WormMine: Gene WBGene00006798

• WormBase Gene ID: WBGene00006798
• Gene Name: unc-64
• Sequence Name: F56A8.7
• Brief Description: unc-64 encodes syntaxin, a plasma membrane receptor for intracellular vesicles that is orthologous to vertebrate syntaxin 1A (OMIM:186590) and Drosophila Syx1A; UNC-64 is required for normal locomotion and possibly also for insulin secretion; as an essential component of the core synaptic vesicle fusion machinery, UNC-64 interacts with UNC-13, a diacylglycerol-binding protein, and SNB-1/synaptobrevin; UNC-64 trafficking from the endoplasmic reticulum to the plasma membrane is mediated by UNC-18, an SM (Sec1, Munc18) family member; unc-64 mutations can be suppressed by mutations in slo-1, a calcium-activated potassium channel; UNC-64 is expressed ubiquitously in the nervous system and in secretory cells such as the vulval uv1 cell and the excretory gland cells.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein-folding chaperone binding activity. Involved in several processes, including chemical synaptic transmission; positive regulation of anterior/posterior axon guidance; and ventral cord development. Located in axon; basolateral plasma membrane; and somatodendritic compartment. Expressed in several structures, including excretory gland cell; hermaphrodite gonad; intestine; nervous system; and rectal gland cell. Human ortholog(s) of this gene implicated in several diseases, including Creutzfeldt-Jakob disease; Hirschsprung's disease; and generalized epilepsy with febrile seizures plus 9. Is an ortholog of human STX1A (syntaxin 1A).
• Biotype: SO:0001217
• Genetic Position: III :21.1995 ±0.007471
• Length (nt): 6630

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006798

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F56A8.7a.2	F56A8.7a.2	2567	III: 13277258-13283887
Transcript:F56A8.7b.1	F56A8.7b.1	1003	III: 13277259-13283887
Transcript:F56A8.7a.1	F56A8.7a.1	1017	III: 13277261-13282340

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F56A8.7a	F56A8.7a	876	III: 13277369-13277382
CDS:F56A8.7b	F56A8.7b	876	III: 13277369-13277382

13 RNAi Result

• WBRNAi00107785
• WBRNAi00107786
• WBRNAi00089743
• WBRNAi00048624
• WBRNAi00095402
• WBRNAi00006429
• WBRNAi00028226
• WBRNAi00095401
• WBRNAi00090278
• WBRNAi00090120
• WBRNAi00089960
• WBRNAi00095372
• WBRNAi00095371

105 Allele

• gk963887
• gk963904
• gk963552
• gk190136
• gk190139
• gk190140
• gk190137
• gk190138
• gk190143
• gk190144
• gk190141
• gk190142
• gk190145
• gk190146
• gk190147
• gk190150
• gk190148
• gk190149
• WBVar00245152
• WBVar01607328
• WBVar01607327
• WBVar00182607
• WBVar00182606
• WBVar01823354
• h13228
• e240
• e246
• gk555153
• gk455957
• gk418285

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006798
• Start: 13277258
• End: 13283887
• 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

162 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.	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:A-class-motor-neurons_larva_enriched
	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
	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
	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
	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 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 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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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 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
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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
Starvation	Starvation-induced transcripts that showed significantly increased expression in post dauer animals comparing to wild type control.	edgeR	WBPaper00053713:Starvation-induced_postdauer_vs_control_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell 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:A-class-motor-neurons_L2-larva_expressed

14 Expression Patterns

• Primary Identifier: Expr15232
• Pattern: Unc-64 isoform A and B.

• Primary Identifier: Expr13063
• Pattern: In wild-type animals, UNC-64A::GFP is strongly expressed in most neurons.
• Subcellular Localization: The two isoforms of UNC-64 are both localized to the plasma membrane via their transmembrane domains at the C terminus.

• Primary Identifier: Expr1423
• Pattern: Syntaxin was expressed in the vast majority of all neurons. In addition, syntaxin expression was high in intestinal nuclei, in the spermatheca, and in the uv1 cells of the vulva.
• Subcellular Localization: nuclei

• Primary Identifier: Expr1424
• Remark: The expression pattern from the GFP, lacZ, and antibody studies were consistent, except that GFP reporter expression was observed in the intestine only with syntaxin C fusions. This expression was limited to the posterior half of the intestine. It is possible that sequences that direct gut expression are absent from the GFP clones since sequences further upstream of the initiation codon are present in the lacZ constructs.
• Pattern: Syntaxin A and C were expressed in neurons and in five nonneuronal tissues. By contrast, expression of syntaxin B was limited to the five nonneuronal cell types. Also stained were the uv1 secretory cells of the vulva, the excretory gland cells, the distal tip cells, the spermatheca, and the intestinal muscle. In the uv1 cells, GFP fluorescence was concentrated subcellularly.
• Subcellular Localization: In neurons, syntaxin A and C were found ubiquitously on neuronal cell bodies, axons, and dendrites.

• Primary Identifier: Expr1448
• Remark: Reporter gene fusion type not specified.
• Pattern: The gene is specifically expressed in neurons, and the transcript is exclusively localized also in neurons. unc-64 transcript is not detectable in hermaphrodite specific neurons. unc-64 gene is expressed in almost all neurons constituting the head ganglion.

• Primary Identifier: Expr2036033
• 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: Expr1032868
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1422
• Remark: Syntaxin = unc-64 in this article.
• Pattern: Syntaxin was detected in the nervous system. Syntaxin immunoreactivity was very strong and distributed uniformly along the major process bundles: the nerve ring, ventral cord, and dorsal cord. Syntaxin was also detected in the pharyngeal nervous system. Furthermore, syntaxin was detected outside the nervous system. Immunoreactivity was strong in the uv1 cells of the vulva, in the intestine, and in the spermatheca. Detectable levels of syntaxin protein were not observed in other tissues.
• Subcellular Localization: Syntaxin immunoreactivity also was detected in the vast majority of neuronal cell bodies as well as in commissural and dendritic processes.

• Primary Identifier: Expr9329
• Remark: Reporter gene fusion type not specified.
• Subcellular Localization: In wild-type intestinal cells, GFP-UNC-64 predominantly localized to the apical and basolateral plasma membrane.

• Primary Identifier: Expr1152392
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1014577
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017897
• 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: Expr1447
• Remark: syntaxin = unc-64 in this article.
• Pattern: Expressed at embryo, L1, L2, L3, L4 and adult stages.

• Primary Identifier: Expr13064
• Pattern: UNC-64B::GFP is not expressed in the nervous system in wild-type background.

40 GO Annotation

29 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006798
• Start: 13277258
• End: 13283887
• Strand: 1

40 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6630

1 Sequence Ontology Term