WormMine: Gene WBGene00249815

• WormBase Gene ID: WBGene00249815
• Gene Name: F20D12.12
• Sequence Name: F20D12.12
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in germ line based on RNA-seq studies. Is affected by several genes including nuo-6; cua-1; and atfs-1 based on RNA-seq studies. Is affected by four chemicals including rifampin; Sirolimus; and allantoin based on RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 613

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00249815

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F20D12.12.1	F20D12.12.1	207	IV: 7947440-7948052

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F20D12.12	F20D12.12	78	IV: 7947471-7947504

0 RNAi Result

11 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• tm11488
• WBVar02124417
• ttTi3158
• gk206370
• gk635266
• gk691317

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00249815
• Start: 7947440
• End: 7948052
• Strand: 1

2 Data Sets

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

0 Downstream Intergenic Region

19 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_upregulated
	Transcripts that showed significantly increased expression in prg-1(tm872) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:prg-1(tm872)_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 decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin_downregulated
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
Dietary restriction	Transcripts that showed significantly increased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_upregulated
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin_downregulated
	Transcripts with promoter regions binding DREAM protein complex, according to ChIP-seq of E2F-DP (DPL-1 and EFL-1) and MuvB (LIN-9, LIN-37, LIN-52, and LIN-54) of N2 late embryo.	N.A.	WBPaper00053289:DREAM-target
	transcripts that showed significantly increased expression after N2 animals were exposed to 20 uM bortezomib for 4 hours.	Differential expression analyses were performed using limma-voom in Galaxy. Fold change > 2, FDR < 0.05.	WBPaper00062345:bortezomib_4h_upregulated_N2
	transcripts that showed significantly increased expression after zip-1(jy13) animals were exposed to 20 uM bortezomib for 4 hours.	Differential expression analyses were performed using limma-voom in Galaxy. Fold change > 2, FDR < 0.05.	WBPaper00062345:bortezomib_4h_upregulated_zip-1(jy13)
	Transcripts that showed significantly decreased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_downregulated_neural
	Transcripts that showed significantly increased expression in unc-70(cas983) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:unc-70(cas983)_upregulated
	Transcripts that showed significantly decreased expression in lbp-3 overexpression transgenic lines comparing to wild type control animals.	DESeq2 fold change > 2, FDR < 0.05.	WBPaper00064156:lbp-3(overexpress)_downregulated
	Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis.	N.A.	WBPaper00059471:EGL-43_interacting
	Transcripts that showed significantly altered expression in olrn-1(ums9) comparing to in N2 animals.	The Ballgown package from the Bioconductor software suite (version 3.8) was used to run a custom R script in R console(R Version 3.5) to analyze the differential gene expression, visualize the data, and perform statistical tests for differential expressionwith multiple test correction. A gene was considered to be differentially regulated if its fold change versus wild-type was greater thantwo, the adjusted p value was less than 0.05, and its RPKM was greater than one.	WBPaper00059567:olrn-1(ums9)_regulated
	Transcripts that showed significantly decreased expression in cua-1(knu790) comparing to in N2.	FDR < 0.05 and fold change > 2.	WBPaper00066160:cua-1(knu790)_downregulated
	Transcripts that showed significantly decreased expression in nuo-6(qm200);atfs-1(gk3094) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:nuo-6(qm200);atfs-1(gk3094)_downregulated

2 Expression Patterns

• Primary Identifier: Expr2020999
• 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: Expr2002781
• 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: WBGene00249815
• Start: 7947440
• End: 7948052
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 613

1 Sequence Ontology Term