Format

Send to:

Choose Destination

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

Gene ID: 55885, updated on 7-Jun-2020

Summary

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
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

Genomic context

See LMO3 in Genome Data Viewer
Location:
12p12.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (16548372..16610233, complement)
105 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 uncharacterized LOC107984494 Neighboring gene VISTA enhancer hs607 Neighboring gene GOT2 pseudogene 4 Neighboring gene VISTA enhancer hs336 Neighboring gene uncharacterized LOC105369677 Neighboring gene VISTA enhancer hs661 Neighboring gene S-phase kinase associated protein 1 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC26081

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..64843
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001001395.2NP_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
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1, Q9NYC6
    Related
    ENSP00000346689.1, ENST00000354662.5
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  2. NM_001243609.1NP_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
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1, Q9NYC6
    Related
    ENSP00000412479.2, ENST00000441439.6
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  3. NM_001243610.1NP_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
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Related
    ENSP00000413703.1, ENST00000447609.5
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  4. NM_001243611.1NP_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/Swiss-Prot
    Q8TAP4
    Related
    ENSP00000261169.6, ENST00000261169.10
    Conserved Domains (2) summary
    cd09388
    Location:2478
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:88142
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  5. NM_001243612.1NP_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/Swiss-Prot
    Q8TAP4
    Related
    ENSP00000446463.1, ENST00000541295.5
    Conserved Domains (2) summary
    cd09388
    Location:3185
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:95149
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  6. NM_001243613.1NP_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:99153
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cl02475
    Location:1349
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  7. NM_018640.5NP_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
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Related
    ENSP00000440099.1, ENST00000537304.6
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    16548372..16610233 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019643.1XP_016875132.1  LIM domain only protein 3 isoform X2

    Conserved Domains (1) summary
    cd09389
    Location:57111
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  2. XM_006719111.2XP_006719174.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006719174.1

    UniProtKB/Swiss-Prot
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Related
    ENSP00000439275.1, ENST00000534946.5
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  3. XM_011520763.1XP_011519065.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011519065.1

    UniProtKB/Swiss-Prot
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Related
    ENSP00000445193.1, ENST00000537757.5
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  4. XM_024449058.1XP_024304826.1  LIM domain only protein 3 isoform X1

    Related
    ENSP00000442713.1, ENST00000546281.5
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  5. XM_006719110.4XP_006719173.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006719173.1

    UniProtKB/Swiss-Prot
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  6. XM_011520762.1XP_011519064.1  LIM domain only protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011519064.1

    UniProtKB/Swiss-Prot
    Q8TAP4
    UniProtKB/TrEMBL
    A0A024RAT1
    Conserved Domains (2) summary
    cd09388
    Location:1367
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:77131
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
Support Center