WormMine: Gene WBGene00013333

• WormBase Gene ID: WBGene00013333
• Gene Name: degl-1
• Sequence Name: Y57G11C.44
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable sodium channel activity. Predicted to be involved in sodium ion transmembrane transport. Predicted to be located in membrane.
• Biotype: SO:0001217
• Genetic Position: IV :12.4449±
• Length (nt): 776

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00013333

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y57G11C.44c.1	Y57G11C.44c.1	173	IV: 14770650-14770869
Transcript:Y57G11C.44a.1	Y57G11C.44a.1	553	IV: 14770654-14771425
Transcript:Y57G11C.44b.1	Y57G11C.44b.1	264	IV: 14770700-14771127

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y57G11C.44a	Y57G11C.44a	468	IV: 14770700-14770729
CDS:Y57G11C.44b	Y57G11C.44b	264	IV: 14770700-14770729
CDS:Y57G11C.44c	Y57G11C.44c	123	IV: 14770700-14770729

0 RNAi Result

24 Allele

• gk964078
• gk963546
• gk963547
• gk964500
• gk962765
• gk963590
• gk963795
• gk963948
• WBVar02123255
• WBVar02122621
• WBVar02124802
• gk964476
• WBVar02123105
• gk466239
• gk320867
• gk447270
• gk698730
• WBVar00195906
• WBVar00195905
• ok2771
• WBVar01806268
• gk218783
• gk218784
• gk218782

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00013333
• Start: 14770650
• End: 14771425
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

0 Downstream Intergenic Region

28 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
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
	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
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	Transcripts that showed significantly increased 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)_upregulated_neuron
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
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals.	CuffDiff, fold change > 2.	WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
	Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
	Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:flat_dev_expression
Bacteria: B.subtilis	Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult.	edgeR 3.16.5, FDR < 0.05, fold change > 2.	WBPaper00059117:B.subtilis_upregulated
	Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in lin-22(ot267) 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(ot267)_downregulated
	Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12	Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.	WBPaper00040221:DAF-12_target_ALF4
	Genes with variation in expression level across conditions (control, 25C, High-pH-Salt, Liquid, infection).	two-way ANOVA	WBPaper00041174:environmental
Starvation 48 hours at L1 arrest	Transcripts that showed significantly decreased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_downregulated_N2_mRNA
	Transcripts that showed significantly increased expression in fhod-1(tm2363) comparing to in N2 animals.	Differentially expressed genes (defined by false discovery rate (FDR) step up <= 0.05, fold change >1.5) were identified by Gene-Specific Analysis.	WBPaper00060634:fhod-1(tm2363)_upregulated
	Top 300 transcripts enriched in ABplapaaapa, ABprapaaapa 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:Neuroblast_AIZ_FLP
	Top 300 transcripts enriched in ABplapaaap, ABprapaaap 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:Neuroblast_AIZ_FLP_RMG
	Genes with significant variation in expression level only across environments(control, 25C, High-pH-Salt, Liquid, infection), but no genotypic variation (AB2, CB4856, RC301, CB4857, N2, HC445).	two-way ANOVA	WBPaper00041174:environmental_prime
Bacteria infection: Stenotrophomonas maltophilia	Transcripts that showed significantly decreased expression after fed with S. maltophilia strains JCMS or K279a for 24 hours at 25C, comparing to control animals fed with OP50.	Benjamini-Hochberg fold change >= 1.5, p-value < 0.05.	WBPaper00055137:S.maltophilia_downregulated
	Single-cell RNA-Seq cell group 25_1 expressed in neuron.	scVI 0.6.0	WBPaper00065841:25_1
	Top 300 transcripts enriched in IL2L, IL2R, IL2DL, IL2DR, IL2VL, IL2VR 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:IL2
	Transcripts enriched in IL2_LR according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:IL2_LR_enriched

5 Expression Patterns

• Primary Identifier: Expr1161124
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1035954
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2026308
• 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: Expr2008069
• 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: Expr1018890
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

8 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00013333
• Start: 14770650
• End: 14771425
• Strand: -1

8 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 776

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00032779

0 Upstream Intergenic Region