WormMine: Gene WBGene00019698

• WormBase Gene ID: WBGene00019698
• Gene Name: riok-1
• Sequence Name: M01B12.5
• Brief Description: riok-1 encodes, by alternative splicing, two isoforms of a putative RIO kinase required for viability, fertility, endocytosis, and fat storage; RIOK-1 was identified as a negative regulator of endo-siRNA generation in C. elegans by a clonal screen (suppressor of siRNA gene 3, susi-3); RIOK-1 is orthologous to human RIOK1; the sterile phenotype of riok-1(RNAi) is specifically enhanced by lin-35(n2239), indicating that RIOK-1 and LIN-35 may interact in vivo; in eri-1(mg366);GFP::NRDE-3 worms, the mutated susi-3 could redistribute NRDE-3 from the cytoplasm to the nucleus.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable protein serine/threonine kinase activity. Involved in several processes, including gamete generation; positive regulation of vulval development; and regulation of intracellular signal transduction. Predicted to be located in cytosol. Predicted to be part of preribosome, small subunit precursor. Expressed in gonad; nervous system; and vulva. Is an ortholog of human RIOK1 (RIO kinase 1).
• Biotype: SO:0001217
• Genetic Position: I :-4.48576 ±0.003734
• Length (nt): 11253

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00019698

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:M01B12.5a.1	M01B12.5a.1	2040	I: 3085014-3096218
MRNA	Transcript:M01B12.5a.2	M01B12.5a.2	1596	I: 3091268-3096266
NcPrimaryTranscript	Transcript:M01B12.5b	M01B12.5b	2240	I: 3091283-3096206

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:M01B12.5a	M01B12.5a	1521	I: 3091283-3091814

37 RNAi Result

• WBRNAi00034336
• WBRNAi00050723
• WBRNAi00073218
• WBRNAi00114397
• WBRNAi00114542
• WBRNAi00114543
• WBRNAi00073220
• WBRNAi00088191
• WBRNAi00088314
• WBRNAi00114547
• WBRNAi00114544
• WBRNAi00070955
• WBRNAi00112509
• WBRNAi00073219
• WBRNAi00114525
• WBRNAi00025968
• WBRNAi00114398
• WBRNAi00003998
• WBRNAi00025969
• WBRNAi00114396
• WBRNAi00114395
• WBRNAi00114548
• WBRNAi00088117
• WBRNAi00024075
• WBRNAi00088058
• WBRNAi00088506
• WBRNAi00114545
• WBRNAi00114546
• WBRNAi00088396
• WBRNAi00088273

327 Allele

• gk963902
• gk964159
• WBVar01691743
• WBVar01430910
• WBVar01430917
• WBVar01430916
• WBVar01430920
• WBVar01430909
• WBVar01602814
• WBVar01602813
• WBVar01602812
• WBVar01602811
• WBVar01602817
• WBVar01602816
• WBVar01602815
• WBVar01269028
• WBVar01269361
• WBVar01269250
• WBVar01269139
• WBVar01269917
• WBVar01269806
• WBVar01269584
• WBVar01269473
• WBVar01269695
• WBVar01268917
• WBVar01820631
• WBVar01820632
• WBVar01545908
• WBVar00031816
• WBVar00031821

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00019698
• Start: 3085014
• End: 3096266
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrI_3084877..3085013
• Length (nt): 137
• Chromosome Location: I: 3084877-3085013
• Organism: Caenorhabditis elegans

94 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Bacteria infection: Staphylococcus aureus	mRNAs that showed increased expression 8 hours after hlh-30(tm1978) animals were infected by S. aureus.	DESeq, p <= 0.05	WBPaper00045314:S.aureus-induced_hlh-30(tm1978)
Bacteria infection: Staphylococcus aureus	mRNAs that showed increased expression 8 hours after N2 animals were infected by S. aureus.	DESeq, p <= 0.05	WBPaper00045314:S.aureus-induced_N2
	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
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
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
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	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
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
hypergravitational 15xg force for 4 days via centrifugation.	Transcripts that showed significantly decreased expression in animals grew under the hypergravitational 15xg force for 4 days via centrifugation.	N.A.	WBPaper00061274:hypergravity_15xg_downregulated
24 hours of AgNPs exposure.	Genes downregulated more than 2 fold after 24 hours of AgNPs exposure.	Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL).	WBPaper00034661:AgNPs_downregulated
	Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2.	DESeq2	WBPaper00052884:emb-4(hc60)_upregulated
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh, triggered by the dafachronic acid (DA) growth hormone6). Cluster 2 genes' expression gradually increased into dauer.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster2
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 20C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_20C_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
Bacteria infection: Xenorhabdus nematophila	Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila.	Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets.	WBPaper00041606:CE_X.nematophila_regulated
control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h).	Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)).	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_UVC-EtBr-exposed_48h

6 Expression Patterns

• Primary Identifier: Expr11860
• Remark: Temporal description
• Pattern: Fluorescence was observed in all developmental stages after hatching with strong expression in the nervous system and the somatic gonad during L2-L4 larval stages. Additionally, GFP signals were detected in the uterus as well as in the spermatheca of adult worms. Strong riok-1 expression was seen in the head neurons required for chemotaxis like the AWC neurons, the nerve ring (RID/RIF neurons), in inhibitory motor neurons (DA/DD/VA/VD), mechanosensory neurons (ALML/PLML), as well as in the tail sensory neurons (DVA/PDA). GFP was also detected in both nerve cords and associated commissures. In the L2-larva, GFP expression was observed in the somatic gonad as well as in the ventral nerve cord. In the L3-larva, riok-1 expression is maintained in the somatic gonad in ventral uterine (VU/AC) cells. After commitment, riok-1 is expressed in the anchor cell. In contrast, GFP expression could not be detected in the ventral precursor cells (VPCs) in the hypodermis. In the L4-larva, riok- 1 is expressed in the vulF cells of the vulva, cells of the uterus and the uterine seam cells (utse). In young adult worms, the riok-1 expression is maintained in the cells of vulva and the uterus.

• Primary Identifier: Expr1021317
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1038509
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1154420
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2015361
• 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: Expr2033595
• 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).

24 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00019698
• Start: 3085014
• End: 3096266
• Strand: -1

24 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 11253

1 Sequence Ontology Term