WormMine: AnatomyTerm WBbt:0004742

• Definition: Neuron class of one pharyngeal interneuron, anterior sensory.
• Name: I3 neuron
• Primary Identifier: WBbt:0004742
• Synonym: I3

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree MSaaaaapaa	MSaaaaapaa nucleus		WBbt:0002101

2 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Single-cell RNA-Seq cell group 58_1 expressed in neuron.	scVI 0.6.0	WBPaper00065841:58_1
	Transcripts enriched in I3 according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:I3_enriched

41 Expression Patterns

• Primary Identifier: Expr67
• Remark: Legacy Data: Author "Lynch AS" "Bauer PK" "Hope IA"Date 1996-06.
• Pattern: One nucleus in the anterior part of the pharyngeal metacorpus shows expression. The expression is relatively weak and rare compared to most of the patterns described here, but is reproducible and so is included. The position and singularity of expression suggests the pharyngeal interneuron I3 as the cell of interest.

• Primary Identifier: Expr11755
• Remark: Isoform 1b.1

• Primary Identifier: Expr1688
• Remark: The cellular expression pattern for nlp-3 fragments was indistinguishable from the cellular expression pattern for nlp-3 subcloned constructs. Transgenic lines were generated by coinjection of the nlp::gfp construct (5070 ng/ul) and lin-15 rescue construct (pJM24,100 ng/ul) into lin-15(n765ts) animals. At least two independent transgenic lines were analyzed for each nlp gene; 5-10 animals were scored per line. 1,1'-Dioctadecyl-3,3,3',3 -tetramethylindodicarbocyanine perchlorate (Molecular Probes) was used to stain amphid and phasmid neurons to facilitate identification.
• Pattern: Expressed in ADF, ASE, ASH, AWB, ASJ, BAG, HSN, I1, I2, I3, I4, MI, M3, NSMR, 3 head neurons, VNC, oocytes, I6, M2, pm1VL, intestine.

• Primary Identifier: Expr15571

• Primary Identifier: Expr15572

• Primary Identifier: Expr15573

• Primary Identifier: Expr822
• Remark: C43H6.9 = glr-7
• Pattern: I3, I2, I6, MI, NSM, I1(?).

• Primary Identifier: Expr15579

• Primary Identifier: Expr823
• Remark: F22A3.3 = glr-8
• Pattern: I1, I2, MC, NSM, M3 (left/right), I3, MI M4, M3 (left/right), I6, M5, BDU, ALM, PLM, URB (left/right)

• Primary Identifier: Expr15583

• Primary Identifier: Expr2937
• Pattern: Both ahr-1:GFP reporters are expressed during embryonic and larval development. Expression is first detected in two cells 260 min after the first cleavage. By midembryogenesis (pre-comma stage), 14 cells express the pJ360 ahr-1:GFP fusion gene. At the 2-fold stage of embryogenesis, two cells express ahr-1:GFP in the tail, and the remaining fluorescing cells are in the forming head. During the first larval stage. ahr-1:GFP is expressed in 28 neurons, several blast cells, and two phasmid socket cells. The neurons that express ahr-1:GFP include ALNR/ALNL, AQR/PQR, AVM/PVM, BDUR/BDUL, PLMR/PLML, PLNR/PLNL, PHCL/PHCR, PVWL/PVWR, RMEL/RMER, SDQR/SDQL, and URXR/URXL. The T.pa, T.ppa, and T.ppp blast cells in the tail express ahr-1:GFP, as do all of their descendents, including the PHso1 and PHso2 phasmid socket cells. ahr-1:GFP is also expressed in the MI and I3 neurons in the pharynx and the G2 and W blast cells. Four additional cells in the head express ahr-1:GFP, tentatively identified as the ASK and RIP neurons.
• Subcellular Localization: The pJ360 construct includes the entire ahr-1 genomic sequence, and transgenic animals express this fusion protein in a subset of neuronal nuclei. The pHT102 transgene lacks most of the ahr-1 coding sequence and labels axons as well as nuclei.

• Primary Identifier: Expr15586

• Primary Identifier: Expr15651

• Primary Identifier: Expr15652

• Primary Identifier: Expr15589

• Primary Identifier: Expr15591

• Primary Identifier: Expr15598

• Primary Identifier: Expr11622
• Pattern: Expression of ceh-34::gfp transgene began during embryogenesis. CEH-34::GFP was localized to the nuclei of expressing cells. During embryonic morphogenesis and larval development and throughout adulthood, expression of the ceh-34::gfp transgene was seen predominantly in pharyngeal cells. The ceh-34::gfp transgene was expressed in all pharyngeal neurons (M4, I1, MI, I3, M3, NSM, MC, I2, I4, I5, I6, M1, M2, and M5), some pharyngeal muscle cells (pm1 and pm2) and pharyngeal epithelial cells (e1 and e3), and some body wall muscles around the anterior pharynx.

• Primary Identifier: Expr8850
• Remark: Picture: Fig 3.
• Pattern: Neuronal Expression: AVA, AVB, AVE, PVC, AIB, AUA, AVG, RIB, RIC, SAA, SIA, SIB, RIF, RIM, RMD, RME, SMD, DA, DB, VA, VB, M5, NSM, MC, I3, MI?. Non-neuronal Expression: rectal epithelium, body wall muscle, spermethecae, vulva muscle.

• Primary Identifier: Expr15604

• Primary Identifier: Expr14590
• Pattern: Embryonic expression of exc-7 was first observed at the bean stage. By reverse lineaging with use of SIMI-Biocell software, we confirm the identity of one of the expressing cells at this stage as the excretory canal cell. In L1 animals, broad expression in the head, ventral nerve cord (VNC), and tail was observed. In young adults, expression is notably observed in vulva cells. In the nervous system specifically, expression is observed in many neurons throughout the body, but unlike Drosophila Elav, exc-7::gfp it is not panneuronally expressed. We confirmed previously reported expression in cholinergic VNC MNs, but absence of GABAergic VNC MNs, consistent with previous reports (Fujita et al., 1999; Loria et al., 2003) and consistent with exc-7 functioning in cholinergic, but not GABAergic neurons to control alternative splicing (Norris et al., 2014). exc-7::gfp is also expressed in some non-neuronal cell types, including muscle and hypodermis, but not in the gut. A previous report showed that exc-7 is only transiently and weakly expressed in the excretory cell, which, based on exc-7's excretory mutant phenotype, has puzzled researchers (Fujita et al., 2003). We find that the gfp tagged exc-7 locus is strongly and continuously expressed in the excretory canal cell.

• Primary Identifier: Expr15608

• Primary Identifier: Expr15369

• Primary Identifier: Expr15611

• Primary Identifier: Expr3759
• Pattern: ser-7::gfp DNA injected into C. elegans at 0.5-0.05 ng/Ul produced lines that exhibited marked GFP fluorescence in a number of pharyngeal neurons, including the MCs, M4, I2s, I3, M5 and occasionally in the M3s, I4, I6 and M2s. Strong GFP fluorescence was also observed in the vulval muscles.

• Primary Identifier: Expr97
• Remark: Other strains injected with this plasmid are UL278 and UL279. The expression in these strains are consistent with that shown in UL280 but they are not as extensive.
• Pattern: In some L1 larvae the cell body and process of the I3 interneuron show expression. Late larval stages and adults show expression in the large nuclei of the intestine. Staining is strongest in the posterior nuclei. Strong staining is seen in the muscle nuclei of the pharynx with diffuse staining also seen in the pharyngeal muscle. The cell body and part of the process of either the I6 interneuron or the M1 or M2 pharyngeal motoneuron stain as well. Other nuclei in the head and body show expression and these are probably neuronal. This pattern may be due to an incomplete promoter (0.8kb). b-galactosidase is first expressed in late embryonic stages, in nuclei that are most likely pharyngeal.

• Primary Identifier: Expr597
• Remark: Reporter gene fusion type not specified. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). tba-2 in this article is referred as alpha-2 tubulin, while the same authors referred it as tba-2 in later publications such as cgc2176.
• Pattern: Following hatching, 6 pharyngeal muscle cells stain becoming increasingly intense during larval and adult development. 6-7 neurons are stained in the ventral cord identified as DB motor neurons. Late larval and adult stages, staining of the set of DB and VB motor neurons in the ventral cord and their axonal processes along the ventral cord shows higher intensity of staining in late larval and adult stages. At L4, Pharyngeal muscles and the motor neurons show intense staining in L4 and adult stages. Fusion gene expressed in intestinal nuclei showing a gradient of expression, high staining in the posterior most intestinal nuclei in the tail region to a lower intensity of staining in the anterior intestinal nuclei. Intestinal staining decreases (L3-L4) and adult stages. Staining is detected in entire intestinal organ. Expression in neurons includes a set of DB and VB (19 cells) in the ventral nerve cord, a pair of posterior mechanosensory receptor neuron PLML and PLMR a single interneuron PVT in the pre-anal ganglion and a single neuron ALA in dorsal ganglion in the head.

• Primary Identifier: Expr2607
• Pattern: Earliest expression with the antibody was seen in a small cluster in late-gastrulation embryos. From their position, these cells may be the precursors of the pharyngeal cells that express GFP in the L1 larva. ceh-2 expression was found restricted to eleven cells (fourteen nuclei) of five types in the anterior pharynx (corpus) of larvae and adults: the I3 neuron that lies embedded in the dorsal sector of the pharynx muscle; the pairs of NSM and M3 motoneurons in the left and right subventral sectors; the three m2 muscle cells, each possessing two nuclei resulting from cell fusion during development; and the three e2 epithelial cells with the anterior-most pharynx nuclei.
• Subcellular Localization: Antibody staining is nuclear as expected for a transcription factor.

• Primary Identifier: Expr2890
• Remark: The whole-mount in situ hybridization database by the Kohara Lab [NEXTDB Ver. 3.0 beta (July 07, 2001), yk112c4, shows that the gene is expressed transiently in the midembryonic stage.
• Pattern: Expression was detected in some neurons in the head and pharynx of larvae and adult animals. The neurons expressing Ce-TBX-2 was identified in adult animals: they were amphid sensory neurons AWB, AWC, ASJ, and pharyngeal neurons I1, I3, I5, M1, M2, M5, NSM.
• Subcellular Localization: Most Ce-TBX-2 protein molecules were localized in the cytoplasm and not in the nuclei of all the neurons that express this protein. The mutations ut180 and ut192 did not change the localization.

• Primary Identifier: Expr15370

9 Life Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	The first stage larva. At 25 Centigrade, it ranges 14-25.5 hours after fertilization, 0-11.5 hours after hatch.		L1 larva Ce	WBls:0000024
	The whole period of embryogenesis in the nematode Caenorhabditis elegans, from the formation of an egg until hatching.		embryo Ce	WBls:0000003
	The C. elegans life stage spanning 620-800min(hatch) after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. A stage after elongation is over. The last stage of embryogenesis. Also called pre-hatched embryo, late embryo or morphogenetic embryo.		fully-elongated embryo Ce	WBls:0000021
	The C. elegans life stage spanning 350-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The stage that embryo starts elongation until elongation is over.		elongating embryo Ce	WBls:0000015
	The C. elegans life stage spanning 390-420min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo looks like a comma. A stage between bean embryo and 1.5-fold embryo.		comma embryo Ce	WBls:0000017
	The C. elegans life stage spanning 460-520min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and double fold. A stage between 1.5-fold embryo and 3-fold embryo.		2-fold embryo Ce	WBls:0000019
	The C. elegans life stage spanning 520-620min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and tripple fold. A stage between 2-fold embryo and fully-elongated embryo. Also called pretzel embryo or pretzel stage.		3-fold embryo Ce	WBls:0000020
	The C. elegans life stage spanning 420-460min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. The shape of embryo is elongated and fold back 50%. A stage between comma embryo and 2-fold embryo.		1.5-fold embryo Ce	WBls:0000018
	The C. elegans life stage spanning 350-390min after first cleavage at 20 Centigrade. Cell number remains at ~560 cells, with some new cells generated and some cells go through programmed cell death. Emrbyo elongation started but have not formed comma shape yet. The shape of embryo looks like a lima bean. A stage right before comma embryo. Also called lima embryo or lima bean stage.		bean embryo Ce	WBls:0000016

3 Parents

Definition	Name	Synonym	Primary Identifier
posterior segment of pharyngeal corpus.	metacorpus		WBbt:0003711
interneuron of the pharyngeal nervous system.	pharyngeal interneuron		WBbt:0003668
embryonic cell	MSaaaaapa		WBbt:0006202