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

Gene ID: 54923, updated on 23-Nov-2021

Summary

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
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
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Genomic context

See LIME1 in Genome Data Viewer
Location:
20q13.33
Exon count:
7
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (63735701..63739103)
105.20201022 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 regulator of telomere elongation helicase 1 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ADP ribosylation factor related protein 1 Neighboring gene zinc finger CCCH-type and G-patch domain containing Neighboring gene LIME1 eExon liver enhancer Neighboring gene SLC2A4 regulator Neighboring gene zinc finger and BTB domain containing 46 Neighboring gene ZBTB46 antisense RNA 1

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

Phenotypes

Associated conditions

Description Tests
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
Process Evidence Code Pubs
involved_in B cell receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of MAP kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of NIK/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of phosphatidylinositol 3-kinase signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of release of sequestered calcium ion into cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of B cell receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular space HDA PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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_001305654.2NP_001292583.1  lck-interacting transmembrane adapter 1 isoform 2 precursor

    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/Swiss-Prot
    Q9H400
    UniProtKB/TrEMBL
    A0A087WT39
  2. NM_001305655.2NP_001292584.1  lck-interacting transmembrane adapter 1 isoform 2 precursor

    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/Swiss-Prot
    Q9H400
    UniProtKB/TrEMBL
    A0A087WT39
    Related
    ENSP00000477561.1, ENST00000480139.5
  3. NM_017806.4NP_060276.2  lck-interacting transmembrane adapter 1 isoform 1 precursor

    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
    Q9H400
    Related
    ENSP00000309521.3, ENST00000309546.8
    Conserved Domains (1) summary
    pfam15332
    Location:27259
    LIME1; Lck-interacting transmembrane adapter 1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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