WormMine: Gene WBGene00006937

• WormBase Gene ID: WBGene00006937
• Gene Name: wah-1
• Sequence Name: Y56A3A.32
• Brief Description: wah-1 encodes a putative flavin-adenine dinucleotide (FAD)-bindingoxidoreductase orthologous to mammalian PDCD8 (AIF; OMIM:300169, mutatedin Harlequin mice); WAH-1 is required for apoptotic DNA degratation,SCRM-1 phospholipid scramblase activity, phosphatidylserine exposure,rapid apoptosis during embryonic development, and rapid engulfment ofapoptotic cells in the germline; WAH-1 is also required for normallyrapid growth and large brood sizes, and has a subtle proapoptoticfunction revealed in ced-3 or ced-4 mutant backgrounds; WAH-1 isexpressed in most, if not all, cells of embryos and larvae; WAH-1 isnormally mitochondrial, but can be released into the cytosol and nucleusby EGL-1 and CED-3; residues 380-550 of WAH-1 specifically bind SCRM-1in vitro, but not SCRM-2 through SCRM-4, and WAH-1 binding is requiredin liposomes for more than residual SCRM-1 activity; WAH-1 also bindsand activates CPS-6, promoting apoptotic DNA degradation, and transgeniccoexpression of WAH-1 with CPS-6 specifically induces ectopicCED-3-dependent apoptosis in touch receptor neurons; CPS-6 shares agenetic pathway with WAH-1, whereas CED-3, CED-4, CED-8, and NUC-1 actindependently of it; WAH-1 is paralogous to C. elegans F20D6.11 andhuman AIFM3 (AIFL).
• Organism: Caenorhabditis elegans
• Automated Description: Enables enzyme binding activity. Involved in apoptotic DNA fragmentation and positive regulation of phosphatidylserine exposure on apoptotic cell surface. Located in cytosol; mitochondrion; and nucleus. Human ortholog(s) of this gene implicated in Alzheimer's disease; X-linked recessive disease (multiple); and dilated cardiomyopathy 1H. Is an ortholog of human AIFM1 (apoptosis inducing factor mitochondria associated 1).
• Biotype: SO:0001217
• Genetic Position: III :13.7988 ±0.058612
• Length (nt): 9424

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006937

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:Y56A3A.32a.1	Y56A3A.32a.1	2274	III: 11990167-11999590
NcPrimaryTranscript	Transcript:Y56A3A.32b	Y56A3A.32b	2423	III: 11990200-11999452
MRNA	Transcript:Y56A3A.32c.1	Y56A3A.32c.1	1449	III: 11994077-11999452

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y56A3A.32a	Y56A3A.32a	2103	III: 11990200-11990314
CDS:Y56A3A.32c	Y56A3A.32c	1449	III: 11994077-11994103

26 RNAi Result

• WBRNAi00037550
• WBRNAi00012282
• WBRNAi00105945
• WBRNAi00106065
• WBRNAi00106074
• WBRNAi00106105
• WBRNAi00022823
• WBRNAi00022824
• WBRNAi00022825
• WBRNAi00022826
• WBRNAi00071369
• WBRNAi00071370
• WBRNAi00109990
• WBRNAi00007413
• WBRNAi00057600
• WBRNAi00111781
• WBRNAi00026870
• WBRNAi00098351
• WBRNAi00077720
• WBRNAi00110649
• WBRNAi00110651
• WBRNAi00110652
• WBRNAi00109138
• WBRNAi00109908
• WBRNAi00109941
• WBRNAi00109974

295 Allele

• otn9896
• gk963887
• gk964363
• gk964364
• gk963799
• gk187352
• gk187353
• gk187354
• gk187355
• gk187356
• gk187357
• gk187358
• gk187359
• gk187360
• gk187361
• gk187362
• gk187363
• gk187364
• gk187365
• gk187366
• otn8644
• WBVar00180864
• WBVar00180865
• WBVar00180866
• WBVar00180867
• WBVar00180860
• WBVar00180861
• WBVar00180862
• WBVar00180863
• WBVar00180869

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006937
• Start: 11990167
• End: 11999590
• 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

91 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
	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
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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 decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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 sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 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_24h_downregulated
	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
	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 altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) 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(tm1630)_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
	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

6 Expression Patterns

• Primary Identifier: Expr2036183
• 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: Expr1032952
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2018046
• 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: Expr1015675
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1161017
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2263
• Subcellular Localization: WAH-1::GFP was widely expressed in embryos and larvae, displaying a punctate, cytoplasmic staining pattern similar to the mitochondrial localization pattern of CPS-6. The staining pattern of WAH-1::GFP coincided with that of Mitotracker Red, a mitochondria-specific fluorescent dye, confirming that WAH-1 localized within mitochondria.

20 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006937
• Start: 11990167
• End: 11999590
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 9424

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00051132

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_11989934..11990166
• Length (nt): 233
• Chromosome Location: III: 11989934-11990166
• Organism: Caenorhabditis elegans