WormMine: Gene WBGene00002891

• WormBase Gene ID: WBGene00002891
• Gene Name: let-767
• Sequence Name: C56G2.6
• Brief Description: let-767 encodes a steroid dehydrogenase required for embryogenesis, molting, and female reproduction; LET-767 is orthologous to human HSD17B3 (OMIM:605573, mutated in pseudohermaphroditism), HSD17B12 (OMIM:609574), and HSDL1; in vitro, LET-767 catalytically converts androstenedione and estrone into testosterone and estradiol, and in vivo probably catalyzes the synthesis of endogeneous steroid hormones from cholesterol; LET-767 is expressed from embryos to adults, and is zygotically expressed in the intestine, but a maternal-effect lethal allele (let-767[s2464]) also exists, indicating that LET-767 is probably also provided maternally; LET-767 is paralogous to STDH-1/-4; some let-767 transcripts are spliced to SL2, indicating that let-767 may belong to an operon with C56G2.7.
• Organism: Caenorhabditis elegans
• Automated Description: Enables long-chain-fatty-acyl-CoA reductase activity and testosterone dehydrogenase [NAD(P)+] activity. Involved in several processes, including establishment or maintenance of epithelial cell apical/basal polarity; long-chain fatty acid biosynthetic process; and steroid metabolic process. Located in apical cortex and endoplasmic reticulum. Expressed in hypodermis; intestine; and pharynx. Used to study obesity. Human ortholog(s) of this gene implicated in 17-beta hydroxysteroid dehydrogenase 3 deficiency and Alzheimer's disease. Is an ortholog of human HSD17B12 (hydroxysteroid 17-beta dehydrogenase 12).
• Biotype: SO:0001217
• Genetic Position: III :-1.38862 ±0.00385
• Length (nt): 1462

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002891

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C56G2.6a.2	C56G2.6a.2	1106	III: 6338508-6339969
Transcript:C56G2.6c.1	C56G2.6c.1	1103	III: 6338509-6339955
Transcript:C56G2.6a.1	C56G2.6a.1	1043	III: 6338511-6339832
Transcript:C56G2.6b.1	C56G2.6b.1	1002	III: 6338598-6339955

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C56G2.6a	C56G2.6a	951	III: 6338598-6338930
CDS:C56G2.6c	C56G2.6c	1014	III: 6338598-6338930
CDS:C56G2.6b	C56G2.6b	1002	III: 6338598-6338930

23 RNAi Result

• WBRNAi00095545
• WBRNAi00085408
• WBRNAi00043289
• WBRNAi00024923
• WBRNAi00008564
• WBRNAi00117240
• WBRNAi00102768
• WBRNAi00106534
• WBRNAi00065017
• WBRNAi00090851
• WBRNAi00106541
• WBRNAi00075436
• WBRNAi00117237
• WBRNAi00002493
• WBRNAi00030211
• WBRNAi00086014
• WBRNAi00096843
• WBRNAi00103235
• WBRNAi00086015
• WBRNAi00117235
• WBRNAi00117236
• WBRNAi00117239
• WBRNAi00117238

17 Allele

• gk964518
• gk176393
• s2176
• s2464
• s2819
• WBVar01656827
• gk808077
• WBVar01900736
• gk888194
• gk557657
• gk935055
• gk921659
• WBVar01645044
• gk553841
• gk679677
• s2716
• WBVar01722614

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002891
• Start: 6338508
• End: 6339969
• 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_chrIII_6335840..6338507
• Length (nt): 2668
• Chromosome Location: III: 6335840-6338507
• Organism: Caenorhabditis elegans

132 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 that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	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
	Genes that were downregulated 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)_downregulated
	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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	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
	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)
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 vit-2(ac3); zcIs4, comparing to parenting strain SJ4005 [zcIs4].	Differential gene expression analysis was then performed on normalized samples. Genes exhibiting at least twofold change and a false-discovery rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00051305:vit-2(ac3)_downregulated
	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 increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3

9 Expression Patterns

• Primary Identifier: Expr1031371
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8146
• Remark: Picture: Figure S1.
• Pattern: Expression of LET-767::GFP was observed in embryos. Strong expression was detected in larval intestine. Weaker expression was detected in pharyngeal region and in the hypodermis.
• Subcellular Localization: Subcellular localization of LET-767::GFP was detected in intestinal cells. Accumulation of LET-767::GFP at the apical surface of intestinal cells was observed.

• Primary Identifier: Expr16547
• Pattern: To trace the expression of LET-767, we generated a single-copy integrated strain for the translational expression of let-767::gfp. The green fluorescence of LET-767::GFP was observed mainly in the intestine and hypodermis, the major sites for lipid synthesis and storage (Watts and Ristow, 2017). LET-767 is expressed on both the endoplasmic reticulum and lipid droplets.

• Primary Identifier: Expr2698
• Remark: No GO_term assigned.
• Pattern: Transgenic animals carrying this construct express gfp in the gut, with a notable absence of expression in the gut nuclei. This pattern of expression is seen from the first larval stage through to adulthood in both hermaphrodites and males. GFP was not detected at any stage of embryogenesis.
• Subcellular Localization: Expression is absent from the gut nuclei.

• Primary Identifier: Expr2013077
• 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: Expr1026440
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2699
• Pattern: The let-767 transcript is present from embryos to adults as revealed by RT-PCR using RNA preparations from successive developmental stages and let-767-specific primers.

• Primary Identifier: Expr1147267
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031309
• 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).

21 GO Annotation

1 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002891
• Start: 6338508
• End: 6339969
• Strand: -1

21 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1462

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00000883

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_6339970..6340112
• Length (nt): 143
• Chromosome Location: III: 6339970-6340112
• Organism: Caenorhabditis elegans