WormMine: Gene WBGene00005246

• WormBase Gene ID: WBGene00005246
• Gene Name: srh-21
• Sequence Name: C02E7.2
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be located in membrane.
• Biotype: SO:0001217
• Genetic Position: V :-3.69531 ±0.001676
• Length (nt): 1587

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00005246

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C02E7.2.1	C02E7.2.1	1282	V: 4926671-4928257

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C02E7.2	C02E7.2	993	V: 4926671-4926705

3 RNAi Result

• WBRNAi00039421
• WBRNAi00009995
• WBRNAi00028346

36 Allele

• gk963301
• WBVar02060018
• gk963591
• gk963553
• gk964259
• gk964351
• gk963850
• WBVar01861826
• WBVar01861828
• WBVar01861827
• WBVar01861829
• WBVar01861831
• WBVar01861830
• WBVar01861833
• WBVar01861832
• WBVar01861835
• WBVar01861834
• WBVar01861837
• WBVar01861836
• WBVar01861839
• WBVar01861838
• gk537697
• gk453912
• gk389903
• gk551214
• gk391780
• WBVar01549187
• ttTi2868
• gk955360
• gk234069

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00005246
• Start: 4926671
• End: 4928257
• Strand: 1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_4928258..4928277
• Length (nt): 20
• Chromosome Location: V: 4928258-4928277
• Organism: Caenorhabditis elegans

27 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	Transcripts of coding genes that showed significantly decreased 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_depleted_coding-RNA
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	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
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_RNAseq
	Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_daf-16
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C.	Transcripts that showed significantly increased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C.	DESeq2, fold change > 2.	WBPaper00061081:E.faecalis_upregulated_N2
	Transcripts that showed significantly decreased expression in unc-70(cas983) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:unc-70(cas983)_downregulated
Bacteria infection: Erwinia carotovora	Genes down-regulated in animals infected with Erwinia carotovora compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Erwinia_carotovora_downregulated
	Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult.	Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed.	WBPaper00049377:MWCNT_downregulated
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_9
	Transcripts that showed significantly decreased expression in drh-3(rrr2) comparing to in N2.	edgeR, log2 fold change > 2 or < -2.	WBPaper00053888:drh-3(rrr2)_downregulated
	Transcripts that showed significantly decreased expression in set-2(zr2012) 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(zr2012)_downregulated
	Transcripts that showed significantly decreased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_downregulated
	Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis.	N.A.	WBPaper00059471:EGL-43_interacting
	Coexpression clique No. 90, ckr-1-T09B9.3, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:ckr-1-T09B9.3
	Transcripts that showed significantly decreased expression in spc-1(cas971) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:spc-1(cas971)_downregulated
	Genes that are down-regulated in wild-type N2 larvae compared to elt-2(ca15);elt-7(tm840) larvae.	RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq. 2 with Cook's cutoff filtering set to FALSE. Genes were counted as differentially expressed if they registered a Benjamini-Hochberg corrected p-value less than 0.05 and a log2-fold change greater than 1.2 between any pair-wise conditional comparison.	WBPaper00053606:N2_vs_elt-2(ca15);elt-7(tm840)_downregulated
feeding/starvation	The third of four clusters of genes up-regulated during L1 arrest.	For each average expression value, the larger of the model-based error and empirical error was reported. ANOVA and T-tests were also computed in Rosetta Resolver using the reported errors. Expression values, errors, and P-values corresponding to transcript detection, ANOVAs, and T-tests were exported from Rosetta Resolver and analyzed elsewhere.	WBPaper00032948:StarveUp3
	Single-cell RNA-Seq cell group 47_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:47_0
	Transcripts enriched in ASH according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASH_enriched
	Top 300 transcripts enriched in ASHL, ASHR 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:ASH
	Single-cell RNA-Seq cell group 47_1 expressed in neuron.	scVI 0.6.0	WBPaper00065841:47_1
	Genes that showed significantly increased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in water samples collected from Lake Stobensee in Berlin in August.	Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5.	WBPaper00046853:AOBr_LakeStobenseeAug_upregulated
	mRNAs that showed decreased expression after 100ug\/L microcystin-LR exposure.	Differentially expressed genes (DEGs) were identified with a random-variance t-test and an SAM (Significance Analysis of Microarrays) test. Gene expression differences were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3 and the fold-change compared to control at least <= 0.67 or >= 1.5.	WBPaper00045807:microcystin-LR_downregulated

4 Expression Patterns

• Primary Identifier: Expr2034642
• 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: Expr1020518
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2016436
• 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: Expr1143536
• 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: WBGene00005246
• Start: 4926671
• End: 4928257
• Strand: 1

1 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1587

1 Sequence Ontology Term

• Name: gene

0 Strains

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_4926216..4926670
• Length (nt): 455
• Chromosome Location: V: 4926216-4926670
• Organism: Caenorhabditis elegans