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Aliases for LMO3 Gene

Aliases for LMO3 Gene

  • LIM Domain Only 3 2 3 5
  • Neuronal-Specific Transcription Factor DAT1 3 4
  • Rhombotin-3 3 4
  • RBTNL2 3 4
  • RBTN3 3 4
  • RHOM3 3 4
  • LIM Domain Only 3 (Rhombotin-Like 2) 3
  • LIM Domain Only Protein 3 3
  • Rhombotin-Like 2 2
  • Rhom-3 3
  • LMO-3 4

External Ids for LMO3 Gene

Previous HGNC Symbols for LMO3 Gene

  • RBTNL2

Previous GeneCards Identifiers for LMO3 Gene

  • GC12U990051
  • GC12M016593
  • GC12M016594
  • GC12M016701
  • GC12M016469

Summaries for LMO3 Gene

Entrez Gene Summary for LMO3 Gene

  • The protein encoded by this gene belongs to the rhombotin family of cysteine-rich LIM domain oncogenes. This gene is predominantly expressed in the brain. Related family members, LMO1 and LMO2 on chromosome 11, have been reported to be involved in chromosomal translocations in T-cell leukemia. Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]

GeneCards Summary for LMO3 Gene

LMO3 (LIM Domain Only 3) is a Protein Coding gene. An important paralog of this gene is LMO1.

Gene Wiki entry for LMO3 Gene

Additional gene information for LMO3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LMO3 Gene

Genomics for LMO3 Gene

GeneHancer (GH) Regulatory Elements for LMO3 Gene

Promoters and enhancers for LMO3 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
GH12J016605 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 650.7 +4.5 4545 2.5 MXI1 FOXA2 SUZ12 ZNF398 ZNF335 POLR2A IKZF1 SCRT2 MLLT1 ZBTB26 LMO3 GC12P016607 GC12P016604 MGST1
GH12J016611 Enhancer 0.9 UCNEbase dbSUPER 650.7 -0.3 -328 0.4 NANOG POU5F1 ATF7 MEF2B KLF5 ETS1 LMO3 GC12P016610 GC12P016607 GC12P016622
GH12J016832 Promoter 0.8 EPDnew 650.1 -221.8 -221762 0.1 SMAD1 IKZF1 ZNF207 EBF1 MEF2B MLLT1 IKZF2 LMO3 GC12M016744 GC12P016797 GC12P016793 LOC105369677
GH12J016610 Enhancer 0.7 UCNEbase dbSUPER 650.7 +0.2 214 0.4 MLLT1 LMO3 GC12P016610 GC12P016607
GH12J016608 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.7 +2.5 2459 0.1 LMO3 GC12P016607 GC12P016610 MGST1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LMO3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LMO3 gene promoter:
  • GR-alpha
  • GR
  • IRF-7A
  • Nkx2-5
  • aMEF-2

Genomic Locations for LMO3 Gene

Genomic Locations for LMO3 Gene
chr12:16,548,372-16,610,594
(GRCh38/hg38)
Size:
62,223 bases
Orientation:
Minus strand
chr12:16,701,307-16,763,528
(GRCh37/hg19)
Size:
62,222 bases
Orientation:
Minus strand

Genomic View for LMO3 Gene

Genes around LMO3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMO3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMO3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LMO3 Gene

Proteins for LMO3 Gene

  • Protein details for LMO3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TAP4-LMO3_HUMAN
    Recommended name:
    LIM domain only protein 3
    Protein Accession:
    Q8TAP4
    Secondary Accessions:
    • B4DG90
    • B4DH35
    • Q58A66
    • Q58A67
    • Q8N974
    • Q9UDD5

    Protein attributes for LMO3 Gene

    Size:
    145 amino acids
    Molecular mass:
    16594 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LMO3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMO3 Gene

Post-translational modifications for LMO3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LMO3 Gene

Domains & Families for LMO3 Gene

Gene Families for LMO3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LMO3 Gene

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LMO3: view

No data available for UniProtKB/Swiss-Prot for LMO3 Gene

Function for LMO3 Gene

Molecular function for LMO3 Gene

GENATLAS Biochemistry:
Lim domain only 3

Phenotypes From GWAS Catalog for LMO3 Gene

Gene Ontology (GO) - Molecular Function for LMO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LMO3: view
genes like me logo Genes that share phenotypes with LMO3: view

Animal Model Products

miRNA for LMO3 Gene

miRTarBase miRNAs that target LMO3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LMO3 Gene

Localization for LMO3 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 LMO3 gene
Compartment Confidence
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for LMO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 23823477
genes like me logo Genes that share ontologies with LMO3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for LMO3 Gene

Pathways & Interactions for LMO3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LMO3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0035360 positive regulation of peroxisome proliferator activated receptor signaling pathway IDA 23823477
GO:0045600 positive regulation of fat cell differentiation IMP 23823477
GO:0070373 negative regulation of ERK1 and ERK2 cascade IDA 23823477
genes like me logo Genes that share ontologies with LMO3: view

No data available for Pathways by source and SIGNOR curated interactions for LMO3 Gene

Drugs & Compounds for LMO3 Gene

No Compound Related Data Available

Transcripts for LMO3 Gene

Unigene Clusters for LMO3 Gene

LIM domain only 3 (rhombotin-like 2):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LMO3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16a ·
SP1: - - - - - - - - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - - -
SP7: - - - - - - - -
SP8: - - - - - - -
SP9: - - - - - - - - - - - - - - - - - - - - - - -
SP10: - - - - - - - - - - - - - - - - - - - - -
SP11: - - - - - - - - - - - - - - - - - -
SP12: - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - - - - -
SP14: - - - - - - - - - - - - - - - - - -
SP15: - - - - - - - - - - - - - - - -
SP16: - - - - - - - - - - - - - -
SP17: - - - - - - - - - - - - -
SP18: - - - - - - - -
SP19: - - - - - - - -
SP20: - - - - - -
SP21: - - - - -
SP22: - - - - -
SP23: - - - - - - - - - - - - - - - - - - - - - - - - -
SP24: - -
SP25: - -
SP26: - - - - - - - - - - - - - - - - - - - - - - -
SP27: - - - - - - - - - - - - - - - - -
SP28: - - - -
SP29: -
SP30:
SP31: - - - - -
SP32:

ExUns: 16b · 16c ^ 17a · 17b · 17c · 17d ^ 18 ^ 19a · 19b · 19c · 19d ^ 20a · 20b · 20c · 20d · 20e ^ 21a · 21b · 21c · 21d · 21e · 21f · 21g · 21h · 21i
SP1: - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - -
SP7: - - - - -
SP8: - - - - - - - -
SP9: - - - - - - - -
SP10: - - - - - - - -
SP11: - - - - - - - -
SP12: - - - - -
SP13: - - - - - - - - - -
SP14: - - - - - - -
SP15: - - - - - - - - - -
SP16: - - - - - - - -
SP17: - - - - - - - -
SP18: - - - - - - - - - -
SP19: - - -
SP20: - - - - - - - -
SP21: - - - - - - - - - -
SP22: - - - - - - - -
SP23: - - - - - - - -
SP24: - - - - - - - -
SP25: - - - - - - - - - -
SP26: - - - - - -
SP27: - -
SP28: - - - - - - - - - -
SP29: - - - - - - - -
SP30: - - - - - - -
SP31: - -
SP32:

Relevant External Links for LMO3 Gene

GeneLoc Exon Structure for
LMO3
ECgene alternative splicing isoforms for
LMO3

Expression for LMO3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LMO3 Gene

mRNA differential expression in normal tissues according to GTEx for LMO3 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x4.8), Brain - Amygdala (x4.4), Brain - Frontal Cortex (BA9) (x4.1), and Brain - Anterior cingulate cortex (BA24) (x4.1).

Protein differential expression in normal tissues from HIPED for LMO3 Gene

This gene is overexpressed in Uterus (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LMO3 Gene



Protein tissue co-expression partners for LMO3 Gene

NURSA nuclear receptor signaling pathways regulating expression of LMO3 Gene:

LMO3

SOURCE GeneReport for Unigene cluster for LMO3 Gene:

Hs.504908

Evidence on tissue expression from TISSUES for LMO3 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with LMO3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LMO3 Gene

Orthologs for LMO3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LMO3 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Lmo3 34
  • 88 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LMO3 34
  • 88 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LMO3 34
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LMO3 34
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LMO3 34
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LMO3 34
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves LMO3 34
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LMO3 34
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.6611 33
zebrafish
(Danio rerio)
Actinopterygii lmo3 34
  • 76 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010391 33
  • 69.05 (n)
fruit fly
(Drosophila melanogaster)
Insecta Bx 34
  • 22 (a)
OneToMany
Species where no ortholog for LMO3 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • 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 LMO3 Gene

ENSEMBL:
Gene Tree for LMO3 (if available)
TreeFam:
Gene Tree for LMO3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMO3: view image

Paralogs for LMO3 Gene

Paralogs for LMO3 Gene

(26) SIMAP similar genes for LMO3 Gene using alignment to 11 proteins:

  • LMO3_HUMAN
  • C9JE61_HUMAN
  • F5GYZ6_HUMAN
  • F5GZR3_HUMAN
  • F5H2N9_HUMAN
  • F5H3S4_HUMAN
  • F5H4K9_HUMAN
  • F5H4T0_HUMAN
  • F5H655_HUMAN
  • F6TDU8_HUMAN
  • Q05D86_HUMAN
genes like me logo Genes that share paralogs with LMO3: view

Variants for LMO3 Gene

Sequence variations from dbSNP and Humsavar for LMO3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000057979 -- 16,571,474(-) A/G intron_variant
rs1000114524 -- 16,597,654(-) T/G intron_variant
rs1000149954 -- 16,553,826(-) G/C intron_variant
rs1000166838 -- 16,598,084(-) T/C intron_variant
rs1000198643 -- 16,597,521(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LMO3 Gene

Variant ID Type Subtype PubMed ID
nsv832339 CNV gain 17160897
nsv1042630 CNV loss 25217958
nsv1037881 CNV loss 25217958
nsv1037740 CNV loss 25217958

Variation tolerance for LMO3 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.02; 0.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMO3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMO3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMO3 Gene

Disorders for LMO3 Gene

Additional Disease Information for LMO3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LMO3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LMO3 Gene

Publications for LMO3 Gene

  1. LMO3 interacts with p53 and inhibits its transcriptional activity. (PMID: 19995558) Larsen S … Nakagawara A (Biochemical and biophysical research communications 2010) 3 22 58
  2. LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. (PMID: 15930276) Aoyama M … Nakagawara A (Cancer research 2005) 3 22 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Identification of dopamine responsive mRNAs in glial cells by suppression subtractive hybridization. (PMID: 11489251) Shi J … Xie Y (Brain research 2001) 2 3 58

Products for LMO3 Gene

Sources for LMO3 Gene

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