WormMine: Gene WBGene00269382

• WormBase Gene ID: WBGene00269382
• Gene Name: F33D11.16
• Sequence Name: F33D11.16
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in several structures, including VB2; epithelial cell; hypodermis; rectal gland cell; and somatic neurons based on single-cell RNA-seq studies. Is affected by several genes including etr-1; ilc-17.1; and hda-2 based on RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 756

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00269382

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F33D11.16a.1	F33D11.16a.1	473	I: 5838095-5838850
Transcript:F33D11.16b.1	F33D11.16b.1	120	I: 5838635-5838754

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F33D11.16a	F33D11.16a	189	I: 5838283-5838301
CDS:F33D11.16b	F33D11.16b	120	I: 5838635-5838754

0 RNAi Result

10 Allele

• gk962858
• gk962706
• gk963902
• gk964505
• WBVar01694791
• WBVar02033005
• gk678947
• gk828172
• gk727097
• gk842776

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00269382
• Start: 5838095
• End: 5838850
• Strand: 1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_5838851..5840281
• Length (nt): 1431
• Chromosome Location: I: 5838851-5840281
• Organism: Caenorhabditis elegans

23 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
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 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
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_N2_mRNA
	Transcripts enriched in Rectal_gland according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:Rectal_gland_enriched
	Transcripts that showed significantly increased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_upregulated
Wounding: 2 hours after a single stab of a microinjection needle to either anterior or posterior body of lateral hyp7 (avoid the gonad) 24 hr after the L4 stage.	Transcripts that showed significantly increased expression 2 hours after animals had a single stab of a microinjection needle to either anterior or posterior body of lateral hyp7 (avoid the gonad) 24 hr after the L4 stage.	The cutoff for differential expressed genes (DEGs) were: Benjamini-Hochberg adjustedP-valueless than 0.05 and fold change larger than 1.5.	WBPaper00059987:Wounding_upregulated
	Single-cell RNA-Seq cell group 74_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:74_0
	Transcripts that showed significantly altered expression at RMG neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_RMG
	Transcriptions that showed significantly decreased expression in daf-16(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:daf-16(RNAi)_downregulated
	Top 300 transcripts enriched in AINL, AINR 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:AIN
	Top 300 transcripts enriched in RIVL, RIVR 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:RIV
	Top 300 transcripts enriched in AVKL, AVKR 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:AVK
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved aptf-1(gk794) animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_aptf-1(gk794)_mRNA
	Single-cell RNA-Seq cell group 6_1 expressed in neuron.	scVI 0.6.0	WBPaper00065841:6_1
	Single-cell RNA-Seq cell group 30_1 expressed in hypodermis.	scVI 0.6.0	WBPaper00065841:30_1
	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
	Single-cell RNA-Seq cell group 30_3 expressed in gland.	scVI 0.6.0	WBPaper00065841:30_3
	Single-cell RNA-Seq cell group 146_0 expressed in epithelium.	scVI 0.6.0	WBPaper00065841:146_0
	Top 300 transcripts enriched in pharyngeal-intestinal valve 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:Pharyngeal_intestinal_valve
	Single-cell RNA-Seq cell group 30_4 expressed in valve.	scVI 0.6.0	WBPaper00065841:30_4
	Transcripts that showed significantly decreased expression in pals-25(jy111) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-25(jy111)_downregulated

2 Expression Patterns

• Primary Identifier: Expr2021465
• 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: Expr2003253
• 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).

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00269382
• Start: 5838095
• End: 5838850
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 756

1 Sequence Ontology Term