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

    Gene ID: 4004, updated on 5-May-2013
    Official Symbol
    LMO1provided by HGNC
    Official Full Name
    LIM domain only 1 (rhombotin 1)provided by HGNC
    Primary source
    HGNC:6641
    See related
    Ensembl:ENSG00000166407; HPRD:01738; MIM:186921; Vega:OTTHUMG00000165833
    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]
    Location :
    11p15
    Sequence :
    Chromosome: 11; NC_000011.9 (8245851..8290182, complement)
    See LMO1 in Epigenomics, MapViewer

    Chromosome 11 - NC_000011.9Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3, subunit F Neighboring gene tubby homolog (mouse) Neighboring gene resistance to inhibitors of cholinesterase 3 homolog (C. elegans) Neighboring gene serine/threonine kinase 33 Neighboring gene tripartite motif containing 66

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. Manning AK, et al. Nat Genet, 2012 May 13. PMID 22581228.
    2. Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1). Beuten J, et al. Carcinogenesis, 2011 Sep. PMID 21602560.
    3. Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Wang K, et al. Nature, 2011 Jan 13. PMID 21124317.
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614.
    5. Genome-wide pleiotropy of osteoporosis-related phenotypes: the Framingham Study. Karasik D, et al. J Bone Miner Res, 2010 Jul. PMID 20200953.

    See all (28) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. genetic variants within LMO1 are associated with acute lymphoblastic leukemia and identify this gene as a strong candidate for precursor B-cell leukemogenesis.
      Title: Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1).
    2. data show that common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma, but also may influence the likelihood of further somatic alterations at this locus, leading to malignant progression
      Title: Integrative genomics identifies LMO1 as a neuroblastoma oncogene.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide pleiotropy of osteoporosis-related phenotypes: the Framingham Study.
    5. The present data suggest that TGF-beta, LMO1, possibly RUNX3, and GSDM form a regulatory pathway for directing the pit cells to apoptosis.
      Title: GASDERMIN, suppressed frequently in gastric cancer, is a target of LMO1 in TGF-beta-dependent apoptotic signalling.
    6. 60% of transgenic mice that overexpressed both OLIG2 and LMO1 developed pre-T lymphoblastic lymphoma/leukemia with large thymic tumor masses.
      Title: OLIG2 (BHLHB1), a bHLH transcription factor, contributes to leukemogenesis in concert with LMO1.
    Submit: New GeneRIF Correction

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    P25800 P23771 GATA3    HPRD  PubMed  
    P25800 Q86U70 LDB1    HPRD  PubMed  
    P25800 P12980 LYL1    HPRD  PubMed  
    P25800 Q02575 NHLH1    HPRD  PubMed  
    P25800 P17542 TAL1    HPRD  PubMed  
    P25800 Q16559 TAL2    HPRD  PubMed  
    BioGRID:110190 BioGRID:108895 GATA3    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 
    BioGRID:110190 BioGRID:110244 LYL1    BioGRID  PubMed Two-hybrid 
    BioGRID:110190 BioGRID:112749 TAL1    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex; Two-hybrid 
    BioGRID:110190 BioGRID:112750 TAL2    BioGRID  PubMed Two-hybrid 

    Markers

    Genotypes

    Homology

    Clone Names

    • MGC116692

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    negative regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
    		  
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    		  
    Component Evidence Code Pubs
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Preferred Names
    rhombotin-1
    Names
    rhombotin-1
    LMO-1
    LIM domain only protein 1
    T-cell translocation gene 1
    cysteine-rich protein TTG-1
    T-cell translocation protein 1

    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.

    mRNA and Protein(s)

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

      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/TrEMBL
      E9PSF5
      UniProtKB/TrEMBL
      Q8IXR0
      Related
      ENSP00000404538, OTTHUMP00000231157, ENST00000428101, OTTHUMT00000386504
      Conserved Domains (2) summary
      cd09388
      Location:23 – 77
      Blast Score: 262
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:87 – 141
      Blast Score: 257
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    2. NM_002315.2 → NP_002306.1  rhombotin-1 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC091013, AW006226, BP218183, M26682
      Consensus CDS
      CCDS44534.1
      UniProtKB/Swiss-Prot
      P25800
      Related
      ENSP00000338207, OTTHUMP00000231156, ENST00000335790, OTTHUMT00000386503
      Conserved Domains (2) summary
      cd09388
      Location:24 – 78
      Blast Score: 262
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:88 – 142
      Blast Score: 257
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    RNA

    1. NR_073006.1 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, AW006226, BC096058, BP218183, M26682

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000011.9 Reference GRCh37.p10 Primary Assembly

      Range
      8245851..8290182, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000143.1 Alternate HuRef

      Range
      7913914..7958156, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018922.1 Alternate CHM1_1.0

      Range
      8170435..8214746, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01028688.1 (51651..70313) None
    genomic ABBA01028689.1 None
    genomic ABBA01028690.1 (23995..29180) None
    genomic AC091013.7 (126394..165943) None
    genomic AJ277662.1 CAC14587.1
    genomic AMYH01003374.1 (142727..187038) None
    genomic CH471064.2 EAW68626.1
    genomic U73635.1 None
    mRNA AW006226.1 None
    mRNA BC039512.1 AAH39512.1
    mRNA BC069673.1 AAH69673.1
    mRNA BC069752.1 AAH69752.1
    mRNA BC069793.1 AAH69793.1
    mRNA BC096056.3 AAH96056.1
    mRNA BC096057.3 AAH96057.1
    mRNA BC096058.1 AAH96058.1
    mRNA BP218183.1 None
    mRNA M26682.1 AAA36819.1
    mRNA X64244.1 None
    other-genetic HQ448387.1 ADQ32867.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    P25800.1 GenPept UniProtKB/Swiss-Prot:P25800

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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      Supplemental Content

      Table of contents

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      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • GAP
        GAP Links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
      • GEO Profiles
        Related GEO
      • HomoloGene
        Links between HomoloGene and Gene are provided by the HomoloGene group when a gene is included in a HomoloGene record.
      • Map Viewer
        These links are maintained by the Map Viewer group and are provided when a GeneID is annotated on a map for the same species.
      • Nucleotide
        Link to related Nucleotide entry
      • OMIM
        Links between OMIM and Gene are calculated by Gene based on MIM numbers included in the summary and phenotype sections of the Gene record.
      • Probe
        Related Probe entry
      • Protein
        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
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        Gene Genotype Report
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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