WormMine: Gene WBGene00013300

• WormBase Gene ID: WBGene00013300
• Gene Name: lgc-7
• Sequence Name: Y57G11C.2
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable excitatory extracellular ligand-gated monoatomic ion channel activity and transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential. Predicted to be involved in excitatory postsynaptic potential and monoatomic ion transmembrane transport. Predicted to be located in neuron projection; plasma membrane; and synapse. Predicted to be part of transmembrane transporter complex. Human ortholog(s) of this gene implicated in several diseases, including alcohol dependence; drug dependence (multiple); and irritable bowel syndrome. Is an ortholog of human HTR3A (5-hydroxytryptamine receptor 3A) and HTR3E (5-hydroxytryptamine receptor 3E).
• Biotype: SO:0001217
• Genetic Position: IV :12.3871 ±0.005186
• Length (nt): 5153

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00013300

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y57G11C.2.1	Y57G11C.2.1	1329	IV: 14709586-14714738

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y57G11C.2	Y57G11C.2	1320	IV: 14709595-14709706

4 RNAi Result

• WBRNAi00057691
• WBRNAi00021140
• WBRNAi00037599
• WBRNAi00066358

95 Allele

• gk964078
• gk963546
• gk963547
• gk964500
• gk962765
• gk963590
• gk963795
• gk963948
• gk964199
• WBVar02067872
• WBVar02122620
• gk961130
• WBVar00195773
• gk960962
• WBVar01732695
• WBVar01821522
• WBVar01821523
• gk947066
• h6227
• gk715399
• gk729618
• gk802634
• gk852193
• gk821250
• gk633927
• gk664281
• gk881992
• gk739607
• gk594518
• gk451512

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00013300
• Start: 14709586
• End: 14714738
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_14714739..14714754
• Length (nt): 16
• Chromosome Location: IV: 14714739-14714754
• Organism: Caenorhabditis elegans

29 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
24 hours of AgNPs exposure.	Genes downregulated more than 2 fold after 24 hours of AgNPs exposure.	Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL).	WBPaper00034661:AgNPs_downregulated
	Genes that showed significantly decreased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control.	To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed.	WBPaper00046548:dafachronic-acid_downregulated
control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint.	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_EtBr-exposed_48h
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Psora_downregulated
	Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_downregulated_neuron
	Top 300 transcripts enriched in MC neuron, MCL, MCR according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:MC
	Transcripts that showed significantly decreased expression in lin-22(ot269) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot269)_downregulated
	Single-cell RNA-Seq cell group 135_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:135_0
	Genes that were regulated by DAF-12 in response to germline loss, identified by comparing differentially expression genes between glp-1(e2141ts, 25C) vs. glp-1(e2141ts, 20C) and daf-12;glp-1(e2141ts, 25C) vs. daf-12;glp-1(e2141ts, 20C).	All lists used an Fs:Ptab 0.01 cutoff.	WBPaper00040412:germline-regulated_daf-12_target
	Transcripts enriched in I1 according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:I1_enriched
	Genes up or down regulated by 10e-05M of estrogen. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.	The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.	WBPaper00005124:estrogen_10-5M_regulated
control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vsafter UVC exposure without EtBr treatment, at the -1h timepoint (just prior to the third UVC dose (48h)).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:control_vs_UVC-exposed_48h
	Transcripts that showed significantly decreased expression in eat-2(ad1113) comparing to in N2.	DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs.	WBPaper00065746:eat-2(ad1113)_downregulated
	Transcripts that showed significantly decreased expression in Day 8 adults comparing to in Day 1 adults in neuron cells.	t-test, fold change > 2, p-value < 0.01.	WBPaper00062590:Aging_downregulated_neuron
	Transcripts that showed significantly decreased expression in scc-1(ubs19) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19)_downregulated
	Transcripts that showed significantly decreased expression in alh-4(hj221) deletion allele comparing to in N2.	N.A.	WBPaper00061653:alh-4(hj221)_downregulated
	Single-cell RNA-Seq cell group 53_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:53_0
	Transcripts enriched in I6 according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:I6_enriched
	Transcripts that showed significantly decreased expression in scc-1(ubs19);coh-1(ubs26) comparing to in control animals.	DESeq2 v.1.34, fold change > 2, FDR < 0.05.	WBPaper00067078:scc-1(ubs19);coh-1(ubs26)_downregulated
	Transcripts down regulated in the FACS isolated neurons from daf-2(e1370), comparing to N2.	DESeq. differential expression was tested using the generalized linear model (GLM) likelihood ratio test, threshold for detection of DEGs was set at p-value < 0.05.	WBPaper00048988:daf-2(e1370)_downregulated_neuron

4 Expression Patterns

• Primary Identifier: Expr2013138
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1022704
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031370
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1161103
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

18 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00013300
• Start: 14709586
• End: 14714738
• Strand: 1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5153

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00050961

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_14709033..14709585
• Length (nt): 553
• Chromosome Location: IV: 14709033-14709585
• Organism: Caenorhabditis elegans