LMO2 Gene (Protein Coding)

LIM Domain Only 2

GC11M033858
GIFtS:
43
LMO2 encodes a cysteine-rich, two LIM-domain protein that is required for yolk sac erythropoiesis. The LMO2 protein has a central and crucial role in hematopoietic development and is highly conserved. The LMO2 transcription start site is located approximately 25 kb downstream from the 11p13 T-cell translocation cluster (11p13 ttc), where a number T-cell acute lymphoblastic leuk... See more...

Aliases for LMO2 Gene

Aliases for LMO2 Gene

  • LIM Domain Only 2 2 3 5
  • T-Cell Translocation Protein 2 3 4
  • Cysteine-Rich Protein TTG-2 3 4
  • T-Cell Translocation Gene 2 2 3
  • LIM Domain Only Protein 2 3 4
  • Rhombotin-Like 1 2 3
  • Rhombotin-2 3 4
  • RBTNL1 3 4
  • LMO-2 3 4
  • RBTN2 3 4
  • RHOM2 3 4
  • TTG2 3 4

External Ids for LMO2 Gene

Previous HGNC Symbols for LMO2 Gene

  • RBTNL1

Previous GeneCards Identifiers for LMO2 Gene

  • GC11M035411
  • GC11M034557
  • GC11M033919
  • GC11M033844
  • GC11M033836
  • GC11M033576
  • GC11M033880

Summaries for LMO2 Gene

Entrez Gene Summary for LMO2 Gene

  • LMO2 encodes a cysteine-rich, two LIM-domain protein that is required for yolk sac erythropoiesis. The LMO2 protein has a central and crucial role in hematopoietic development and is highly conserved. The LMO2 transcription start site is located approximately 25 kb downstream from the 11p13 T-cell translocation cluster (11p13 ttc), where a number T-cell acute lymphoblastic leukemia-specific translocations occur. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Nov 2008]

GeneCards Summary for LMO2 Gene

LMO2 (LIM Domain Only 2) is a Protein Coding gene. Diseases associated with LMO2 include Severe Combined Immunodeficiency, X-Linked and Lymphoblastic Lymphoma. Among its related pathways are Hematopoietic Stem Cell Differentiation and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. Gene Ontology (GO) annotations related to this gene include chromatin binding and RNA polymerase II regulatory region sequence-specific DNA binding. An important paralog of this gene is LMO1.

UniProtKB/Swiss-Prot Summary for LMO2 Gene

  • Acts with TAL1/SCL to regulate red blood cell development. Also acts with LDB1 to maintain erythroid precursors in an immature state.

Gene Wiki entry for LMO2 Gene

Additional gene information for LMO2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LMO2 Gene

Genomics for LMO2 Gene

GeneHancer (GH) Regulatory Elements for LMO2 Gene

Promoters and enhancers for LMO2 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
GH11J033867 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 501.7 +22.8 22760 5.1 NRF1 ZBTB11 ZBTB26 MYC CTBP1 PRPF4 ZNF341 EZH2 NFRKB KDM5B LMO2 lnc-FBXO3-2 ABTB2 lnc-LMO2-3
GH11J033890 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 508.4 -0.8 -791 5.4 ZSCAN5C SIN3A NRF1 SP1 EP300 POLR2A AFF1 TRIM28 RELA HES1 LMO2 LOC105376621 HSALNG0083550 CSTF3
GH11J033912 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 15.8 -20.5 -20472 1.2 SP1 GTF2E2 JUND FOS ZNF639 EP300 ZBTB11 AFF1 TRIM28 CTBP1 LMO2 ENSG00000184566 piR-42491-027 lnc-CAPRIN1-5
GH11J033928 Enhancer 1.3 ENCODE CraniofacialAtlas dbSUPER 13.2 -41.3 -41342 9.7 EP300 ZBTB11 AFF1 CTBP1 TAF9B ZNF341 RBM25 OSR2 HDAC3 NR2F2 LMO2 ENSG00000184566 NAT10 lnc-CAPRIN1-5 lnc-LMO2-2 piR-42491-027
GH11J033920 Enhancer 1.1 Ensembl ENCODE dbSUPER 13.2 -28.4 -28412 3.4 SP1 EP300 RELA TRIM22 POLR2A EZH2 BCL11A TCF12 CBFB USF2 LMO2 ENSG00000184566 APIP piR-42491-027 lnc-CAPRIN1-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LMO2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LMO2

Top Transcription factor binding sites by QIAGEN in the LMO2 gene promoter:
  • AML1a

Genomic Locations for LMO2 Gene

Genomic Locations for LMO2 Gene
chr11:33,858,576-33,892,289
(GRCh38/hg38)
Size:
33,714 bases
Orientation:
Minus strand
chr11:33,880,122-33,913,836
(GRCh37/hg19)
Size:
33,715 bases
Orientation:
Minus strand

Genomic View for LMO2 Gene

Genes around LMO2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LMO2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LMO2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for LMO2 Gene

Proteins for LMO2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for LMO2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P25791-RBTN2_HUMAN
    Recommended name:
    Rhombotin-2
    Protein Accession:
    P25791
    Secondary Accessions:
    • Q9HD58

    Protein attributes for LMO2 Gene

    Size:
    158 amino acids
    Molecular mass:
    18358 Da
    Quaternary structure:
    • Interacts via its LIM domains with ELF2 and LDB1. Also interacts with basic helix-loop-helix protein TAL1/SCL and can assemble in a complex with LMO2 and TAL1/SCL (By similarity). Interacts with BEX2 and KDM5A.
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
    SequenceCaution:
    • Sequence=AAF98804.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305}; Sequence=AAH73973.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=CAA43430.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for LMO2 Gene

    Alternative splice isoforms for LMO2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LMO2 Gene

Protein Expression for LMO2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LMO2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LMO2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LMO2 Gene

Domains & Families for LMO2 Gene

Gene Families for LMO2 Gene

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

Protein Domains for LMO2 Gene

Blocks:
  • Zn-binding protein, LIM
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LMO2 Gene

GenScript: Design optimal peptide antigens:
  • T-cell translocation protein 2 (RBTN2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P25791

UniProtKB/Swiss-Prot:

RBTN2_HUMAN :
  • The second LIM zinc-binding domain interacts with KDM5A.
Domain:
  • The second LIM zinc-binding domain interacts with KDM5A.
genes like me logo Genes that share domains with LMO2: view

Function for LMO2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for LMO2 Gene

UniProtKB/Swiss-Prot Function:
Acts with TAL1/SCL to regulate red blood cell development. Also acts with LDB1 to maintain erythroid precursors in an immature state.
GENATLAS Biochemistry:
LIM domain only 2,rhombotin 2,involved in association with LMO1 (and others),in the formation of multimeric DNA-binding complex for the generation of hematopoietic lineages and angiogenesis (in mice)

Phenotypes From GWAS Catalog for LMO2 Gene

Gene Ontology (GO) - Molecular Function for LMO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 16314316
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IDA 16314316
GO:0001102 RNA polymerase II activating transcription factor binding IPI 16314316
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 16314316
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with LMO2: view
genes like me logo Genes that share phenotypes with LMO2: view

Animal Models for LMO2 Gene

MGI Knock Outs for LMO2:

Animal Model Products

CRISPR Products

miRNA for LMO2 Gene

miRTarBase miRNAs that target LMO2

Transcription Factor Targets for LMO2 Gene

Selected GeneGlobe predicted Target genes for LMO2

Clone Products

  • Addgene plasmids for LMO2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for LMO2 Gene

Localization for LMO2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LMO2 Gene

Nucleus.

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 LMO2 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LMO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005667 transcription factor complex IDA 16314316
genes like me logo Genes that share ontologies with LMO2: view

Pathways & Interactions for LMO2 Gene

genes like me logo Genes that share pathways with LMO2: view

Pathways by source for LMO2 Gene

1 BioSystems pathway for LMO2 Gene
1 KEGG pathway for LMO2 Gene

SIGNOR curated interactions for LMO2 Gene

Activates:

Gene Ontology (GO) - Biological Process for LMO2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development TAS 1923511
GO:0042789 mRNA transcription by RNA polymerase II IDA 16314316
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 16314316
GO:0097067 cellular response to thyroid hormone stimulus IDA 19375645
GO:1902036 regulation of hematopoietic stem cell differentiation TAS --
genes like me logo Genes that share ontologies with LMO2: view

Drugs & Compounds for LMO2 Gene

Products:

  1. Drug

(2) Drugs for LMO2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for LMO2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LMO2: view

Transcripts for LMO2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for LMO2 Gene

3 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for LMO2

Alternative Splicing Database (ASD) splice patterns (SP) for LMO2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b
SP1: - -
SP2: -
SP3: - -
SP4: - - - -
SP5:
SP6:
SP7:

Relevant External Links for LMO2 Gene

GeneLoc Exon Structure for
LMO2

Expression for LMO2 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LMO2 Gene

mRNA expression in normal human tissues for LMO2 Gene
mRNA expression by GTEx for LMO2 GenemRNA expression by BioGPS for LMO2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LMO2 Gene

This gene is overexpressed in Fetal Liver (48.0) and Placenta (21.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LMO2 Gene



Protein tissue co-expression partners for LMO2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LMO2

SOURCE GeneReport for Unigene cluster for LMO2 Gene:

Hs.34560

Evidence on tissue expression from TISSUES for LMO2 Gene

  • Nervous system(4.4)
  • Kidney(4.3)
  • Intestine(4.2)
  • Blood(3)
  • Bone marrow(2.5)
  • Lymph node(2.4)
  • Heart(2)
genes like me logo Genes that share expression patterns with LMO2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LMO2 Gene

Orthologs for LMO2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LMO2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia LMO2 31
  • 99 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia LMO2 31 30
  • 98.53 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia LMO2 31
  • 94 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Lmo2 17 31 30
  • 92.27 (n)
rat
(Rattus norvegicus)
 Mammalia Lmo2 30
  • 91.82 (n)
dog
(Canis familiaris)
 Mammalia LOC609006 30
  • 90.76 (n)
LMO2 31
  • 82 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia LMO2 31
  • 82 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LMO2 31 30
  • 89.87 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia LMO2 31
  • 99 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lmo2 30
  • 83.01 (n)
African clawed frog
(Xenopus laevis)
 Amphibia lmo2-A 30
zebrafish
(Danio rerio)
 Actinopterygii lmo2 31 30 30
  • 79.78 (n)
 OneToOne
Species where no ortholog for LMO2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LMO2 Gene

ENSEMBL:
Gene Tree for LMO2 (if available)
TreeFam:
Gene Tree for LMO2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LMO2: view image

Paralogs for LMO2 Gene

Paralogs for LMO2 Gene

(16) SIMAP similar genes for LMO2 Gene using alignment to 1 proteins:

  • RBTN2_HUMAN
genes like me logo Genes that share paralogs with LMO2: view

Variants for LMO2 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LMO2 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
771440 Benign: not provided 33,859,497(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LMO2 Gene

Structural Variations from Database of Genomic Variants (DGV) for LMO2 Gene

Variant ID Type Subtype PubMed ID
esv1115754 CNV insertion 17803354
nsv1069574 CNV deletion 25765185
nsv1118207 CNV deletion 24896259
nsv1147622 CNV insertion 26484159
nsv509398 CNV insertion 20534489
nsv519717 CNV loss 19592680
nsv526555 CNV loss 19592680

Variation tolerance for LMO2 Gene

Residual Variation Intolerance Score: 44.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.85; 17.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LMO2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LMO2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LMO2 Gene

Disorders for LMO2 Gene

MalaCards: The human disease database

(17) MalaCards diseases for LMO2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
severe combined immunodeficiency, x-linked
  • scidx1
lymphoblastic lymphoma
  • lymphoma, lymphoblastic
acute t cell leukemia
  • precursor t lymphoblastic leukemia
ureteral lymphoma
  • lymphoma of ureter
leukemia
  • leukemias
- elite association - COSMIC cancer census association via MalaCards
Search LMO2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RBTN2_HUMAN
  • Note=A chromosomal aberration involving LMO2 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(11,14)(p13;q11) with TCRD.

Genatlas disease for LMO2 Gene

acute lymphoblastic leukemia (T-ALL),with translocations t(11;14)(p13;q11),t(7;11)(p35;p13)

Additional Disease Information for LMO2

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 LMO2: view

Publications for LMO2 Gene

  1. Human Bex2 interacts with LMO2 and regulates the transcriptional activity of a novel DNA-binding complex. (PMID: 16314316) Han C … Peng X (Nucleic acids research 2005) 3 4 23 54
  2. T-cell oncogene rhombotin-2 interacts with retinoblastoma-binding protein 2. (PMID: 9129143) Mao S … Goorha RM (Oncogene 1997) 3 4 23 54
  3. TTG-2, a new gene encoding a cysteine-rich protein with the LIM motif, is overexpressed in acute T-cell leukaemia with the t(11;14)(p13;q11). (PMID: 1923511) Royer-Pokora B … Ludwig WD (Oncogene 1991) 3 4 23 54
  4. The rhombotin family of cysteine-rich LIM-domain oncogenes: distinct members are involved in T-cell translocations to human chromosomes 11p15 and 11p13. (PMID: 2034676) Boehm T … Rabbitts TH (Proceedings of the National Academy of Sciences of the United States of America 1991) 2 3 23 54
  5. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 41 54

ExternalLinks

View latest publications for LMO2 gene in Mastermind

Products for LMO2 Gene

  • Addgene plasmids for LMO2

Sources for LMO2 Gene