WormMine: Gene WBGene00235279

• WormBase Gene ID: WBGene00235279
• Gene Name: Y67D8C.22
• Sequence Name: Y67D8C.22
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be involved in sensory perception of sound. Predicted to be located in membrane. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness. Is an ortholog of human CLRN2 (clarin 2).
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 6155

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00235279

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y67D8C.22a.1	Y67D8C.22a.1	805	IV: 3070153-3076307
Transcript:Y67D8C.22b.1	Y67D8C.22b.1	201	IV: 3070153-3070353

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y67D8C.22a	Y67D8C.22a	678	IV: 3070153-3070418
CDS:Y67D8C.22b	Y67D8C.22b	201	IV: 3070153-3070353

3 RNAi Result

• WBRNAi00057994
• WBRNAi00021273
• WBRNAi00110941

99 Allele

• gk963722
• gk962726
• gk391994
• gk861086
• gk415351
• gk419777
• gk878096
• gk543175
• gk697082
• gk589384
• gk722211
• gk722210
• gk688110
• gk507444
• gk524697
• gk629779
• gk655348
• gk461959
• gk540120
• gk627600
• gk871956
• gk814069
• gk893288
• gk868037
• gk507967
• gk582384
• gk880248
• gk400718
• gk471797
• gk920845

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00235279
• Start: 3070153
• End: 3076307
• Strand: -1

4 Data Sets

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

0 Downstream Intergenic Region

36 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
	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
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_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
	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
	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 increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_upregulated
	Transcripts that showed significantly decreased expression after animals grew in 500 uM glycine from hatch till 1-day post L4 adult, comparing to untreated animals.	Differential expression was assessed using a nempirical Bayes moderated t-test within limmas linear model framework including the precision weights estimated by voom.Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Curator applied threshold: fold change > 2, adjusted p-value < 0.01.	WBPaper00056330:glycine_downregulated
	Transcripts that showed significantly decreased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_downregulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_upregulated
	Transcripts that showed significantly increased expression in atfs-1(et15) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:atfs-1(et15)_upregulated
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated_P.aeruginosa-infection
	Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_daf-16
Bacteria diet: complex environmental microbiotas	Transcripts that showed significantly decreased expression after L1 larva grew on soil microbiota at 25C for 3 days.	N.A.	WBPaper00056139:soil-microbiota_downregulated
Bacteria: B.subtilis	Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult.	edgeR 3.16.5, FDR < 0.05, fold change > 2.	WBPaper00059117:B.subtilis_upregulated
	Transcripts that showed significantly increased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_upregulated
	Transcripts that showed significantly increased expression in jmjd-5(zr1234) comparing to in N2 animals.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-5(zr1234)_upregulated
	Transcripts that showed significantly decreased expression in nuo-6(qm200) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:nuo-6(qm200)_downregulated
	Transcripts that showed significantly increased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage.	edgeR (version 3.24.3), fold change > 4, FDR < 0.01.	WBPaper00062456:doxycycline_upregulated_N2_transcript
	Transcripts that showed significantly decreased expression in nuo-6(qm200) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:nuo-6(qm200)_downregulated
	siRNAs that showed significantly higher expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine).	DESeq2 v1.13.8, fold change > 2, FDR < 0.01.	WBPaper00056161:hermaphrodite_enriched_siRNA
	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 jmjd-1.2(zr1010) comparing to in N2 animals.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-1.2(zr1010)_upregulated
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_downregulated
	Transcripts that showed significantly decreased expression in atfs-1(et18) comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(et18)_downregulated
	Transcripts uniquely expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_enriched
	Transcripts that showed significantly decreased expression in eat-2(ad1113) comparing to in N2.	DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs.	WBPaper00065746:eat-2(ad1113)_downregulated

2 Expression Patterns

• Primary Identifier: Expr2026450
• 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: Expr2008208
• 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).

3 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00235279
• Start: 3070153
• End: 3076307
• Strand: -1

3 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6155

1 Sequence Ontology Term

• Name: gene

0 Strains

0 Upstream Intergenic Region