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Aliases for LIME1 Gene

Aliases for LIME1 Gene

  • Lck Interacting Transmembrane Adaptor 1 2 3 5
  • Lck-Interacting Membrane Protein 3 4
  • Lck-Interacting Molecule 3 4
  • LIME 3 4
  • Lck-Interacting Transmembrane Adapter 1 3
  • DJ583P15.4 3

External Ids for LIME1 Gene

Previous GeneCards Identifiers for LIME1 Gene

  • GC20P061839
  • GC20P062366
  • GC20P059100

Summaries for LIME1 Gene

Entrez Gene Summary for LIME1 Gene

  • 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]

GeneCards Summary for LIME1 Gene

LIME1 (Lck Interacting Transmembrane Adaptor 1) is a Protein Coding gene. An important paralog of this gene is ENSG00000273047.

UniProtKB/Swiss-Prot for LIME1 Gene

  • Involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and TCR (T-cell antigen receptor)-mediated T-cell signaling in T-cells. In absence of TCR signaling, may be involved in CD4-mediated inhibition of T-cell activation. Couples activation of these receptors and their associated kinases with distal intracellular events such as calcium mobilization or MAPK activation through the recruitment of PLCG2, GRB2, GRAP2, and other signaling molecules.

Gene Wiki entry for LIME1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIME1 Gene

Genomics for LIME1 Gene

Regulatory Elements for LIME1 Gene

Enhancers for LIME1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F063680 1.1 Ensembl ENCODE 28.6 -43.2 -43192 24.9 HDGF PKNOX1 MLX ZFP64 SIN3A ZNF548 FOS PAF1 ZNF263 SP3 LIME1 RTEL1 MIR647 MIR1914 SLC2A4RG ENSG00000229299 ENSG00000237371 ARFRP1 C20orf181 ZBTB46-AS1
GH20F063630 1.2 FANTOM5 Ensembl ENCODE 22.1 -99.2 -99184 12.4 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF48 ZNF121 GLIS2 LIME1 STMN3 GMEB2 ENSG00000237371 RTEL1 HELZ2 TNFRSF6B PCMTD2 FNDC11 ZGPAT
GH20F063735 0.6 ENCODE 19.7 +2.6 2560 6.8 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 LIME1 RTEL1 ENSG00000237371 ARFRP1 ENSG00000273047 SLC2A4RG
GH20F063787 0.9 Ensembl ENCODE 18.8 +50.1 50118 0.8 HDGF CTCF ATF1 MXI1 ZNF792 SAP130 ARID4B ZSCAN9 ZNF2 RAD21 LIME1 ZBTB46 C20orf181 ENSG00000229299 SLC2A4RG ZGPAT DNAJC5 PIR46452 PIR49937
GH20F063782 0.6 ENCODE 17.9 +46.0 46003 0.4 CTCF SAP130 ARID4B ZNF384 DMAP1 ZNF48 RAD21 TEAD3 ZFHX2 ZNF600 LIME1 ZBTB46-AS1 ENSG00000229299 ZBTB46 SLC2A4RG C20orf181 ZGPAT ZNF512B PRPF6 SAMD10
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LIME1 on UCSC Golden Path with GeneCards custom track

Promoters for LIME1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001839246 1217 1401 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF48 GLIS2 FOS DEK PAF1

Genomic Location for LIME1 Gene

Chromosome:
20
Start:
63,736,283 bp from pter
End:
63,739,107 bp from pter
Size:
2,825 bases
Orientation:
Plus strand

Genomic View for LIME1 Gene

Genes around LIME1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LIME1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LIME1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIME1 Gene

Proteins for LIME1 Gene

  • Protein details for LIME1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H400-LIME1_HUMAN
    Recommended name:
    Lck-interacting transmembrane adapter 1
    Protein Accession:
    Q9H400
    Secondary Accessions:
    • E1P5K5
    • E1P5K6
    • Q5JWJ2
    • Q6XYB3
    • Q9NX69

    Protein attributes for LIME1 Gene

    Size:
    295 amino acids
    Molecular mass:
    31288 Da
    Quaternary structure:
    • When phosphorylated in response to BCR activation, interacts with LYN, PIK3R1, PLCG2, and GRB2 (By similarity). When phosphorylated in response to TCR stimulation and/or CD4 co-stimulation, interacts with LCK, CSK, FYN, PTPN11/SHP2, GRB2, PIK3R1 and GRAP2.

    Alternative splice isoforms for LIME1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIME1 Gene

Post-translational modifications for LIME1 Gene

  • Palmitoylation of Cys-28 and Cys-31 is required for raft targeting.
  • Phosphorylated on tyrosines upon TCR activation and/or CD4 coreceptor stimulation, or upon BCR stimulation; which leads to the recruitment of SH2-containing proteins.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LIME1 Gene

Domains & Families for LIME1 Gene

Protein Domains for LIME1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LIME1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LIME1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for LIME1 Gene

Function for LIME1 Gene

Molecular function for LIME1 Gene

UniProtKB/Swiss-Prot Function:
Involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and TCR (T-cell antigen receptor)-mediated T-cell signaling in T-cells. In absence of TCR signaling, may be involved in CD4-mediated inhibition of T-cell activation. Couples activation of these receptors and their associated kinases with distal intracellular events such as calcium mobilization or MAPK activation through the recruitment of PLCG2, GRB2, GRAP2, and other signaling molecules.
genes like me logo Genes that share phenotypes with LIME1: view

Animal Models for LIME1 Gene

MGI Knock Outs for LIME1:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LIME1 Gene

Localization for LIME1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIME1 Gene

Cell membrane; Single-pass type III membrane protein. Note=Present in lipid rafts. Recruited to the immunological synapse upon conjugation of T-cell with antigen-presenting cell.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LIME1 Gene COMPARTMENTS Subcellular localization image for LIME1 gene
Compartment Confidence
extracellular 5
plasma membrane 4

Gene Ontology (GO) - Cellular Components for LIME1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LIME1: view

Pathways & Interactions for LIME1 Gene

SuperPathways for LIME1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LIME1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0050852 T cell receptor signaling pathway IEA --
GO:0050853 B cell receptor signaling pathway IEA --
genes like me logo Genes that share ontologies with LIME1: view

No data available for Pathways by source and SIGNOR curated interactions for LIME1 Gene

Drugs & Compounds for LIME1 Gene

(1) Drugs for LIME1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with LIME1: view

Transcripts for LIME1 Gene

Unigene Clusters for LIME1 Gene

Lck interacting transmembrane adaptor 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIME1 Gene

No ASD Table

Relevant External Links for LIME1 Gene

GeneLoc Exon Structure for
LIME1
ECgene alternative splicing isoforms for
LIME1

Expression for LIME1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LIME1 Gene

Protein differential expression in normal tissues from HIPED for LIME1 Gene

This gene is overexpressed in Nasal epithelium (58.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for LIME1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LIME1 Gene:

LIME1

SOURCE GeneReport for Unigene cluster for LIME1 Gene:

Hs.233220

mRNA Expression by UniProt/SwissProt for LIME1 Gene:

Q9H400-LIME1_HUMAN
Tissue specificity: Expressed in peripheral blood lymphocytes, lymphoid tissues, and liver. Present in T-cells and plasma cells, and in various hematopoietic cell lines (at protein level).
genes like me logo Genes that share expression patterns with LIME1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for LIME1 Gene

Orthologs for LIME1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LIME1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LIME1 34
  • 99.77 (n)
-- 35
  • 95 (a)
OneToMany
cow
(Bos Taurus)
Mammalia LIME1 34
  • 79.1 (n)
-- 35
  • 63 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Lime1 34 16 35
  • 76.04 (n)
dog
(Canis familiaris)
Mammalia LIME1 34
  • 75.23 (n)
-- 35
  • 53 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Lime1 34
  • 74.83 (n)
Species where no ortholog for LIME1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LIME1 Gene

ENSEMBL:
Gene Tree for LIME1 (if available)
TreeFam:
Gene Tree for LIME1 (if available)

Paralogs for LIME1 Gene

Paralogs for LIME1 Gene

genes like me logo Genes that share paralogs with LIME1: view

Variants for LIME1 Gene

Sequence variations from dbSNP and Humsavar for LIME1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1056441 -- 63,738,996(+) CGGGC(C/T)GCCAG upstream-variant-2KB, utr-variant-3-prime
rs111770147 -- 63,734,458(+) CAGGC(C/T)GTGGG intron-variant, upstream-variant-2KB
rs112243416 -- 63,739,393(+) GGGGT(-/G)GTGGA downstream-variant-500B, upstream-variant-2KB
rs112253079 -- 63,736,925(+) GATCC(C/G)CAAGA intron-variant
rs112564671 -- 63,738,735(+) CTCAG(A/G)GCCCT upstream-variant-2KB, reference, synonymous-codon, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LIME1 Gene

Variant ID Type Subtype PubMed ID
dgv523n27 CNV loss 19166990
dgv7677n54 CNV loss 21841781
dgv7678n54 CNV loss 21841781
dgv7679n54 CNV gain 21841781
dgv7680n54 CNV gain 21841781
dgv7681n54 CNV loss 21841781
dgv7682n54 CNV loss 21841781
dgv7683n54 CNV gain+loss 21841781
dgv7684n54 CNV loss 21841781
esv2722959 CNV deletion 23290073
esv2758806 CNV gain+loss 17122850
esv29394 CNV loss 19812545
esv7227 CNV loss 19470904
nsv1059142 CNV gain 25217958
nsv1139762 CNV duplication 24896259
nsv1160690 CNV deletion 26073780
nsv428381 CNV gain+loss 18775914
nsv470563 CNV loss 18288195
nsv586614 CNV gain 21841781
nsv586615 CNV gain 21841781
nsv586618 CNV gain 21841781
nsv586621 CNV gain 21841781
nsv586633 CNV loss 21841781
nsv586643 CNV gain 21841781
nsv586644 CNV gain 21841781
nsv953308 CNV deletion 24416366

Variation tolerance for LIME1 Gene

Gene Damage Index Score: 2.94; 49.22% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIME1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LIME1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIME1 Gene

Disorders for LIME1 Gene

Relevant External Links for LIME1

Genetic Association Database (GAD)
LIME1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIME1

No disorders were found for LIME1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LIME1 Gene

Publications for LIME1 Gene

  1. Transmembrane adaptor molecules: a new category of lymphoid-cell markers. (PMID: 16160011) Tedoldi S. … Horejsi V. (Blood 2006) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PMID: 15498874) Wan D. … Gu J. (Proc. Natl. Acad. Sci. U.S.A. 2004) 3 4 64
  5. LIME, a novel transmembrane adaptor protein, associates with p56lck and mediates T cell activation. (PMID: 14610044) Hur E.M. … Yun Y. (J. Exp. Med. 2003) 3 4 64

Products for LIME1 Gene

Sources for LIME1 Gene

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