WormMine: Gene WBGene00195240

• WormBase Gene ID: WBGene00195240
• Gene Name: Y39B6A.69
• Sequence Name: Y39B6A.69
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in ABplppppaa and ABprppppaa based on single-cell RNA-seq studies. Is affected by several genes including hrpr-1; mrps-5; and hpl-2 based on RNA-seq and microarray studies. Is affected by four chemicals including Psoralens; allantoin; and Sirolimus based on RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 150

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00195240

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y39B6A.69.1	Y39B6A.69.1	150	V: 19152279-19152428

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y39B6A.69	Y39B6A.69	150	V: 19152279-19152428

0 RNAi Result

7 Allele

• gk963271
• gk962705
• gk963489
• gk963304
• gk963809
• gk963637
• WBVar01992301

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00195240
• Start: 19152279
• End: 19152428
• Strand: -1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_19149158..19152278
• Length (nt): 3121
• Chromosome Location: V: 19149158-19152278
• Organism: Caenorhabditis elegans

26 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals.	The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed.	WBPaper00053402:cco-1(RNAi)_upregulated
	Transcripts that showed significantly increased expression in his-3(RNAi) comparing to in vector control animals.	The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed.	WBPaper00053402:his-3(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_downregulated
	Transcripts that showed significantly increased 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)_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)_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 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
	Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_upregulated
	Transcripts that showed significantly increased exression in animals exposed to 100uM cadmium for 24 hours.	DESeq2 v1.20.0, fold change > 2, FDR < 0.05.	WBPaper00065029:cadmium_upregulated
Bacteria infection: N.ausubeli	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ausubeli_regulated
	Genes identified as up-regulated at a 5% false discovery rate through RNAseq experiments with three tatn-1(qd182) and three N2 RNA samples.	ANOVA with FDR <= 0.05.	WBPaper00044656:tatn-1(qd182)_upregulated
	Transcripts that showed significantly increased expression in pals-22(jy3) comparing to in N2 animals.	limma-voom, fold change > 2, FDR < 0.05	WBPaper00064532:pals-22(jy3)_upregulated
	Transcripts that showed significantly increased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_upregulated
	Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals.	Fold change > 4, p-value < 0.01	WBPaper00056330:mrps-5(RNAi)_upregulated
	Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals.	DESeq2, fold change > 4, FDR < 0.05.	WBPaper00064661:lpd-3(ok2138)_upregulated
moderate static magnetic field	Transcripts that showed significantly increased expression after exposure to moderate static magnetic field.	N.A.	WBPaper00064509:static-magnetic-field_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Psora-Allantoin_downregulated
	Transcripts that showed significantly increased expression in cco-1/cox-5B(RNAi) animals comparings to animals injected with vector control.	LimmaVoom. The genes with a BenjaminiHochbergadjusted P value < 0.05 were defined as statistically significant. Genes whose expressions were significantly upregulated with log2FC > 0.393.	WBPaper00064637:cox-5B(RNAi)_upregulated
	Genes that showed significantly increased expression in hrp-2(RNAi) animals comparing to in control animals.	DESeq2, adjusted p-value < 0.1, log2 Fold change >= 2 or <= -2.	WBPaper00050504:hrp-2(RNAi)_upregulated
	Top 300 transcripts enriched in ABplppppaa, ABprppppaa 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:Parent_of_PVP_and_rect_V
Bacteria: C.neoformans strain H99	Transcripts that showed significantly increased expression after infection by C. neoformans H99.	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:C.neoformans_H99_upregulated
Bacteria infection: N.ferruginous	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ferruginous_regulated
Bacteria infection: N.ironsii	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ironsii microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.ironsii_regulated
Bacteria infection: N.parisii	Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.parisii microsporidia spores for 72 hours at 21C starting from L1 larva stage.	FDR < 0.01	WBPaper00065086:JU1400_N.parisii_regulated
Virus infection: Orsay infected at L3 larva stage for 12 hours.	Transcripts that showed signicantly increased expression after Orsay virus infection to rde-1(ne219) animals.	edgeR, FDR < 0.05.	WBPaper00051137:Orsay-virus_upregulated_rde-1(ne219)

3 Expression Patterns

• Primary Identifier: Expr2007378
• 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: Expr1159705
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2025613
• 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: WBGene00195240
• Start: 19152279
• End: 19152428
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 150

1 Sequence Ontology Term