WormMine: Gene WBGene00009610

• WormBase Gene ID: WBGene00009610
• Gene Name: oac-28
• Sequence Name: F41D3.5
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable acyltransferase activity, transferring groups other than amino-acyl groups. Predicted to be involved in polysaccharide biosynthetic process. Predicted to be located in membrane.
• Biotype: SO:0001217
• Genetic Position: I :13.1057±
• Length (nt): 2937

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00009610

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F41D3.5.1	F41D3.5.1	2022	I: 12259912-12262848

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F41D3.5	F41D3.5	2022	I: 12259912-12260175

6 RNAi Result

• WBRNAi00046972
• WBRNAi00046973
• WBRNAi00003648
• WBRNAi00003653
• WBRNAi00107928
• WBRNAi00107929

13 Allele

• gk962706
• gk963849
• gk962859
• gk964175
• gk963095
• gk964202
• gk964201
• WBVar02123567
• gk963738
• gk836218
• WBVar02121103
• WBVar02122512
• WBVar02124530

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00009610
• Start: 12259912
• End: 12262848
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_12258804..12259911
• Length (nt): 1108
• Chromosome Location: I: 12258804-12259911
• Organism: Caenorhabditis elegans

25 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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 in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_downregulated
	Genes with significantly increased expression in eat-2(ad465) treated with 2% DMSO for 72 hours, comparing to in N2 treated with 2% DMSO for 72 hours.	Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes.	WBPaper00048989:eat-2(ad465)_upregulated_in-DMSO
	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
	Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.	Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction.	WBPaper00040560:hpl-2_embryo_downregulated
	Transcripts that showed significantly decreased expression in pals-22(jy3) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-22(jy3)_downregulated
	Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_downregulated
	Transcripts that showed significantly decreased expression in bcf-1(ylf1) comparing to in N2 adult animals.	DESeq2	WBPaper00064933:bcf-1(ylf1)_downregulated_transcript
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
	Genes from eat-2(ad465) animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO.	Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes.	WBPaper00048989:eat-2(ad465)_rapamycin_upregulated
	Transcripts that showed significantly decreased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:hmg-3(bar24)_downregulated
	Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 20C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_downregulated_20C
	Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray
	Transcripts that showed significantly decreased expression in animals after 24 hour exposure to 100ug per ml silica nanoparticles (SiNPs).	The random variance model (RVM)t-test was applied toidentify differentially expressed mRNAs and miRNAsbetween the SiNPs-treated group and the control group. P-value <0.05 and fold change (FC) >1.5 were considered as the threshold screening between the SiNP-treated groupand the control group.	WBPaper00060100:SiNP_downregulated_mRNA
	Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_downregulated
	Transcripts that showed significantly decreased expression in pals-25(icb98) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-25(icb98)_downregulated
	Genes that are upregulated by 0.2M ethanol treatment.	Differences in gene expression levels between the two groups of worms were analyzed with Cufflinks 1.0.3, using a cutoff of twofold difference and FDR corrected p < 0.05.	WBPaper00041954:ethanol_upregulated
	Transcripts that showed significantly increased expression in spt-16(RNAi) comparing to in vector control worm at L4 larva stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:spt-16(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in vha-12(ok281) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.01	WBPaper00066743:vha-12(ok281)_downregulated
	Transcripts that showed significantly decreased expression in hmg-4(RNAi) comparing to in vector control worm at L4 larva stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:hmg-4(RNAi)_downregulated
	Genes that showed expression changes over the aging time course.	One-way analysis of variance (ANOVA) was used to identify 201 genes that show expression changes over the aging time course (p < 0.001)	WBPaper00005475:Aging-regulated
	Transcripts that showed significantly decreased expression in etr-1(lq61) comparing to in N2 animals at L1 larva stage.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:etr-1(lq61)_downregulated
	Transcripts that showed significantly decreased expression in eat-2(ad465) animals treated with luc2 RNAi comparing to in wild type animals treated with luc2 RNAi.	Fold change > 2, FDR < 0.05	WBPaper00066595:eat-2(ad465)_downregulated_luc2(RNAi)
	Transcripts that showed more than 4 fold of expression in CB4856 comparing to in N2 animals.	DESeq2, fold change > 4.	WBPaper00053909:N2_vs_CB4856_downregulated

1 Expression Patterns

• Primary Identifier: Expr1150840
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

4 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00009610
• Start: 12259912
• End: 12262848
• Strand: -1

4 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2937

1 Sequence Ontology Term