Seroatlas · Human Serome Atlas

LIME1

Lck-interacting transmembrane adapter 1

Also known as: dJ583P15.4, FLJ20406, LIME, LIME1_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9H400
Gene: LIME1
Ensembl: ENSG00000203896
Chromosome: 20
Canonical length: 295 aa
Protein class: Predicted intracellular proteins

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

295 residues, UniProt reviewed canonical sequence.

>Q9H400|LIME1
     1  MGLPVSWAPP ALWVLGCCAL LLSLWALCTA CRRPEDAVAP RKRARRQRAR LQGSATAAEA
    61  SLLRRTHLCS LSKSDTRLHE LHRGPRSSRA LRPASMDLLR PHWLEVSRDI TGPQAAPSAF
   121  PHQELPRALP AAAATAGCAG LEATYSNVGL AALPGVSLAA SPVVAEYARV QKRKGTHRSP
   181  QEPQQGKTEV TPAAQVDVLY SRVCKPKRRD PGPTTDPLDP KGQGAILALA GDLAYQTLPL
   241  RALDVDSGPL ENVYESIREL GDPAGRSSTC GAGTPPASSC PSLGRGWRPL PASLP

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LIME1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 1
Mean surface accessibility (rSASA): 0.71
Highest tissue expression: 259 nTPM

Expression across tissuesHPA

Tissue

liver: 259 nTPM
kidney: 57 nTPM
spleen: 42 nTPM
cerebellum: 28 nTPM
basal ganglia: 25 nTPM
small intestine: 18 nTPM

Single-cell type

conjunctival goblet cells: 1 nCPM
plasma cells: 0.4 nCPM
astrocytes: 0.2 nCPM
nk-cells: 0.2 nCPM
t-cells: 0.2 nCPM
brain excitatory neurons: 0.1 nCPM

Immune cell

plasmacytoid DC: 751 nTPM
T-reg: 691 nTPM
memory CD4 T-cell: 439 nTPM
memory CD8 T-cell: 412 nTPM
naive CD8 T-cell: 320 nTPM
gdT-cell: 316 nTPM

Brain region

basal ganglia: 15 nTPM
white matter: 13 nTPM
cerebral cortex: 13 nTPM
thalamus: 11 nTPM
medulla oblongata: 9.6 nTPM
cerebellum: 9.2 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.65
gnomAD pLI: 0
gnomAD missense Z: 1.06
DepMap mean gene effect: 0.13
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

protein kinase binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

Lck-interacting transmembrane adapter 1
Lck-interacting transmembrane adapter 1

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LIME1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads LIME1 as an antibody target. Whether an autoantibody or antibody against LIME1 could matter depends on whether native LIME1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LIME1 is annotated at the cell surface, where native LIME1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label LIME1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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