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

    Gene ID: 4004, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See LMO1 in Genome Data Viewer
    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_000011.10Genomic 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: 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. 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. 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. LMO1 is a novel oncogene in colorectal cancer and its overexpression is a new predictive marker for anti-EGFR therapy. Liu J, et al. Tumour Biol, 2014 Aug. PMID 24845030
    4. LMO1 is a novel oncogene in lung cancer, and its overexpression is a new predictive marker for anti-EGFR therapy. Zhang Y, et al. Med Oncol, 2014 Aug. PMID 25037573
    5. Candidate Gene Association Analysis of Neuroblastoma in Chinese Children Strengthens the Role of LMO1. Lu J, et al. PLoS One, 2015. PMID 26030754, Free PMC Article

    See all (56) 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)

    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_2024_08

    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, F5H3S4

    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, F5H3S4

    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

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

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