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LMO1 LIM domain only 1 [ Homo sapiens (human) ]

Gene ID: 4004, updated on 9-Dec-2018

Summary

Official Symbol
LMO1provided by HGNC
Official Full Name
LIM domain only 1provided by HGNC
Primary source
HGNC:HGNC:6641
See related
Ensembl:ENSG00000166407 MIM:186921
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
TTG1; RBTN1; RHOM1
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See LMO1 in Genome Data Viewer
Location:
11p15.4
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (8224304..8268635, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (8245851..8290182, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RIC3 acetylcholine receptor chaperone Neighboring gene uncharacterized LOC101927936 Neighboring gene VISTA enhancer hs1859 Neighboring gene uncharacterized LOC105376536 Neighboring gene serine/threonine kinase 33 Neighboring gene tripartite motif containing 66 Neighboring gene ribosomal protein L27a

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
NHGRI GWA Catalog
A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.
NHGRI GWA Catalog
Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma.
NHGRI GWA Catalog
Integrative genomics identifies LMO1 as a neuroblastoma oncogene.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC116692

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
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
rhombotin-1
Names
LIM domain only 1 (rhombotin 1)
LIM domain only protein 1
LMO-1
T-cell translocation gene 1
T-cell translocation protein 1
cysteine-rich protein TTG-1

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_032827.2 RefSeqGene

    Range
    9777..49326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270428.1NP_001257357.1  rhombotin-1 isoform b

    See identical proteins and their annotated locations for NP_001257357.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC091013, AW006226, BC039512
    Consensus CDS
    CCDS58118.1
    UniProtKB/Swiss-Prot
    P25800
    Related
    ENSP00000404538.2, ENST00000428101.6
    Conserved Domains (2) summary
    cd09388
    Location:2377
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:87141
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  2. NM_002315.3NP_002306.1  rhombotin-1 isoform a

    See identical proteins and their annotated locations for NP_002306.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC091013
    Consensus CDS
    CCDS44534.1
    UniProtKB/Swiss-Prot
    P25800
    Related
    ENSP00000338207.3, ENST00000335790.7
    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)

RNA

  1. NR_073006.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC091013, AW006226, BC096058, BP218183, M26682

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    8224304..8268635 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520099.2XP_011518401.1  rhombotin-1 isoform X2

    See identical proteins and their annotated locations for XP_011518401.1

    UniProtKB/TrEMBL
    E9PK83
    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. XM_006718228.3XP_006718291.1  rhombotin-1 isoform X1

    Conserved Domains (2) summary
    cd09388
    Location:61115
    LIM1_LMO1_LMO3; The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
    cd09389
    Location:125179
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
  3. XM_011520098.2XP_011518400.1  rhombotin-1 isoform X2

    See identical proteins and their annotated locations for XP_011518400.1

    UniProtKB/TrEMBL
    E9PK83
    Related
    ENSP00000435456.1, ENST00000534484.1
    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_011520100.1XP_011518402.1  rhombotin-1 isoform X3

    Conserved Domains (1) summary
    cd09389
    Location:54108
    LIM2_LMO1_LMO3; The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)
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