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

Gene ID: 54923, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63735701..63739103)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65555977..65559374)
105.20220307 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 ADP ribosylation factor 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

Expression

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  • 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

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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. Non-T cell activation linker regulates ERK activation in Helicobacter pylori-infected epithelial cells. Rieke C, et al. Cell Signal, 2010 Mar. PMID 19879355

See all (25) 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)

Genotypes

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_2023_10

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

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