WormMine: Gene WBGene00022433

• WormBase Gene ID: WBGene00022433
• Gene Name: Y108F1.5
• Sequence Name: Y108F1.5
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable helicase activity. Is an ortholog of human DHX35 (DEAH-box helicase 35).
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 1083

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00022433

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y108F1.5.1	Y108F1.5.1	444	X: 272930-274012

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y108F1.5	Y108F1.5	444	X: 272930-273323

3 RNAi Result

• WBRNAi00001479
• WBRNAi00075519
• WBRNAi00075512

24 Allele

• gk963652
• gk962800
• gk964065
• gk964321
• WBVar02123605
• WBVar00074196
• WBVar02123945
• WBVar02123727
• WBVar02123607
• WBVar02121495
• gk532412
• gk820744
• gk925551
• gk657519
• gk351632
• WBVar02026564
• gk950386
• WBVar01617890
• WBVar01992429
• WBVar02048356
• gk268727
• gk268726
• WBVar01689942
• ok3700

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00022433
• Start: 272930
• End: 274012
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_270940..272929
• Length (nt): 1990
• Chromosome Location: X: 270940-272929
• Organism: Caenorhabditis elegans

22 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
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
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 decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) 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:hda-1(ne4752)_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 that show significant variation due to strain by stage interaction.	An analysis of variance (one-way ANOVA) test was used to see which genes changed significantly over developmental time, using the strain and stage of each array as the parameters. qvalue, an R-package, was used to obtain false-discovery rates (FDR). Significant genes have an FDR of less than .05.	WBPaper00032479:CB4856vsN2_LifeStageProfile_Variation
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(gk437) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(gk437)_adult
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in N2 animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_N2_adult
	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
	Transcripts that showed significantly decreased expression in emb-4(hc60) comparing to in N2.	DESeq2	WBPaper00052884:emb-4(hc60)_downregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure.	Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.	DESeq2, FDR < 0.05	WBPaper00056868:P.aeruginosa_upregulated_smallRNA
	Transcripts that showed significantly decreased 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)_downregulated_neuron
	Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals.	edgeR p-value < 0.01 and fold change > 4.	WBPaper00061613:human-amyloid-beta_upregulated
	Transcripts that showed significantly increased expression in animals treated with 25ug per mL tunicamycin for 4 hours, comparing to control animals.	Fold-change > 1.5, ANOVA P values < 0.05.	WBPaper00055482:Tunicamycin_upregulated
Bacteria infection: Photorhabdus luminescens	Genes with decreased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_downregulated_RNAseq
	Transcripts that showed differential expression in adult N2 vs adult mir-34(OverExpression) animals at 25C.	N.A.	WBPaper00050488:N2_vs_mir-34(OverExpression)_regulated_adult_25C
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 20C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_20C
	Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_20C
	Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 25C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_25C
	Transcripts that showed differential expression in adult mir-34(OverExpression) vs adult N2 animals at 20C.	N.A.	WBPaper00050488:mir-34(OverExpression)_vs_N2_regulated_adult_20C
	Transcripts that showed significantly decreased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:downregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly decreased expression in hlh-26(ok1453) animals exposed to E. faecium for 8 hours, comparing to N2 animals exposed to E. faecium for 8 hours.	Fold change > 2.	WBPaper00062585:hlh-26(ok1453)_downregulated_E.faecium

3 Expression Patterns

• Primary Identifier: Expr1014615
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2025227
• 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: Expr1158822
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

1 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00022433
• Start: 272930
• End: 274012
• Strand: -1

1 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1083

1 Sequence Ontology Term