WormMine: Gene WBGene00001446

• WormBase Gene ID: WBGene00001446
• Gene Name: flp-3
• Sequence Name: W07E11.2
• Brief Description: flp-3 encodes nine copies of a GTMRFamide-containing peptide that is predicted to function as a neuropeptide that inhibits pharyngeal action potential in a manner similar to octopamine without having a significant effect on basal resting membrane potential; flp-3 is expressed in three pairs of neurons IL1D, OLL, URB.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in negative regulation of action potential; neuropeptide signaling pathway; and regulation of nematode pharyngeal pumping. Predicted to be located in extracellular region. Expressed in head; motor neurons; sensory neurons; somatic nervous system; and in male.
• Biotype: SO:0001217
• Genetic Position: X :1.73922 ±0.001345
• Length (nt): 1019

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001446

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W07E11.2.1	W07E11.2.1	874	X: 10091946-10092964

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W07E11.2	W07E11.2	555	X: 10092219-10092334

4 RNAi Result

• WBRNAi00054945
• WBRNAi00054946
• WBRNAi00019697
• WBRNAi00027743

26 Allele

• gk964260
• gk962707
• e2819
• gk885683
• gk592921
• gk406349
• gk458785
• gk370199
• gk808837
• gk742463
• gk798935
• gk546328
• gk438348
• WBVar01888349
• WBVar01888347
• WBVar01888348
• tm10563
• gk291121
• gk291120
• gk291119
• ok3265
• tm13075
• pk361
• WBVar01551569
• WBVar01551568
• syb2634

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001446
• Start: 10091946
• End: 10092964
• 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

165 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
	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
	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
	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
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
	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 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 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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	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 the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
	Transcripts that showed significantly increased expression in clk-1(qm30) 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:clk-1(qm30)_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) 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:daf-2(e1370)_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 in wdr-23(mac32) embryos from parents fed with E. coliHB101, comparing to N2 embryos parents fed with E. coli HB101.	DESeq2, Fold Change > 2 or < 0.5.	WBPaper00059566:wdr-23(mac32)_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

14 Expression Patterns

• Primary Identifier: Expr1030869
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr16037
• Pattern: In addition to other neuron classes, flp-3 is expressed in the IL1 head mechanosensory neurons and the nerve ring.

• Primary Identifier: Expr2701
• Remark: Reporter gene fusion type not specified.
• Pattern: GFP expressed cells are only seen in the anterior head region.

• Primary Identifier: Expr15831
• Pattern: Expression analysis of a FLP-3 translational fusion (pflp-3::flp- 3::mCherry) confirmed previous expression analyses of the neuropeptide within male-specific spicule neurons. Transcriptional reporters have shown robust flp-3 expression in the amphid IL1 neurons, as well as the sensory PQR and the male-specific interneuron, CP9, although our translational fusion exhibited no PQR or CP9 expression. Previous studies employed 1-2kb regions of promoter sequence driving GFP expression,while our construct employs a 4 kb region, thereby incorporating further regulatory elements that may restrict expression patterns. By including the full coding sequence in our translational fusion, we have also incorporated the regulatory elements found within the introns of the flp-3 gene.Interestingly, we observed localization of mCherry within sensory cilia of male dorsal and ventral IL1 neurons, as well as in puncta spanning their dendrites, consistent with peptide packing into dense core vesicles. Previous studies have observed dense core vesicles within, and being released from, dendritic arbors, supporting our findings that FLP-3 is packaged within the dendrites of the IL1 neurons. We found an identical expression pattern within the IL1 cilia and dendritic puncta of hermaphrodites as well. In males, our flp-3 construct also exhibited male-specific tail expression in the SPD spicule neurons.

• Primary Identifier: Expr3005
• Pattern: Expressed in IL1 and PQR. Male specific expression in SP and CP9.

• Primary Identifier: Expr2011845
• 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: Expr15350

• Primary Identifier: Expr15832
• Pattern: Expression analysis of a FLP-3 translational fusion (pflp-3::flp- 3::mCherry) confirmed previous expression analyses of the neuropeptide within male-specific spicule neurons. Transcriptional reporters have shown robust flp-3 expression in the amphid IL1 neurons, as well as the sensory PQR and the male-specific interneuron, CP9, although our translational fusion exhibited no PQR or CP9 expression. Previous studies employed 1-2kb regions of promoter sequence driving GFP expression,while our construct employs a 4 kb region, thereby incorporating further regulatory elements that may restrict expression patterns. By including the full coding sequence in our translational fusion, we have also incorporated the regulatory elements found within the introns of the flp-3 gene.Interestingly, we observed localization of mCherry within sensory cilia of male dorsal and ventral IL1 neurons, as well as in puncta spanning their dendrites, consistent with peptide packing into dense core vesicles. Previous studies have observed dense core vesicles within, and being released from, dendritic arbors, supporting our findings that FLP-3 is packaged within the dendrites of the IL1 neurons. We found an identical expression pattern within the IL1 cilia and dendritic puncta of hermaphrodites as well. In males, our flp-3 construct also exhibited male-specific tail expression in the SPD spicule neurons.

• Primary Identifier: Expr2381
• Remark: Immunostaining increased in neuronal cell bodies of unc-104 KIF1A mutants, whereas staining in axons was proportionately diminished. In addition, a broader expression pattern was observed in unc-104 KIF1A mutants compared with wild-type controls, because retention in the cell bodies enabled identification of previously undetected neurons. Protein_Description: FMRFamide related peptides (FaRPs).
• Pattern: Nerve ring and other neuronal processes.
• Subcellular Localization: In wild-type animals, FaRPs immunostaining was most concentrated in the nerve ring and other neuronal processes, whereas neuronal cell bodies had lower levels of expression.

• Primary Identifier: Expr2030083
• 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: Expr10034
• Pattern: FLP-3-derived VENUS is expressed in the dorsal nerve cord.

• Primary Identifier: Expr1158480
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1475
• Pattern: Expressed in all stages

• Primary Identifier: Expr1016444
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

7 GO Annotation

1 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001446
• Start: 10091946
• End: 10092964
• Strand: -1

7 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1019

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00037364
• WBStrain00055068

0 Upstream Intergenic Region