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    LMO3 LIM domain only 3 [ Homo sapiens (human) ]

    Gene ID: 55885, updated on 14-Nov-2024

    Summary

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    Official Symbol
    LMO3provided by HGNC
    Official Full Name
    LIM domain only 3provided by HGNC
    Primary source
    HGNC:HGNC:6643
    See related
    Ensembl:ENSG00000048540 MIM:180386; AllianceGenome:HGNC:6643
    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
    RBTN3; RHOM3; RBTNL2; Rhom-3
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 41.7), lung (RPKM 13.9) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LMO3 in Genome Data Viewer
    Location:
    12p12.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (16548372..16610174, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (16425771..16487621, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (16701306..16761148, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene microsomal glutathione S-transferase 1 Neighboring gene SPT16 homolog, facilitates chromatin remodeling subunit pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:16602892-16603466 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:16603467-16604039 Neighboring gene VISTA enhancer hs607 Neighboring gene NANOG hESC enhancer GRCh37_chr12:16703865-16704366 Neighboring gene VISTA enhancer hs336 Neighboring gene GOT2 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:16757530-16758030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:16762919-16763418 Neighboring gene VISTA enhancer hs661 Neighboring gene uncharacterized LOC105369677 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:17135721-17136920 Neighboring gene S-phase kinase associated protein 1 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism.
      Title: LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism.
    2. Circ_0007385 promotes the proliferation and inhibits the apoptosis of non-small cell lung cancer cells via miR-337-3p-dependent regulation of LMO3.
      Title: Circ_0007385 promotes the proliferation and inhibits the apoptosis of non-small cell lung cancer cells via miR-337-3p-dependent regulation of LMO3.
    3. Hyperglycemia affects neuronal differentiation and Nestin, FOXO1, and LMO3 mRNA expression of human Wharton's jelly mesenchymal stem cells of children from diabetic mothers.
      Title: Hyperglycemia affects neuronal differentiation and Nestin, FOXO1, and LMO3 mRNA expression of human Wharton's jelly mesenchymal stem cells of children from diabetic mothers.
    4. Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway.
      Title: Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway.
    5. LMO3 reprograms visceral adipocyte metabolism during obesity.
      Title: LMO3 reprograms visceral adipocyte metabolism during obesity.
    6. MicroRNA-381 inhibits lung adenocarcinoma cell biological progression by directly targeting LMO3 through regulation of the PI3K/Akt signaling pathway and epithelial-to-mesenchymal transition.
      Title: MicroRNA-381 inhibits lung adenocarcinoma cell biological progression by directly targeting LMO3 through regulation of the PI3K/Akt signaling pathway and epithelial-to-mesenchymal transition.
    7. our results suggest that LMO3-BORCS5 fusion oncogene plays an essential role in tumorigenesis
      Title: Newly identified LMO3-BORCS5 fusion oncogene in Ewing sarcoma at relapse is a driver of tumor progression.
    8. These results suggest that LMO3 promotes hepatocellular carcinoma (HCC) cell invasion and anoikis inhibition by interacting with LATS1 and suppressing Hippo signaling. LMO3 may serve as a potential therapeutic target for HCC in future
      Title: LMO3 promotes hepatocellular carcinoma invasion, metastasis and anoikis inhibition by directly interacting with LATS1 and suppressing Hippo signaling.
    9. These results suggested that LMO3 promotes Gastric Cancer cell invasion and proliferation mainly through Akt/mTOR and Akt/GSK3beta signaling.
      Title: LMO3 promotes gastric cancer cell invasion and proliferation through Akt-mTOR and Akt-GSK3β signaling.
    10. SH3BP5, LMO3, and SNAP25 were expressed in diffuse large B-cell lymphoma cells and associated with clinical features.
      Title: Expressions of SH3BP5, LMO3, and SNAP25 in diffuse large B-cell lymphoma cells and their association with clinical features.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    • MGC26081

    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 ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of glucocorticoid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of peroxisome proliferator activated receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    LIM domain only protein 3
    Names
    LIM domain only 3 (rhombotin-like 2)
    dopamine associated transcription factor-1
    neuronal-specific transcription factor DAT1
    rhombotin-3

    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_029785.2 RefSeqGene

      Range
      7053..64843
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001001395.2 → NP_001001395.1  LIM domain only protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001001395.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' non-coding exon compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AF258348, AK294474, AL050152, BQ029059, DA780743
      Consensus CDS
      CCDS8678.1
      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000346689.1, ENST00000354662.5
      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. NM_001243609.1 → NP_001230538.1  LIM domain only protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001230538.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs at the 5' end compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AB044746, AF258348, AL050152, BQ029059, DA780743
      Consensus CDS
      CCDS8678.1
      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000412479.2, ENST00000441439.6
      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)

    3. NM_001243610.1 → NP_001230539.1  LIM domain only protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001230539.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs at the 5' end compared to variant 1. Variants 1-4 encode the same isoform (1).
      Source sequence(s)
      AL050152, BC050085, BQ029059
      Consensus CDS
      CCDS8678.1
      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000413703.1, ENST00000447609.5
      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. NM_001243611.1 → NP_001230540.1  LIM domain only protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001230540.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame upstream start codon, and an isoform (2) with a longer N-terminus compared to isoform 1.
      Source sequence(s)
      AB044745, AL050152, BC026311, BQ029059, DC324870
      Consensus CDS
      CCDS58211.1
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000261169.6, ENST00000261169.10
      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)

    5. NM_001243612.1 → NP_001230541.1  LIM domain only protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001230541.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame upstream start codon, and an isoform (3) with a longer N-terminus compared to isoform 1.
      Source sequence(s)
      AK294474, AL050152, BQ029059
      Consensus CDS
      CCDS58212.1
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000446463.1, ENST00000541295.5
      Conserved Domains (2) summary
      cd09388
      Location:31 → 85
      LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cd09389
      Location:95 → 149
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

    6. NM_001243613.1 → NP_001230542.1  LIM domain only protein 3 isoform 4

      See identical proteins and their annotated locations for NP_001230542.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs at the 5' end, and contains an additional in-frame coding exon compared to variant 1. This results in a longer isoform (4) with an internal protein segment not found in isoform 1.
      Source sequence(s)
      AK294909, AL050152, BQ029059
      Consensus CDS
      CCDS58210.1
      UniProtKB/Swiss-Prot
      Q8TAP4
      Related
      ENSP00000442786.1, ENST00000540445.5
      Conserved Domains (2) summary
      cd09389
      Location:99 → 153
      LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
      cl02475
      Location:13 → 49
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    7. NM_018640.5 → NP_061110.2  LIM domain only protein 3 isoform 1

      See identical proteins and their annotated locations for NP_061110.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (1). Variants 1-4 encode the same isoform.
      Source sequence(s)
      AL050152, BC026311, BQ029059
      Consensus CDS
      CCDS8678.1
      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      Related
      ENSP00000440099.1, ENST00000537304.6
      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)

    RNA

    1. NR_045012.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs at the 5' end and contains an additional internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF258348, AK294909, AK308826, AL050152, BQ029059, DA780743

    2. NR_045013.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs at the 5' end and uses an alternate donor splice site at an internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF258348, AL050152, BC017777, BQ029059, DA780743
      Related
      ENST00000396205.6

    3. NR_045014.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) differs at the 5' end and uses an alternate donor splice site at an internal exon compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF258348, AL050152, BC017777, BQ029059, DA780743

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      16548372..16610174 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006719111.3 → XP_006719174.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006719174.1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      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_047429153.1 → XP_047285109.1  LIM domain only protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      Related
      ENSP00000439275.1, ENST00000534946.5

    3. XM_006719110.5 → XP_006719173.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_006719173.1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      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_011520762.2 → XP_011519064.1  LIM domain only protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011519064.1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5
      UniProtKB/TrEMBL
      B2R631
      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)

    5. XM_047429156.1 → XP_047285112.1  LIM domain only protein 3 isoform X4

    6. XM_047429154.1 → XP_047285110.1  LIM domain only protein 3 isoform X2

    7. XM_047429155.1 → XP_047285111.1  LIM domain only protein 3 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      16425771..16487621 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372560.1 → XP_054228535.1  LIM domain only protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5

    2. XM_054372559.1 → XP_054228534.1  LIM domain only protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5

    3. XM_054372558.1 → XP_054228533.1  LIM domain only protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B4DG90, B4DH35, Q58A66, Q58A67, Q8N974, Q8TAP4, Q9UDD5

    4. XM_054372562.1 → XP_054228537.1  LIM domain only protein 3 isoform X4

    5. XM_054372561.1 → XP_054228536.1  LIM domain only protein 3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TAP4.1 GenPept UniProtKB/Swiss-Prot:Q8TAP4

    Gene LinkOut

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

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