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

Gene ID: 4004, updated on 3-Apr-2024

Summary

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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
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Genomic context

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Location:
11p15.4
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (8224309..8268787, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (8305646..8350087, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (8245856..8290334, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TUB bipartite transcription factor Neighboring gene RIC3 acetylcholine receptor chaperone Neighboring gene Sharpr-MPRA regulatory region 8819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8214713-8215283 Neighboring gene VISTA enhancer hs1859 Neighboring gene RIC3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8244025-8244526 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8248695-8249355 Neighboring gene uncharacterized LOC105376536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8271693-8272438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8272439-8273182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8281879-8282380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8283311-8283850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8288990-8289574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8289575-8290158 Neighboring gene MPRA-validated peak1191 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:8304411-8304972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8303849-8304410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8339910-8340410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:8347375-8347960 Neighboring gene Sharpr-MPRA regulatory region 11418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8358075-8358892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8359711-8360526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8360626-8361287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:8373273-8373772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4384 Neighboring gene serine/threonine kinase 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4385 Neighboring gene small Cajal body-specific RNA 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3114 Neighboring gene NANOG hESC enhancer GRCh37_chr11:8625413-8625914 Neighboring gene tripartite motif containing 66 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:8692389-8692996 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:8703769-8704968 Neighboring gene ribosomal protein L27a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Circ_0021087 acts as a miR-184 sponge and represses gastric cancer progression by adsorbing miR-184 and elevating FOSB expression. Yu Y, et al. Eur J Clin Invest, 2021 Nov. PMID 34076278
  2. LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies. Hashemi M, et al. J Cell Mol Med, 2020 Jan. PMID 31830377, Free PMC Article
  3. Indirect Down-regulation of Tumor-suppressive let-7 Family MicroRNAs by LMO1 in Neuroblastoma. Saeki N, et al. Cancer Genomics Proteomics, 2018 Sep-Oct. PMID 30194082, Free PMC Article
  4. APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL. Li Z, et al. Leukemia, 2017 Oct. PMID 28260788, Free PMC Article
  5. LMO1 gene polymorphisms contribute to decreased neuroblastoma susceptibility in a Southern Chinese population. He J, et al. Oncotarget, 2016 Apr 19. PMID 27009839, Free PMC Article

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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
A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.
EBI GWAS Catalog
Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma.
EBI GWAS Catalog
Integrative genomics identifies LMO1 as a neuroblastoma oncogene.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC116692

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

  1. NG_032827.3 RefSeqGene

    Range
    9758..49327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_508

mRNA and Protein(s)

  1. 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)

  2. 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

  1. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    8224309..8268787 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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)

  2. 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)

  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)

  4. 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)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    8305646..8350087 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368771.1 → XP_054224746.1  rhombotin-1 isoform X2

    UniProtKB/TrEMBL
    E9PK83

  2. XM_054368770.1 → XP_054224745.1  rhombotin-1 isoform X1

  3. XM_054368772.1 → XP_054224747.1  rhombotin-1 isoform X2

    UniProtKB/TrEMBL
    E9PK83

  4. XM_054368773.1 → XP_054224748.1  rhombotin-1 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P25800.1 GenPept UniProtKB/Swiss-Prot:P25800

Gene LinkOut

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