Details for: LEKR1

Gene ID: 389170

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: LEKR1

Ensembl ID: ENSG00000197980

Description: leucine, glutamate and lysine rich 1

Cell Significance Landscape

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • glutamatergic neuron CL0000679
    CSI 8.29
    rCSI 17.03%
    PRS 88.03
  • ependymal cell CL0000065
    CSI 7.66
    rCSI 15.55%
    PRS 84.07
  • melanocyte CL0000148
    CSI 5.87
    rCSI 4.34%
    PRS 94.22
  • choroid plexus epithelial cell CL0000706
    CSI 4.01
    rCSI 6.56%
    PRS 92.34
  • GABAergic neuron CL0000617
    CSI 3.85
    rCSI 12.9%
    PRS 87.37
  • kidney loop of Henle thin descending limb epithelial cell CL1001111
    CSI 3.78
    rCSI 5.36%
    PRS 95.03
  • Bergmann glial cell CL0000644
    CSI 3.52
    rCSI 4.82%
    PRS 91.61
  • retinal bipolar neuron CL0000748
    CSI 3.15
    rCSI 5.9%
    PRS 91.34
  • ciliated epithelial cell CL0000067
    CSI 2.89
    rCSI 2.54%
    PRS 90.64
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.87
    rCSI 3.56%
    PRS 87.5
  • multi-ciliated epithelial cell CL0005012
    CSI 2.77
    rCSI 2.76%
    PRS 92.48
  • Mueller cell CL0000636
    CSI 2.55
    rCSI 5.81%
    PRS 92.52
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.5
    rCSI 2.99%
    PRS 89.23
  • lung secretory cell CL1000272
    CSI 2.32
    rCSI 5.73%
    PRS 97.16
  • retinal rod cell CL0000604
    CSI 2.31
    rCSI 4.08%
    PRS 93.31
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.31
    rCSI 2.98%
    PRS 89.97
  • retinal cone cell CL0000573
    CSI 2.31
    rCSI 3.72%
    PRS 90.92
  • ciliated cell CL0000064
    CSI 2.27
    rCSI 3.67%
    PRS 91.45
  • lung ciliated cell CL1000271
    CSI 2.14
    rCSI 2.47%
    PRS 92.74
  • podocyte CL0000653
    CSI 2.09
    rCSI 9.31%
    PRS 95.98
  • luminal epithelial cell of mammary gland CL0002326
    CSI 2.09
    rCSI 3.79%
    PRS 97.99
  • cardiac muscle cell CL0000746
    CSI 2
    rCSI 2.87%
    PRS 91.12
  • astrocyte of the cerebral cortex CL0002605
    CSI 1.94
    rCSI 4.36%
    PRS 89.47
  • epithelial cell of proximal tubule CL0002306
    CSI 1.93
    rCSI 4.73%
    PRS 91.81
  • kidney connecting tubule epithelial cell CL1000768
    CSI 1.89
    rCSI 4.79%
    PRS 93.11
  • regular ventricular cardiac myocyte CL0002131
    CSI 1.72
    rCSI 10.76%
    PRS 91.85
  • retinal ganglion cell CL0000740
    CSI 1.67
    rCSI 3.7%
    PRS 89.94
  • amacrine cell CL0000561
    CSI 1.64
    rCSI 4.76%
    PRS 90.93
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 1.6
    rCSI 3.64%
    PRS 90.89
  • diffuse bipolar 6 cell CL4033032
    CSI 1.28
    rCSI 6.75%
    PRS 89
  • S cone cell CL0003050
    CSI 1.25
    rCSI 5.49%
    PRS 92.86
  • parietal epithelial cell CL1000452
    CSI 1.21
    rCSI 3.23%
    PRS 93.4
  • H2 horizontal cell CL0004218
    CSI 1.13
    rCSI 5.61%
    PRS 92.39
  • starburst amacrine cell CL0004232
    CSI 0.78
    rCSI 6.52%
    PRS 85.66
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 0.76
    rCSI 2.88%
    PRS 89.19
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 0.73
    rCSI 2.29%
    PRS 91.14
  • flat midget bipolar cell CL4033033
    CSI 0.72
    rCSI 5.12%
    PRS 89.2
  • central nervous system neuron CL2000029
    CSI 0.59
    rCSI 4.34%
    PRS 91.48
  • ON midget ganglion cell CL4033046
    CSI 0.34
    rCSI 6.86%
    PRS 90.31
  • kidney distal convoluted tubule epithelial cell CL1000849
    CSI 0.32
    rCSI 3.39%
    PRS 93.32

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

Loading network (please wait)...

Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [LEKR1](/details-gene/389170) (leucine, glutamate and lysine rich 1) is a protein-coding gene located on chromosome 3q25.31. While its molecular function remains poorly characterized, expression data reveals a highly specific landscape, suggesting a primary role in the central nervous system and in specialized epithelial tissues. **Overall**, it shows the highest significance in neuronal populations, particularly [glutamatergic neurons](/details-cell/CL0000679), as well as in ciliated cell types like [ependymal cells](/details-cell/CL0000065). Its discovery and annotation are supported by large-scale cDNA and genome sequencing projects ([Link](https://doi.org/10.1038/ng1285), [Link](https://doi.org/10.1038/nature04728)). ## Cellular Roles and Expression Landscape The expression pattern of [LEKR1](/details-gene/389170) points towards specialized functions in distinct cellular contexts, predominantly within the nervous system and epithelial linings. **Overall**, the gene's most significant expression is observed in the central nervous system. It is a top marker for [glutamatergic neurons](/details-cell/CL0000679) (CSI: 8.29) and is also highly significant in various [GABAergic neurons](/details-cell/CL0000617) (CSI: 3.85), including specific cortical interneuron subtypes such as [pvalb GABAergic cortical interneurons](/details-cell/CL4023018) and [VIP GABAergic cortical interneurons](/details-cell/CL4023016). Its importance extends to glial and retinal cells, with high significance in [Bergmann glial cells](/details-cell/CL0000644), [retinal bipolar neurons](/details-cell/CL0000748), [Mueller cells](/details-cell/CL0000636), and [retinal rod cells](/details-cell/CL0000604). This collective enrichment suggests a fundamental role in neuronal signaling, retinal function, or glial support within the CNS. A second prominent feature of [LEKR1](/details-gene/389170) expression is its high significance in specialized epithelial cells, particularly those possessing cilia. It is a defining marker for [ependymal cells](/details-cell/CL0000065) (CSI: 7.66) and [choroid plexus epithelial cells](/details-cell/CL0000706) (CSI: 4.01), which line the brain ventricles and are crucial for cerebrospinal fluid dynamics. This pattern is reinforced by its significance in [ciliated epithelial cells](/details-cell/CL0000067) and [multi-ciliated epithelial cells](/details-cell/CL0005012) found in other tissues. Beyond these primary domains, [LEKR1](/details-gene/389170) also shows notable significance in [melanocytes](/details-cell/CL0000148) and specific renal cells like [kidney loop of Henle thin descending limb epithelial cells](/details-cell/CL1001111). The absence of immune, muscle, or general stromal cell types from the top expressed list underscores its highly specialized role, largely confined to neuroectodermal and specific epithelial lineages. ## Pathways and Molecular Function Detailed functional annotations for [LEKR1](/details-gene/389170) are currently limited. However, its distinct cell-type-specific expression provides strong clues to its potential biological roles. The consistent high expression of [LEKR1](/details-gene/389170) across a diverse array of neuronal and glial cell types is suggestive of a role in fundamental neural processes. These could include synaptic transmission, axon guidance, maintenance of neuronal integrity, or metabolic support provided by glial cells. Its presence in both excitatory ([glutamatergic neurons](/details-cell/CL0000679)) and inhibitory ([GABAergic neurons](/details-cell/CL0000617)) subtypes suggests a function that is broadly applicable to neuronal physiology rather than specific to one mode of neurotransmission. Furthermore, the striking enrichment in multiple types of ciliated cells ([ependymal cells](/details-cell/CL0000065), [choroid plexus epithelial cells](/details-cell/CL0000706), [multi-ciliated epithelial cells](/details-cell/CL0005012)) strongly points towards a potential involvement in the biology of cilia. [LEKR1](/details-gene/389170) may be a structural component of the cilium or axoneme, or it could be involved in the complex processes of ciliogenesis or regulating ciliary motility. ## Research Directions The specific expression profile of [LEKR1](/details-gene/389170) in the absence of well-defined molecular functions makes it a compelling candidate for further investigation. Future research should focus on elucidating its role in both the nervous system and ciliated tissues. **Proposed Hypotheses:** 1. **[LEKR1](/details-gene/389170) is a crucial component for the formation, structure, or function of motile cilia.** Its high significance in [ependymal cells](/details-cell/CL0000065) and other [multi-ciliated epithelial cells](/details-cell/CL0005012) suggests that its absence could lead to defects in ciliary beating or structure, potentially contributing to the pathology of ciliopathies affecting the brain or respiratory tract. 2. **[LEKR1](/details-gene/389170) plays a role in synaptic homeostasis or function in the central nervous system.** Its strong expression in diverse neuronal populations, including [glutamatergic](/details-cell/CL0000679) and [GABAergic](/details-cell/CL0000617) neurons, suggests it may be involved in a core mechanism such as vesicle trafficking, receptor stabilization, or synaptic scaffolding. **Key Experimental Approach:** To test the hypothesis that [LEKR1](/details-gene/389170) is involved in ciliary function (Hypothesis 1), an *in vitro* model of mucociliary differentiation could be employed. Primary human bronchial epithelial cells could be cultured at an air-liquid interface (ALI) to induce differentiation into a ciliated epithelium. Using CRISPR-Cas9 to generate a stable knockout of [LEKR1](/details-gene/389170) in these cells, researchers could then perform a functional and structural analysis. Ciliary beat frequency (CBF) could be quantified using high-speed video microscopy, while ciliary structure could be examined via immunofluorescence staining for core ciliary proteins (e.g., acetylated tubulin) and transmission electron microscopy to assess the ultrastructure of the axoneme. A significant reduction in CBF or observable structural abnormalities in knockout cells compared to wild-type controls would provide strong evidence for a direct role of [LEKR1](/details-gene/389170) in ciliary biology. **Therapeutic Potential:** The therapeutic potential of targeting [LEKR1](/details-gene/389170) is currently speculative. If its role in ciliary function is validated, it could become a gene of interest for understanding human ciliopathies, which can affect multiple organ systems. For neurological disorders, its widespread expression across many essential neuron types in the brain and retina suggests that systemic modulation could carry a high risk of off-target effects. Therefore, any potential therapeutic strategy, such as gene therapy for a loss-of-function ciliopathy, would likely require highly targeted delivery to specific cell populations.

Genular Protein ID: 3720662269

Symbol: LEKR1_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q6ZMV7 D3DNK8 S4R3D4

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 8 Ensembl 2 ExpressionAtlas 1 GeneCards 1 GeneTree 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pharos 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 2 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 neXtProt 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 16641997

Title: The DNA sequence, annotation and analysis of human chromosome 3.

PubMed ID: 16641997

DOI: 10.1038/nature04728

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 132
  • Mass: 16005
  • Checksum: 93DA1A4A64508858
  • Sequence:
    • MDHHIPMHAL PEEIQKMLPE EKVCKYCGVS YLILHEFKAM EEKVKAMEKE MKFYQGSVDR 
EKRLQEKLHS LSQELEQYKI DNKSKTERIY DVGMQLKSQQ NEFQKVKKQL SHLQDELKIK 
YRQSYIFRLC FC

Genular Protein ID: 3136887748

Symbol: J3KP02_HUMAN

Name: N/A

UniProtKB Accession Codes:

J3KP02

Database IDs:

AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 ExpressionAtlas 1 GeneTree 1 HGNC 1 InterPro 1 MANE-Select 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OrthoDB 1 PANTHER 2 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 2 ProteomicsDB 1 RefSeq 3 SAM 2 SMR 1 UCSC 1 VEuPathDB 1 iPTMnet 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 16641997

Title: The DNA sequence, annotation and analysis of human chromosome 3.

PubMed ID: 16641997

DOI: 10.1038/nature04728

Sequence Information:

  • Length: 692
  • Mass: 81229
  • Checksum: 27AFE309512D17ED
  • Sequence:
    • MDHHIPMHAL PEEIQKMLPE EKVCKYCGVS YLILHEFKAM EEKVKAMEKE MKFYQGSVDR 
EKRLQEKLHS LSQELEQYKI DNKSKTERIY DVGMQLKSQQ NEFQKVKKQL SHLQDELKIK 
YRQSYIFSQR LSEYKYFWNK TLSLLTFTKR ELTSIKNEVY DNYQNWTSLK GAVFLQIKSI 
SETALTEIDI LNKSLTVSQR NKVCLEKEMK NLKLLSDAAI LRSQQIRTSR QQEVNLQTRC 
YDLQKEVLDL QCLVEALGLK LQKAVTEMDN YKEMLMNKSN EADDCQRELK KLKFESIISE 
SQHTMLLKEK EDSLMTCQQI YKALQEELTV KEKQEEDIKR RINLAENELE ITKTLLNQTR 
EEVLTLKNER ELMLISHQKS IEQLQETLRQ KLLSDDNWKE KIEAELAKER AQHLVEFEEQ 
ALLFKEETKL QLDIEKEKHQ DVIQKYKKEQ EELQMKISDL ITGATRDLRQ EVTTLKEKLH 
KSHIRYTEES NSKEKEIENL KNLVAEFESR LKKEIDSNDS VSENLRKEME QKSDELKRVM 
LAQTQLIEQF NQSQEENTFL QETVRRECEE RFELTEALSQ AREQLLELSK LRGSLPFSPC 
SLSKGSLTSP AAAVSNHGER SLARLNSEKG IQIPNLRGVS KPTTFPTSDK PKRVRSGVPI 
LPQPHPPRGG ASSANETRQR LAAILRRRRS QQ