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Aliases for LMO1 Gene

Aliases for LMO1 Gene

  • LIM Domain Only 1 2 3 5
  • T-Cell Translocation Protein 1 3 4
  • Cysteine-Rich Protein TTG-1 3 4
  • LIM Domain Only Protein 1 3 4
  • RBTN1 3 4
  • LMO-1 3 4
  • RHOM1 3 4
  • TTG1 3 4
  • LIM Domain Only 1 (Rhombotin 1) 3
  • T-Cell Translocation Gene 1 3
  • Rhombotin-1 3
  • Rhombotin 1 2

External Ids for LMO1 Gene

Previous HGNC Symbols for LMO1 Gene

  • RBTN1

Previous GeneCards Identifiers for LMO1 Gene

  • GC11M009030
  • GC11M008706
  • GC11M008204
  • GC11M008210
  • GC11M008202
  • GC11M007915

Summaries for LMO1 Gene

Entrez Gene Summary for LMO1 Gene

  • 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]

GeneCards Summary for LMO1 Gene

LMO1 (LIM Domain Only 1) is a Protein Coding gene. Diseases associated with LMO1 include Exencephaly and T-Cell Leukemia. An important paralog of this gene is LMO3.

UniProtKB/Swiss-Prot for LMO1 Gene

  • May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Gene Wiki entry for LMO1 Gene

Additional gene information for LMO1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMO1 Gene

Genomics for LMO1 Gene

GeneHancer (GH) Regulatory Elements for LMO1 Gene

Promoters and enhancers for LMO1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J008262 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 650.4 +5.7 5668 1.4 CTCF MXI1 ZBTB6 ZIC2 ZNF335 E2F1 ZFHX2 POLR2A ZBTB48 PRDM10 LMO1 TRIM66 GC11P008258 GC11P008268
GH11J008263 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 650.7 +4.8 4760 0.2 CTCF RAD21 POLR2A SMC3 ZNF143 ZSCAN29 PRDM10 RCOR1 CHD2 EZH2 LMO1 GC11P008268 GC11P008258
GH11J008268 Promoter/Enhancer 0.9 EPDnew dbSUPER 650.7 -0.1 -91 0.1 SUZ12 ZSCAN4 EZH2 GC11P008268 LMO1 GC11M008295
GH11J008231 Enhancer 1.1 Ensembl ENCODE dbSUPER 5.5 +35.2 35226 3.4 CTCF JUN SREBF2 SIN3A ZIC2 GLIS2 POLR2A ZBTB48 SMC3 PRDM10 LMO1 LOC105376536 GC11P008258
GH11J008258 Enhancer 0.8 ENCODE dbSUPER 5 +9.9 9941 1.4 NFYA ZNF189 JUN MAX CEBPB CEBPG EP300 OSR2 JUND POLR2A GC11P008258 LMO1 LOC105376536
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LMO1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LMO1 gene promoter:

Genomic Locations for LMO1 Gene

Genomic Locations for LMO1 Gene
chr11:8,224,304-8,268,716
(GRCh38/hg38)
Size:
44,413 bases
Orientation:
Minus strand
chr11:8,245,851-8,290,263
(GRCh37/hg19)

Genomic View for LMO1 Gene

Genes around LMO1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMO1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMO1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMO1 Gene

Proteins for LMO1 Gene

  • Protein details for LMO1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P25800-RBTN1_HUMAN
    Recommended name:
    Rhombotin-1
    Protein Accession:
    P25800
    Secondary Accessions:
    • E9PSF5
    • Q4VBC5
    • Q8IXR0

    Protein attributes for LMO1 Gene

    Size:
    156 amino acids
    Molecular mass:
    17828 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH39512.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for LMO1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMO1 Gene

Post-translational modifications for LMO1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LMO1 Gene

No data available for DME Specific Peptides for LMO1 Gene

Domains & Families for LMO1 Gene

Gene Families for LMO1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for LMO1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LMO1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LMO1: view

No data available for UniProtKB/Swiss-Prot for LMO1 Gene

Function for LMO1 Gene

Molecular function for LMO1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.
GENATLAS Biochemistry:
LIM domain only 1,rhombotin 1,expressed in rhombomeres

Phenotypes From GWAS Catalog for LMO1 Gene

Gene Ontology (GO) - Molecular Function for LMO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21516116
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LMO1: view
genes like me logo Genes that share phenotypes with LMO1: view

Human Phenotype Ontology for LMO1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LMO1 Gene

MGI Knock Outs for LMO1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for LMO1 Gene

Localization for LMO1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMO1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LMO1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LMO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with LMO1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LMO1 Gene

Pathways & Interactions for LMO1 Gene

No Data Available

SIGNOR curated interactions for LMO1 Gene

Activates:

Gene Ontology (GO) - Biological Process for LMO1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0045944 positive regulation of transcription by RNA polymerase II IMP 20855495
GO:0046013 regulation of T cell homeostatic proliferation IEA --
GO:1902036 regulation of hematopoietic stem cell differentiation TAS --
genes like me logo Genes that share ontologies with LMO1: view

No data available for Pathways by source for LMO1 Gene

Drugs & Compounds for LMO1 Gene

No Compound Related Data Available

Transcripts for LMO1 Gene

Unigene Clusters for LMO1 Gene

LIM domain only 1 (rhombotin 1):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LMO1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c
SP1: - - -
SP2: -
SP3:

Relevant External Links for LMO1 Gene

GeneLoc Exon Structure for
LMO1
ECgene alternative splicing isoforms for
LMO1

Expression for LMO1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LMO1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LMO1 Gene

This gene is overexpressed in Muscle - Skeletal (x7.6), Skin - Not Sun Exposed (Suprapubic) (x6.1), Skin - Sun Exposed (Lower leg) (x4.3), and Brain - Hypothalamus (x4.2).

Protein differential expression in normal tissues from HIPED for LMO1 Gene

This gene is overexpressed in Urine (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LMO1 Gene



Protein tissue co-expression partners for LMO1 Gene

NURSA nuclear receptor signaling pathways regulating expression of LMO1 Gene:

LMO1

SOURCE GeneReport for Unigene cluster for LMO1 Gene:

Hs.654426

mRNA Expression by UniProt/SwissProt for LMO1 Gene:

P25800-RBTN1_HUMAN
Tissue specificity: Expressed mainly in the central nervous. Low level of expression in other tissues including thymus.

Evidence on tissue expression from TISSUES for LMO1 Gene

  • Blood(4.3)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with LMO1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LMO1 Gene

Orthologs for LMO1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LMO1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LMO1 34 33
  • 100 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMO1 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LMO1 34 33
  • 95.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LMO1 34 33
  • 94.87 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LMO1 34
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lmo1 16 34 33
  • 93.16 (n)
rat
(Rattus norvegicus)
Mammalia Lmo1 33
  • 92.9 (n)
chicken
(Gallus gallus)
Aves LMO1 34
  • 97 (a)
OneToOne
LOC100858792 33
  • 84.83 (n)
lizard
(Anolis carolinensis)
Reptilia LMO1 34
  • 94 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.32263 33
zebrafish
(Danio rerio)
Actinopterygii lmo1 34 33 33
  • 85.16 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9759 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000731 33
  • 73.18 (n)
fruit fly
(Drosophila melanogaster)
Insecta Bx 34 35
  • 27 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.9021 33
Species where no ortholog for LMO1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LMO1 Gene

ENSEMBL:
Gene Tree for LMO1 (if available)
TreeFam:
Gene Tree for LMO1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMO1: view image

Paralogs for LMO1 Gene

Paralogs for LMO1 Gene

(23) SIMAP similar genes for LMO1 Gene using alignment to 4 proteins:

  • RBTN1_HUMAN
  • E9PK83_HUMAN
  • Q4VBC4_HUMAN
  • Q9H4D3_HUMAN
genes like me logo Genes that share paralogs with LMO1: view

Variants for LMO1 Gene

Sequence variations from dbSNP and Humsavar for LMO1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs2168101 benign, LIM DOMAIN ONLY-1 POLYMORPHISM 8,233,861(-) C/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000039567 -- 8,241,867(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000101161 -- 8,246,254(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000232443 -- 8,236,942(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000237108 -- 8,252,008(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LMO1 Gene

Variant ID Type Subtype PubMed ID
nsv1040979 CNV gain 25217958
nsv1054339 CNV gain 25217958
nsv469936 CNV loss 18288195
nsv499766 OTHER inversion 21111241
nsv522567 CNV loss 19592680
nsv527329 CNV loss 19592680
nsv553446 CNV loss 21841781
nsv7215 OTHER inversion 18451855
nsv7663 CNV insertion 18451855

Variation tolerance for LMO1 Gene

Residual Variation Intolerance Score: 36.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.35; 7.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMO1 Gene

Human Gene Mutation Database (HGMD)
LMO1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMO1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMO1 Gene

Disorders for LMO1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for LMO1 Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
exencephaly
t-cell leukemia
  • leukemia t-cell
immunodeficiency 18
  • imd18
neuroblastoma
  • neuroblastoma, susceptibility to
acute t cell leukemia
  • precursor t lymphoblastic leukemia
- elite association - COSMIC cancer census association via MalaCards
Search LMO1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RBTN1_HUMAN
  • Note=A chromosomal aberration involving LMO1 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(11,14)(p15;q11) with TCRD.

Genatlas disease for LMO1 Gene

acute lymphoblastic leukemia (T ALL),with translocation t(11;14)(p15;q11),and a LMO1/LDB1 interaction,likely involved in tumorigenesis

Additional Disease Information for LMO1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Tumor Gene Database
(TGDB)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LMO1: view

Publications for LMO1 Gene

  1. Comparative architectural aspects of regions of conserved synteny on human chromosome 11p15.3 and mouse chromosome 7 (including genes WEE1 and LMO1). (PMID: 11528126) Cichutek A … Zabel BU (Cytogenetics and cell genetics 2001) 3 4 22 58
  2. T-cell translocation gene 1 (Ttg-1) encodes a nuclear protein normally expressed in neural lineage cells. (PMID: 1703797) McGuire EA … Korsmeyer SJ (Blood 1991) 2 3 4 58
  3. Integrative genomics identifies LMO1 as a neuroblastoma oncogene. (PMID: 21124317) Wang K … Maris JM (Nature 2011) 3 44 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. GASDERMIN, suppressed frequently in gastric cancer, is a target of LMO1 in TGF-beta-dependent apoptotic signalling. (PMID: 17471240) Saeki N … Sasaki H (Oncogene 2007) 3 22 58

Products for LMO1 Gene

Sources for LMO1 Gene

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