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

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; 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

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results identified one differentially methylated region associated with cerebral palsy within the transcription start site of the LIME1 gene, which plays a key role in inflammatory pathways.
Title: Epigenome-wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation.
these results establish LIME as a transmembrane adaptor protein linking TCR stimulation to IS formation and integrin activation through activation of Vav(Vav guanine nucleotide exchange factor)
Title: LIME mediates immunological synapse formation through activation of VAV.

Submit: New GeneRIF Correction

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 EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH101996 (e-PCR)
- UniSTS:96330

RH75350 (e-PCR)
- UniSTS:83812

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 more info	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)

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
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
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