2A, CEBPE, and LMO1 Gene Polymorphisms to Acute Lymphoblastic Leukemia in a Yemeni Population.
These results suggested that LMO1 gene rs110419 A > G polymorphism may contribute to protection against neuroblastoma
Title: LMO1 gene polymorphisms contribute to decreased neuroblastoma susceptibility in a Southern Chinese population.
A C-to-T single nucleotide transition occurs as a somatic mutation in noncoding sequences 4 kb upstream of the transcriptional start site of the LMO1 oncogene in primary samples from patients with T-cell acute lymphoblastic leukaemia. This conforms to an APOBEC-like cytidine deaminase mutational signature and a new MYB binding site driving high levels of LMO1 expression.
Title: APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL.
LMO1 is an important oncogene that promotes neuroblastoma initiation, progression, and widespread metastatic dissemination.
Title: LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis.
LMO1 appears to be a coactivator of AR involved in the progression of prostate cancer
Title: Upregulated LMO1 in prostate cancer acts as a novel coactivator of the androgen receptor.
data suggest that genetic variants in LMO1 are associated with increased NB risk in Chinese children.
Title: Candidate Gene Association Analysis of Neuroblastoma in Chinese Children Strengthens the Role of LMO1.

Submit: New GeneRIF Correction See all GeneRIFs (20)

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

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed
A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Integrative genomics identifies LMO1 as a neuroblastoma oncogene. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

LMO1 (e-PCR)
- UniSTS:26133

D11S4594 (e-PCR)
- UniSTS:29757

D11S3445 (e-PCR)
- UniSTS:152686

Lmo1 (e-PCR), detects polymorphism
- UniSTS:507031

Lmo1 (e-PCR), detects polymorphism
- UniSTS:143784

Lmo1 (e-PCR), detects polymorphism
- UniSTS:536530

NoName (e-PCR)
- UniSTS:483839

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 transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of T cell homeostatic proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: rhombotin-1

Names: LIM domain only 1 (rhombotin 1); LIM domain only protein 1; LMO-1; T-cell translocation gene 1; T-cell translocation protein 1; cysteine-rich protein TTG-1

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_032827.3 RefSeqGene

Range

9758..49327

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_508

mRNA and Protein(s)

NM_001270428.2 → NP_001257357.1 rhombotin-1 isoform b

See identical proteins and their annotated locations for NP_001257357.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AC091013, AW006226, BC039512

Consensus CDS

CCDS58118.1

UniProtKB/Swiss-Prot

P25800

Related

ENSP00000404538.2, ENST00000428101.6

Conserved Domains (2) summary

cd09388
Location:23 → 77

LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

cd09389
Location:87 → 141

LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
NM_002315.3 → NP_002306.1 rhombotin-1 isoform a

See identical proteins and their annotated locations for NP_002306.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC091013

Consensus CDS

CCDS44534.1

UniProtKB/Swiss-Prot

E9PSF5, P25800, Q4VBC5, Q8IXR0

Related

ENSP00000338207.3, ENST00000335790.8

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)

RNA

NR_073006.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC091013

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_000011.10 Reference GRCh38.p14 Primary Assembly

Range

8224309..8268787 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520099.3 → XP_011518401.1 rhombotin-1 isoform X2

See identical proteins and their annotated locations for XP_011518401.1

UniProtKB/TrEMBL

E9PK83, F5H3S4

Related

ENSP00000435456.1, ENST00000534484.1

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_006718228.4 → XP_006718291.1 rhombotin-1 isoform X1

Conserved Domains (2) summary

cd09388
Location:61 → 115

LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

cd09389
Location:125 → 179

LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
XM_011520098.3 → XP_011518400.1 rhombotin-1 isoform X2

See identical proteins and their annotated locations for XP_011518400.1

UniProtKB/TrEMBL

E9PK83, F5H3S4

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_011520100.2 → XP_011518402.1 rhombotin-1 isoform X3

Conserved Domains (1) summary

cd09389
Location:54 → 108

LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)