WormMine: Gene WBGene00000905

• WormBase Gene ID: WBGene00000905
• Gene Name: daf-9
• Sequence Name: T13C5.1
• Brief Description: daf-9 encodes a cytochrome P450 of the CYP2 subfamily that by homology is predicted to function as a steroidogenic or fatty acid hydroxylase; DAF-9 likely functions cell nonautonomously in hypodermal and neuronal cells to produce, for the DAF-12 nuclear receptor, a lipophilic hormone whose presence is necessary for bypassing entry into the alternative L3/dauer larval stage and promoting reproductive development; in regulating dauer formation, daf-9 acts downstream of the DAF-2/insulin/IGF receptor and the DAF-7/TGFbeta ligand, suggesting that at least two of the signaling pathways that control dauer formation converge, in part, upon daf-9; in addition, daf-9 activity is required for gonadal cell migration; a DAF-9::GFP fusion is expressed in the XXXL/R head cells at all developmental stages, in hypodermal cells from the L2 to L4 larval stages, and in the spermatheca of adult hermaphrodites.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable heme binding activity; oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen; and steroid hydroxylase activity. Involved in cell-cell signaling; dauer larval development; and regulation of cell migration. Located in neuronal cell body and perinuclear region of cytoplasm. Expressed in several structures, including anterior ganglion; excretory cell; intestine; spermatheca; and vulval muscle.
• Biotype: SO:0001217
• Genetic Position: X :-3.4723 ±0.026809
• Length (nt): 3897

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000905

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T13C5.1a.1	T13C5.1a.1	1999	X: 6196927-6200823
Transcript:T13C5.1b.1	T13C5.1b.1	1674	X: 6198094-6200604
Transcript:T13C5.1c.1	T13C5.1c.1	1824	X: 6198338-6200817

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T13C5.1a	T13C5.1a	1719	X: 6196988-6197016
CDS:T13C5.1b	T13C5.1b	1674	X: 6198094-6198156
CDS:T13C5.1c	T13C5.1c	1611	X: 6198338-6198674

13 RNAi Result

• WBRNAi00067354
• WBRNAi00067938
• WBRNAi00067970
• WBRNAi00068134
• WBRNAi00053258
• WBRNAi00018669
• WBRNAi00084743
• WBRNAi00084744
• WBRNAi00084750
• WBRNAi00084749
• WBRNAi00109099
• WBRNAi00077531
• WBRNAi00092637

76 Allele

• gk964260
• gk576344
• gk486866
• gk927986
• gk797327
• gk770113
• gk743159
• gk785740
• gk389595
• gk827669
• gk854581
• gk761769
• gk366977
• gk776769
• gk699729
• WBVar02064183
• WBVar02064185
• WBVar02064184
• WBVar02064186
• gk586236
• gk365535
• gk834123
• gk807838
• gk426602
• gk523080
• gk336285
• gk651362
• gk475885
• gk388535
• gk653969

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000905
• Start: 6196927
• End: 6200823
• Strand: 1

4 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_6200824..6201874
• Length (nt): 1051
• Chromosome Location: X: 6200824-6201874
• Organism: Caenorhabditis elegans

122 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
	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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis 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:E.faecalis_24hr_upregulated_TilingArray
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_upregulated
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2.	DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1.	WBPaper00046012:tdp-1(ok803)_upregulated
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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 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)
	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 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)_upregulated
	Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Transcripts that showed significantly increased expression in adr-1(tm668) and adr-1(gv6) comparing to in N2 at embryo stage.	DESeq FDR <= 0.05	WBPaper00056617:adr-1_upregulated_embryo_transcript
	Transcripts that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:Aging_downregulated_mRNA_N2
	Transcripts that showed significantly decreased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:mir-71(n4115)_downregulated_mRNA
	Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
	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 xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Transcripts that showed significantly increased expression in isp-1(qm150) 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:isp-1(qm150)_upregulated
	Transcripts that showed significantly increased 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)_upregulated
	Transcripts that showed significantly increased expression among animals treated with 400mM sucrose and 500 mg per ml stearic acid from L1 to L4 larva stage comparing to animals grown up on control plates.	CuffDiff, FDR <= 0.05, fold change >= 2.	WBPaper00059253:sucrose_stearic-acid_upregulated
	Transcripts that showed significantly increased expression in mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4345)_upregulated
	Transcripts that showed significantly increased expression in spt-16(RNAi) comparing to in vector control worm at L4 larva stage.	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:spt-16(RNAi)_upregulated
	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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated

10 Expression Patterns

• Primary Identifier: Expr16190
• Pattern: We examined the daf-9::GFP expression pattern in males and observed expression within the pharynx, gut, and hypodermis, as well as in the XXX cells, but did not observe expression in the male gonad.

• Primary Identifier: Expr2915
• Remark: When this transgene was introduced into daf-2(e1370) and daf-7(e1372) mutant animals grown at the non-permissive temperature (25 centigrades), hypodermal expression of daf-9::GFP was absent in dauers, even though the daf-9::GFP expression in XXXL/R persisted. The lack of hypodermal daf-9::GFP expression was also noted in wild-type dauer animals derived from starvation. The daf-9::GFP transgene was unable to suppress dauer arrest of daf-2(e1370) and daf-7(e1372) animals (n>100) at the restrictive temperature (25 centigrades) and enhanced dauer arrest of these animals at the permissive temperature (15 centigrades).
• Pattern: daf-9::GFP is expressed in a pair of cells in the anterior ganglion in L1 larvae, which persists in all larval stages and in adults, in the hypodermis from the mid-L2 stage to the end of L4 stage, and in the spermatheca of adult hermaphrodites. The daf-9::GFP-expressing head cells have been identified as XXXL/R, which are thought to be embryonic hypodermal cells.

• Primary Identifier: Expr2916
• Remark: No detailed description on cellular expression patterns in other tissue or life stages.
• Reporter Gene: daf-9 constructs were made by standard molecular techniques using genomic fragments or isoform B cDNA amplified with gene-specific primers and cloned in front of gfp. daf-9::gfp contains 7.16 kb upstream promoter and the entire genomic daf-9-coding region, including introns with gfp fused at the C terminus. This construct was used to make integrant dhIs59, dhIs64 and extrachromosomal dhEx66.
• Pattern: In favorable environments (abundant food and cholesterol, 20 centigrades, low pheromone) hypodermal daf-9 was weakly expressed.

• Primary Identifier: Expr1790
• Pattern: daf-9 was strikingly expressed in a ventral pair of bilateral neurons identified as the IL1Vs or URAVs in the anterior ganglia. Neuronal expression first appeared shortly before hatch, increased greatly during larval development, and perdured in reproductive and postreproductive adults. By mid-L2, DAF-9 also appeared in the cytoplasm of the hypodermis, the syncitial epidermis surrounding the worm, but was absent from midline epidermal seam cells. Levels peaked around the L2 molt and diminished during L4. In some cases, transient expression was seen in L3 vulval blast cells. daf-9 was also expressed within the hermaphrodite spermatheca starting in late L4 larvae, and continuing even in old adults. In some extrachromosomal lines, sporadic weak expression was seen in the excretory cell, a few unidentified head neurons, and vulval muscles. In males, daf-9 was expressed in IL1V/URAVs and hypodermis but not somatic gonad. In dauer larvae, daf-9 was strongly expressed in IL1V/URAV and specifically extended into axonal but not dendritic processes. No hypodermal expression was evident in dauers. In post-dauer stages, daf-9 was expressed in a pattern similar to reproductively growing animals, except expression was absent in the hypodermis.
• Subcellular Localization: DAF-9 was perinuclear, consistent with residence in endoplasmic reticulum.

• Primary Identifier: Expr1803
• Remark: When injected into the germline of daf-9(m540), it fully rescued the Daf-c phenotype (Table 3), indicating that the gfp reporter must be expressed in cells required for daf-9 function.
• Pattern: The DAF-9::GFP fusion protein was expressed mainly in a pair of neurons anterior to the nerve ring, and the signal was detected in all stages from late embryos to adult. Expression in embryos was observed only in those which developed at 25C. The intensity of the signal was not noticeably different in stages from L2 to adult, or in the dauer larva, but was fainter in embryos and L1 larvae. Weak expression was also observed in the spermathecae of older adults raised at 25C. Two cells strongly expressing GFP were identified as right and left ventral Inner Labial-1 (IL1) neurons, but right and left ventral URA neurons could not be excluded. In some transgenic animals, DAF-9::GFP was only expressed in one of the ventral cells. The positions of these two cell bodies are variable, with one occasionally found anterior to the metacorpus.
• Subcellular Localization: The DAF-9::GFP fusion protein was very finely localized within the cell bodies, whereas GFP driven by the same promoter, but without daf-9 coding sequences, diffused throughout the cell body.

• Primary Identifier: Expr1804
• Pattern: The expression of these transgenes in N2 and m540 genetic backgrounds was the same. In addition to the pair of IL1/URA neurons, one to four other cells likely to be neurons posterior to the nerve ring occasionally gave faint signals. These latter cells were not seen in the DAF-9::GFP full-length construct.

• Primary Identifier: Expr2010784
• 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: Expr1156841
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1017558
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029021
• 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).

23 GO Annotation

131 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000905
• Start: 6196927
• End: 6200823
• Strand: 1

23 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3897

1 Sequence Ontology Term