WormMine: Gene WBGene00004921

• WormBase Gene ID: WBGene00004921
• Gene Name: snt-1
• Sequence Name: F31E8.2
• Brief Description: snt-1 encodes two proteins, SNT-1A and SNT-1B, orthologous to synaptotagmin; SNT-1 is required for synaptic vesicle exocytosis and neurotransmitter release as well as for synaptic vesicle recycling via clathrin-mediated endocytosis; accordingly, snt-1 activity is required for a variety of behaviors including pharyngeal pumping, locomotion, and defecation; SNT-1A and SNT-1B isoforms are expressed in neurons, with SNT-1A typically expressed at higher levels, and in a greater number of neurons, than SNT-1B; in addition, SNT-1B is exclusively expressed in the excretory duct cell and a group of tail neurons including DVB, a GABAergic neuron required for defecation.
• Organism: Caenorhabditis elegans
• Automated Description: Enables calcium ion binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Involved in several processes, including defecation; regulation of nematode pharyngeal pumping; and synaptic vesicle endocytosis. Located in synaptic vesicle. Expressed in several structures, including excretory gland cell; gonad; nervous system; pharyngeal gland cell; and rectal gland cell. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 7. Is an ortholog of human SYT1 (synaptotagmin 1).
• Biotype: SO:0001217
• Genetic Position: II :0.115793 ±0.000262
• Length (nt): 5471

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004921

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F31E8.2a.1	F31E8.2a.1	1785	II: 6810963-6816433
Transcript:F31E8.2b.1	F31E8.2b.1	1332	II: 6810968-6815979

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F31E8.2a	F31E8.2a	1326	II: 6810968-6811083
CDS:F31E8.2b	F31E8.2b	1332	II: 6810968-6811083

10 RNAi Result

• WBRNAi00089812
• WBRNAi00046026
• WBRNAi00022346
• WBRNAi00076365
• WBRNAi00027612
• WBRNAi00112395
• WBRNAi00092941
• WBRNAi00089992
• WBRNAi00090151
• WBRNAi00090310

91 Allele

• gk963801
• gk963053
• WBVar01438269
• WBVar01374501
• WBVar01374512
• gk472574
• gk472573
• gk779581
• gk614816
• gk718936
• gk464606
• gk574379
• gk358589
• gk910060
• gk333624
• gk494508
• gk490056
• gk348395
• gk470253
• gk653587
• gk472575
• gk377648
• gk413288
• gk804642
• gk509514
• gk823681
• h10255
• md172
• WBVar00172805
• WBVar00172806

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004921
• Start: 6810963
• End: 6816433
• 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_chrII_6816434..6817749
• Length (nt): 1316
• Chromosome Location: II: 6816434-6817749
• Organism: Caenorhabditis elegans

233 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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
	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_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_expressed
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
	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
	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
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
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	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 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 sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_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 that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	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
	Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage.	fold change > 2	WBPaper00058711:wdr-5(ok1417)_upregulated
	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

11 Expression Patterns

• Primary Identifier: Expr2034211
• 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: Expr15234

• Primary Identifier: Expr8299
• Remark: Picture: Figure 3.
• Reporter Gene: [snt-1::SNT-1A::CFP; snt-1::SNT-1B::YFP]. SNT-1A::CFP and SNT-1B::YFP transgenes were integrated separately, and a strain containing both integrated transgenes was constructed.
• Pattern: Imaging this strain revealed significant differences in SNT-1 isoform expression and localization. The SNT-1A isoform is abundantly expressed in most neurons, and the distribution of this isoform is synaptic, resembling that of the endogenous SNT-1 (see Expr334). In contrast, the SNT-1B isoform is expressed at lower levels and in fewer neurons than SNT-1A. Many neurons express both SNT-1A and -1B, although the relative amount of each isoform varies greatly between individual cells, and some neurons appear to express only the SNT-1A isoform.
• Subcellular Localization: Distribution of SNT-1A is synaptic.

• Primary Identifier: Expr8300
• Remark: Picture: Figure 3.
• Reporter Gene: [snt-1::SNT-1A::CFP; snt-1::SNT-1B::YFP]. SNT-1A::CFP and SNT-1B::YFP transgenes were integrated separately, and a strain containing both integrated transgenes was constructed.
• Pattern: Imaging this strain revealed significant differences in SNT-1 isoform expression and localization. The SNT-1A isoform is abundantly expressed in most neurons, and the distribution of this isoform is synaptic, resembling that of the endogenous SNT-1 (see Expr334). In contrast, the SNT-1B isoform is expressed at lower levels and in fewer neurons than SNT-1A. Many neurons express both SNT-1A and -1B, although the relative amount of each isoform varies greatly between individual cells, and some neurons appear to express only the SNT-1A isoform. Strong exclusive expression of the SNT-1B isoform was also observed in a single ventral cell located just anterior to the terminal bulb of the pharynx; which might be the excretory duct cell. In addition, SNT-1B is strongly expressed in a cluster of tail neurons, including DVB.

• Primary Identifier: Expr1032450
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr334
• Remark: Data modified according to Shawn Lockery's expression pattern curations.
• Pattern: In adult hermaphrodites, strong staining were observed in three synaptic rich structures: nerve ring, ventral cord and dorsal cord processes, sites of neuromuscular junctions onto body wall muscles. Stained majority of the pharyngeal nervous system processes. Less intensive staining of the ventral and dorsal sublateral processes and several processes directed anteriorly from the nerve ring. Staining was often restricted to punctate patches occuring at frequent intervals. In adult males, strong immunostaining was observed in the posterior region of the ventral nerve cord. DVB is the only stained neuronal cell body. Staining also observed in several non-neuronal secretory cells. Four cells in the vulva region (uv1 cells). The vas deferens of adult males, about 20 large circular structures, not surround nuclei, suggesting they were cytoplasmic structures, only observed in adult males. Faint staining in spermathecea of adult hermaphrodites.

• Primary Identifier: Expr1026155
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015976
• 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: Chronogram2081
• Remark: Original chronogram file: chronogram.996.xml
• Reporter Gene: [F31E8.2:gfp] transcriptional fusion.

• Primary Identifier: Expr1149922
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr11534
• Subcellular Localization: In wild-type worms, GFP::SNT-1 fluorescence was expressed at the nerve ring but did not accumulate at the nerve ends of ALM neurons. Results were confirmed by immunostaining.

36 GO Annotation

17 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004921
• Start: 6810963
• End: 6816433
• Strand: 1

36 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5471

1 Sequence Ontology Term