WormMine: Gene WBGene00005296

• WormBase Gene ID: WBGene00005296
• Gene Name: srh-75
• Sequence Name: T04C12.2
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be located in membrane.
• Biotype: SO:0001217
• Genetic Position: V :2.92233 ±0.002185
• Length (nt): 1850

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00005296

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T04C12.2a.1	T04C12.2a.1	1113	V: 11055294-11057143
Transcript:T04C12.2b.1	T04C12.2b.1	993	V: 11055306-11057143

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T04C12.2b	T04C12.2b	993	V: 11055306-11055409
CDS:T04C12.2a	T04C12.2a	1101	V: 11055306-11055409

4 RNAi Result

• WBRNAi00052367
• WBRNAi00018132
• WBRNAi00069441
• WBRNAi00035131

27 Allele

• gk963271
• gk963301
• gk964451
• gk964452
• gk492313
• gk482145
• gk579543
• gk601535
• gk934825
• gk776614
• gk504972
• gk376949
• gk751569
• gk690496
• gk963736
• gk963737
• WBVar01865434
• gk246686
• gk246685
• gk246687
• gk953749
• WBVar00589391
• otn6767
• WBVar00003550
• WBVar00003555
• WBVar01661220
• WBVar01743342

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00005296
• Start: 11055294
• End: 11057143
• Strand: -1

3 Data Sets

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

0 Downstream Intergenic Region

20 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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 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
	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
	Genes enriched in AMsh glia.	Two different statistical methods were used for differential gene expression analysis, DESeq and voom. For DEseq analysis, DESeq2 was applied to normalize count matrix and to perform differential gene expression on the counts using negative binomial distribution; for voom analysis, edgeR was applied to normalize count matrix, and voom was applied for gene differentiation analysis. Significant genes from both analyses were combined. To identify transcripts enriched in AMsh glia compared to other cells (control AMsh versus control non-AMsh), authors used a fold change of 3.5 and an adjusted p value threshold of <0.05.	WBPaper00049489:AMsh-glia_enriched
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
	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
	Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control.	Fold change > 1.2 or < 0.8.	WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray
	Genes that are up or down regulated by more than 2.1 fold with the t-test p-value less than 0.01 are included in this cluster.	Genes that are regulated by more than 2.1 fold with the t-test p-value less than 0.01 are included in this cluster.	WBPaper00024393:strongly_regulated_dauer_genes
	Coexpression clique No. 282, srj-21-srh-32, 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:srj-21-srh-32
Drug treatment: Rhine sediment	Genes with significantly changing transcripts in C. elegans exposed to the Rhine (R) sediment.	[ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube (D) > 1.4 (up-regulated) or < 0.7 (down-regulated)].	WBPaper00033070:Rhine_upregulated
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).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the first UVC dose (3h).	Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -45h timepoint (3 hours after the first UVC dose).	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:UVC-EtBr-exposed_vs_UVC-exposed_3h
	Transcripts that showed significantly increased expression in postdauer adults comparing to adult animals that bypassed the dauger stage.	DESeq 2, FDR < 0.05.	WBPaper00064494:postdauer_upregulated_WholeAnimal
	Transcripts that showed significantly increased expression in ADL neurons of qui-1(db104) comparing to in N2 at day 1 adult stage.	tximport 1.14.2 and DEseq2 1.26.0. Fold change > 2, FDR < 0.05.	WBPaper00062520:qui-1(db104)_upregulated
	Transcripts that showed significantly decreased expression in ikb-1(nr2027) animals at L1 larva stage, comparing to in N2 animals.	Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01.	WBPaper00060445:ikb-1(nr2027)_downregulated_L1
	mRNAs that showed increased 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_upregulated
	Transcripts that showed significantly increased expression after exposure to 0.1ug/L MWCNT from L1 to day 1 adult stage in liquid solutions with OP50.	Fold change > 2.	WBPaper00057254:MWCNT_downregulated_mRNA

4 Expression Patterns

• Primary Identifier: Expr2034712
• 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: Expr1021408
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1155996
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2016514
• 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).

1 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00005296
• Start: 11055294
• End: 11057143
• Strand: -1

1 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1850

1 Sequence Ontology Term

• Name: gene

0 Strains

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_11057144..11058639
• Length (nt): 1496
• Chromosome Location: V: 11057144-11058639
• Organism: Caenorhabditis elegans