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    LIME1 Lck interacting transmembrane adaptor 1 [ Homo sapiens (human) ]

    Gene ID: 54923, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LIME1provided by HGNC
    Official Full Name
    Lck interacting transmembrane adaptor 1provided by HGNC
    Primary source
    HGNC:HGNC:26016
    See related
    Ensembl:ENSG00000203896 MIM:609809; AllianceGenome:HGNC:26016
    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
    LIME; dJ583P15.4
    Summary
    This gene encodes a transmembrane adaptor protein that links the T and B-cell receptor stimulation to downstream signaling pathways via its association with the Src family kinases Lck and Lyn, respectively. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]
    Expression
    Broad expression in kidney (RPKM 23.8), liver (RPKM 18.5) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LIME1 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63735701..63739103)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65555977..65559374)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62367053..62370456)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene uncharacterized LOC124904954 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene ARF related protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene zinc finger CCCH-type and G-patch domain containing Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62368201-62369118 Neighboring gene LIME1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13186 Neighboring gene ZBTB46 antisense RNA 2 Neighboring gene SLC2A4 regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62383144-62384094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62384095-62385046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62385047-62385996 Neighboring gene zinc finger and BTB domain containing 46 Neighboring gene uncharacterized LOC124904956 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62401989-62402163

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Transcript specific regulation of expression influences susceptibility to multiple sclerosis. Ban M, et al. Eur J Hum Genet, 2020 Jun. PMID 31932686, Free PMC Article
    2. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Edwards NJ. Mol Syst Biol, 2007. PMID 17437027, Free PMC Article
    3. Epigenome-wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation. Mohandas N, et al. Clin Epigenetics, 2018. PMID 29484035, Free PMC Article
    4. LIME mediates immunological synapse formation through activation of VAV. Son M, et al. Mol Cells, 2012 Apr. PMID 22395814, Free PMC Article
    5. LIME: a new membrane Raft-associated adaptor protein involved in CD4 and CD8 coreceptor signaling. Brdicková N, et al. J Exp Med, 2003 Nov 17. PMID 14610046, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog

    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

    Potential readthrough

    Included gene: ZGPAT

    Homology

    Clone Names

    • FLJ20406

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in B cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in T cell receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of non-canonical NF-kappaB signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of release of sequestered calcium ion into cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of B cell receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space HDA PubMed 

    General protein information

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    Preferred Names
    lck-interacting transmembrane adapter 1
    Names
    lck-interacting membrane protein
    lck-interacting molecule

    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.

    mRNA and Protein(s)

    1. NM_001305654.2 → NP_001292583.1  lck-interacting transmembrane adapter 1 isoform 2

      See identical proteins and their annotated locations for NP_001292583.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR and uses an alternate splice site in an internal exon resulting in a frameshift, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1. Both variants 2 and 3 encode the same protein (isoform 2).
      Source sequence(s)
      AI763397, AL121845, AY203957
      Consensus CDS
      CCDS82638.1
      UniProtKB/TrEMBL
      A0A087WT39, A0A087WZP9

    2. NM_001305655.2 → NP_001292584.1  lck-interacting transmembrane adapter 1 isoform 2

      See identical proteins and their annotated locations for NP_001292584.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon resulting in a frameshift, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1. Both variants 2 and 3 encode the same protein (isoform 2).
      Source sequence(s)
      AK000413, AL121845
      Consensus CDS
      CCDS82638.1
      UniProtKB/TrEMBL
      A0A087WT39, A0A087WZP9
      Related
      ENSP00000477561.1, ENST00000480139.5

    3. NM_017806.4 → NP_060276.2  lck-interacting transmembrane adapter 1 isoform 1

      See identical proteins and their annotated locations for NP_060276.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK000413, AL121845
      Consensus CDS
      CCDS13536.1
      UniProtKB/Swiss-Prot
      E1P5K5, E1P5K6, Q5JWJ2, Q6XYB3, Q9H400, Q9NX69
      UniProtKB/TrEMBL
      A0A087WUJ1
      Related
      ENSP00000309521.3, ENST00000309546.8
      Conserved Domains (1) summary
      pfam15332
      Location:27 → 259
      LIME1; Lck-interacting transmembrane adapter 1

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      63735701..63739103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      65555977..65559374
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H400.1 GenPept UniProtKB/Swiss-Prot:Q9H400

    Gene LinkOut

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

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