WormMine: Gene WBGene00008117

• WormBase Gene ID: WBGene00008117
• Gene Name: gsr-1
• Sequence Name: C46F11.2
• Brief Description: gsr-1 encodes a glutathionine reductase orthologous to human mitochondrial glutathione reductase (GSR; OMIM:138300); GSR deficiency has been associated with hemolytic anemia; loss of gsr-1 activity, together with that of trxr-1, results in molting defects characterized by a failure to remove old cuticle and reduced, disulfide groups in the cuticle that remain oxidized; gsr-1 expression is reduced in dauer larvae.
• Organism: Caenorhabditis elegans
• Automated Description: Enables glutathione-disulfide reductase (NADPH) activity. Involved in several processes, including cell redox homeostasis; ecdysis, collagen and cuticulin-based cuticle; and response to superoxide. Located in cytosol and mitochondrion. Expressed in several structures, including Epr; Epra; coelomocyte; excretory canal; and hermaphrodite gonad. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; cataract (multiple); hematologic cancer (multiple); and microcytic anemia (multiple). Is an ortholog of human GSR (glutathione-disulfide reductase).
• Biotype: SO:0001217
• Genetic Position: III :-4.91444 ±0.040413
• Length (nt): 2052

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00008117

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C46F11.2a.1	C46F11.2a.1	1573	III: 3650907-3652958
Transcript:C46F11.2b.2	C46F11.2b.2	1481	III: 3651027-3652957
Transcript:C46F11.2b.1	C46F11.2b.1	1468	III: 3651329-3652957

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C46F11.2a	C46F11.2a	1422	III: 3650976-3651010
CDS:C46F11.2b	C46F11.2b	1380	III: 3651336-3651583

20 RNAi Result

• WBRNAi00115516
• WBRNAi00042606
• WBRNAi00012036
• WBRNAi00088162
• WBRNAi00088285
• WBRNAi00006019
• WBRNAi00029866
• WBRNAi00062166
• WBRNAi00088029
• WBRNAi00088070
• WBRNAi00088121
• WBRNAi00088203
• WBRNAi00088244
• WBRNAi00088326
• WBRNAi00088367
• WBRNAi00092175
• WBRNAi00115513
• WBRNAi00115515
• WBRNAi00115517
• WBRNAi00115519

35 Allele

• gk962532
• gk963881
• gk963882
• gk964381
• WBVar01656275
• WBVar01656274
• WBVar01656273
• gk957097
• tm3574
• WBVar01566244
• gk705228
• gk344523
• WBVar01837388
• gk635228
• gk171240
• gk395846
• gk171242
• gk171241
• gk439869
• gk664175
• gk822215
• gk339686
• gk792342
• gk632662
• gk831419
• gk542371
• gk907450
• gk687558
• gk171243
• gk522255

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00008117
• Start: 3650907
• End: 3652958
• 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

120 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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 body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_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
	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
	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 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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:germline-precursors_blastula-embryo_expressed
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	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
	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
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
Oxidative stress.	Genes upregulated by oxidative stress.	Assessed by SAM (Significance Analysis of Microarray) [false discovery rate (FDR) = 11%]	WBPaper00034757:up_by_oxidative_stress
	Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock.	Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).	WBPaper00049942:hsf-1(RNAi)_downregulated

14 Expression Patterns

• Primary Identifier: Expr5516
• Remark: Strain: BC11072
• Reporter Gene: [C46F11.2::gfp] transcriptional fusion. PCR products were amplified using primer A: 5' [CCATCATTTCGGGACTCG] 3' and primer B 5' [CAGCGAAATCGGAGCATT] 3'.
• Pattern: Adult Expression: intestine; Reproductive System; vulval muscle; unidentified cells in tail ; Larval Expression: pharynx; unidentified cells in tail

• Primary Identifier: Expr10836
• Pattern: Bright fluorescence was seen mainly in the intestine, vulval muscle, the pharynx and some unidentified cells in the tail region. Although the overall spatial GFP expression pattern was similar throughout all postembryonic life stages, a general increase in the fluorescence signals was observed during the development from L1 to adult worms.

• Primary Identifier: Expr12985
• Pattern: Transgenic worms expressing a translational GFP fusion spanning a 2.2kb fragment of the gsr-1 promoter plus the complete gsr-1 genomic ORF, showed strong fluorescence in pharynx while weaker labeling was found in hypodermis, intestine, vulva muscle cells, spermatheca, uterine cells, coelomocytes, gonad sheath cells, rectal cells and a couple of unidentified neurons (probably PVPL/R) in the tail.

• Primary Identifier: Expr9187
• Remark: Reporter gene fusion type not specified.
• Pattern: gsr-1::gfp reporter was strongly expressed in the hypodermis and the pharynx.

• Primary Identifier: Expr1033523
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12986
• Pattern: Transgenic worms expressing a translational GFP fusion spanning the gsr-1 ORF from the first intron show labeling in some neurons in the head, excretory channel, intestine and coelomocytes.

• Primary Identifier: Expr12989
• Pattern: Transgenic animals expressing the transcriptional construct Pgsr-1::gfpgsr-1 show expression at approximately 100 min since embryos start developing. In these initial stages, gsr-1 stronger expression is found in E blastomere descendants (intestine precursors) and MS blastomeres descendants (neurons and mesodermic tissues precursors).

• Primary Identifier: Expr2012291
• 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: Expr1026256
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1146589
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12988
• Subcellular Localization: GSR-1a is the mitochondrial isoform of gsr-1.

• Primary Identifier: Expr12987
• Subcellular Localization: GSR-1b is the cytoplasmic isoform of gsr-1.

• Primary Identifier: Expr2030527
• 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: Chronogram1153
• Remark: Original chronogram file: chronogram.2276.xml
• Reporter Gene: [C46F11.2:gfp] transcriptional fusion.

29 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00008117
• Start: 3650907
• End: 3652958
• Strand: 1

29 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2052

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00040328
• WBStrain00051072
• WBStrain00051074
• WBStrain00001618

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_3650833..3650906
• Length (nt): 74
• Chromosome Location: III: 3650833-3650906
• Organism: Caenorhabditis elegans