WormMine: AnatomyTerm WBbt:0003887

• Definition: one member of Amphid neurons, single ciliated endings, probably chemo-sensory; project into ring via commissure from ventral ganglion, make diverse synaptic connections in ring neuropil
• Name: ASIR
• Primary Identifier: WBbt:0003887
• Synonym: lineage name: ABpraapapppa

1 Children

Definition	Name	Synonym	Primary Identifier
nucleus of pedigree ABpraapapppa	ABpraapapppa nucleus		WBbt:0001684

1 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Top 300 transcripts enriched in ASIL, ASIR according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASI

344 Expression Patterns

• Primary Identifier: Expr4693
• Remark: nsy-5 = T16H5.1.
• Pattern: A GFP reporter transgene with 5.8 kb of the nsy-5 promoter was expressed exclusively in sensory neurons and interneurons in the head and tail. The neurons that expressed nsy-5::GFP included AWC, ASH, AFD, ASI, ADL, ASK, BAG, AWB, and ADF (head sensory neurons); ADA, AIZ, RIC, AIY, and AIM (head interneurons); PHA and PHB (tail sensory neurons); and PVC and PVQ (tail interneurons). Expression began about halfway through embryogenesis, was strongest in late embryogenesis and the L1 larval stage, and faded thereafter. Adults maintained weak expression in several neurons, including ASH but not AWC.

• Primary Identifier: Expr4684
• Pattern: GFP expression was detected at most developmental stages, with the spatial expression depending on the developmental stage of the animal. Neuronal expression of hlh-29 was detected in larvae and adults in both amphid and phasmid sockets, in the ALA and PVT neurons, in the chemosensory and mechanosensory neurons, ASI, ASK, PHA, and PQR, and in neurons of the anterior pharyngeal bulb. Weaker expression was also detected in the ASG chemosensory neurons in some transgenic lines. L1 animals show strong expression of hlh-29 in intestinal cells, and weaker expression in the rectal glands and the pharyngeal muscle cell PM1. By L3 stage, intestinal expression of the hlh-29::GFP is limited to the posterior intestinal cells, and PM1 expression is no longer detected. Expression is also detected in the ventral posterior coelomocytes in the later L3-stage larvae, and in the spermatheca and vulval muscles of L4 and adult animals.

• Primary Identifier: Expr4796
• Remark: Reporter gene fusion type not specified.
• Pattern: cnx-1 was expressed ubiquitously in every blastomere of the embryos up to the gastrulation stage but expression became gradually restricted to the head and tail regions at the comma stage during embryogenesis. During post-embryonic development, cnx-1 was expressed prominently in the H-shaped excretory cell, in the neurons of head and tail, in the dorsal and ventral nerve cords, and in the spermatheca. cnx-1 expression was also observed in the spicules of the male tail. The two head neurons expressing cnx-1 are ASK and ADL, and two tail neurons are PHA and PHB. Therefore, cnx-1 is expressed in head neurons including ASK and ASI chemosensory neurons and tail neurons including PHA and PHB.

• Primary Identifier: Expr4403
• Pattern: Strong and consistent expression was observed in a limited number of neurons in the head and tail and coelomocytes. Weaker and/or inconsistent expression of TTX-7::EGFP was detected in nerve cord motor neurons, intestine, and somatic gonad. The head neurons expressing ttx-7::EGFP include AFD and RIA neurons. Also expressed in ASH, ASE, ASJ, AWC, ADF, ADL, ASI, ASK, AWB, VNC motor neurons, etc.
• Subcellular Localization: TTX-7::EGFP was diffusely expressed in the cytoplasm and was not localized to any specific subcellular compartment.

• Primary Identifier: Expr4281
• Reporter Gene: [wrk-1::TM-gfp] translational fusion. wrk-1 expression was determined by means of a reporter construct (wrk1::TM::gfp), in which 4 kb of sequences upstream of the ATG start codon, all exons, and the first three introns of the wrk-1 locus were fused in frame to gfp. This construct is able to rescue the phenotype of wrk-1 mutant animals. See Transgene otEx2389. [wrk-1::gfp] transcriptional fusion in which 4 kb of sequences upstream of the ATG start codon was fused to GFP. See Transgene otEx203 [wrk-1::gfp] translational fusion. See Transgene otEx2522.
• Pattern: The wrk-1 gene is expressed in ventral midline cells, namely in the eMNs. Additional expression is observed in a subset of head neurons, including interneurons (AIY class), sensory neurons (ASI class), and head motoneurons (SMDV/D class), and glial-type sheath and socket cells. Outside the nervous system, the most prominent sites of wrk-1 expression include the intestine, excretory gland cell, distal tip cell, and coelomocytes.

• Primary Identifier: Expr4270
• Pattern: INS-1::Venus, which was confirmed to be functional, was expressed in several amphid chemosensory neurons, ASE, ASI, and ASJ; AIA interneurons; and several other neurons. Of these expression patterns, the fluorescence signal in AIA was the strongest and most consistent between individual animals.
• Subcellular Localization: In AIA neurons, punctate expression patterns in the cell bodies and processes were observed.

• Primary Identifier: Expr4204
• Remark: A translational DYF-2::GFP fusion was found to be localized only in cilia of CSN, thus precluding a confirmation of the cellular expression pattern obtained with the transcriptional dyf-2::gfp fusion or any further cell identification.
• Pattern: dyf-2::gfp expression was observed in only a subset of the ciliated sensory neuron (CSN) class in the worm. GFP signal was observed in seven out of twelve neurons of the amphids, including ASH, ASI, ASJ, ASK, ADL (ciliated neurons that fill with the fluorescent dye DiI) plus two hitherto unidentified amphid neurons. In addition, GFP expression was observed in the phasmid CSN and in neurons identified as AQR and PQR (asymmetric CSN in the head and tail, respectively). No or only very occasional GFP signal was detected in other CSN anterior to the nerve ring in the head of the worm.

• Primary Identifier: Expr4647
• Pattern: Transgenic lines generated with the partial protein fusion construct (for example, ljEx109) expressed TRPA-1:: GFP in the same cells as ljEx107 (see Expr4646), but with some additional cells, including the majority of amphid sensory neurons (for example, ASH, AWA, AWB, ASI and ASK) and the phasmid neurons PHA and PHB.

• Primary Identifier: Expr4648
• Pattern: Transgenic lines generated with the full-length protein fusion construct (for example, ljEx114) expressed TRPA-1:: GFP in the same cells as ljEx107 (see Expr4646), but with some additional cells, including the majority of amphid sensory neurons (for example, ASH, AWA, AWB, ASI and ASK) and the phasmid neurons PHA and PHB. The full-length TRPA-1:: GFP fusion was also expressed in the PVD and PDE in the postdeirid sensilla and the sensory neurons OLQ and IL1. Other neurons in the head and ventral nerve cord also expressed TRPA-1:: GFP.
• Subcellular Localization: The fusion protein was observed at the cilia of sensory neurons, as well as at the cell body.

• Primary Identifier: Expr4546
• Remark: asna-1 has been predicted to be the fourth gene in an operon together with the genes ZK637.2, ZK637.3, and ZK637.4 according to WS160.
• Pattern: An ASNA-1::GFP fusion protein driven by the 430 bp fragment fully rescued asna-1(sv42) and asna-1(ok938). In worms carrying the transgene, like those harboring the longer construct, GFP expression was seen in a restricted set of sensory neurons, in the intestine, and weakly in the hypodermis. Further analysis of the sensory neuron expression revealed that during the L1 and L2 stages, GFP was invariably expressed in ASI, and often also in ASK. In some animals, expression was also seen in ADL; however, in most animals expression was not seen in all three pairs of neurons simultaneously.

• Primary Identifier: Expr4541
• Pattern: Expressed in ASKL/R, ASIL/R, ASJL/R.

• Primary Identifier: Expr4525
• Pattern: Expressed in ASER, ASIL/R, PVT, URXL/R, AIYL/R, intestine.

• Primary Identifier: Expr4526
• Pattern: Expressed in AWAL/R, ASIL/R, RIAL/R, PVT.

• Primary Identifier: Expr4527
• Pattern: Expressed in ASER, ASIL/R, PVT.

• Primary Identifier: Expr4511
• Pattern: RGS-3::GFP expression is seen in seven pairs of head sensory neurons (ASH, ADL, AWB, AWC, ASI, ASJ and ASK) as well as PHA and PHB in the tail.

• Primary Identifier: Expr14133
• Remark: Strain: OH14774
• Pattern: Asymmetric expression in AWC OFF, ASK, ASI

• Primary Identifier: Expr11200
• Remark: Reporter fusion construct for the translational fusion not specified.
• Pattern: Upstream regulatory sequences of cng-2 drove gfp expression exclusively in six pairs of head sensory neurons in the adult. AWC, ASE, ASG, ASI, ASJ, ASK (Fig. 2B).
• Subcellular Localization: When expressed under an ASK-specific promoter the CNG-2 fusion protein was restricted to the ASK cell bodies.

• Primary Identifier: Expr12330
• Remark: A promoter fusion to gfp, daf- 41p::gfp, revealed expression most prominently in anterior and posterior neurons including amphids (e.g. ASE, AWC, ASI, ADL) and phasmid sensory neurons, as well as peripheral neurons and ventral cord motorneurons. We also observed strong expression in body wall muscle and pharynx, as well as occasional expression in vulva, seam and intestine.

• Primary Identifier: Expr13411
• Pattern: The Venus reporter driven by the 5.7 kb npr22 promoter was expressed in many cells mainly in the head region; the npr-22prom::Venus expression was observed in head muscles, the I2 neurons, the MC neurons, the RIH neuron, the AIA neurons, the AUA neurons, the ASK neurons (strong in larval worms), the ASI neurons (strong in larval worms), a few B-type motorneurons in the posterior ventral nerve cord (variable), pharyngeal muscles, body wall muscles (weak), the intestine (weak), and a few classes of unidentified cells anterior to the nerve ring. In the I2, MC, RIH, AIA, AUA, and posterior B-type motorneurons, we confirmed the co-expression of established cell markers.

• Primary Identifier: Expr3175
• Pattern: Expressed in ADF, ADL, AFD, ASE, ASG, ASH, ASI, ASJ, ASK, AWA, AWB, AWC, BAG, PHA, PHB, URX, intestine.

• Primary Identifier: Expr8976
• Remark: Picture: Fig 4E to 4H. npr-5 = Y58G8A.4 in this paper.
• Pattern: The npr-5p::RFP transgene was expressed in a subset of amphid neurons (ADF, ASE, ASG, ASI, ASJ, ASK, AWA, AWB) in the inner labial neuron IL2, in the interneurons AIA and AUA, and in the phasmids (PHA, PHB). Outside the nervous system, npr-5p::RFP was expressed in head, neck, and body muscles throughout larval and adult development.

• Primary Identifier: Expr10641
• Pattern: A ser-6::ser-6::gfp transgene is expressed in head neurons, including the AWB, ADL and ASI sensory neurons, posterior ventral cord motor neurons and the intestine.

• Primary Identifier: Marker49
• Remark: Picture: N.A. Reporter gene fusion type not specified.
• Pattern: Expressed in anterior neurons, including AIY, AIZ, RID, M5, ASI, and labial sensory neurons, VNC motorneurons, midbody neurons HSN, CAN, and PVM, tail neurons DVB, DVC, and PDB, and the nonneuronal excretory cell, uterine muscles. -- according to pers. comm. from Oliver Hobert.

• Primary Identifier: Expr14199
• Pattern: ASH, ASI, AWB (dimmer and less consistent), sometimes you see other neurons in the head (variable), PVT

• Primary Identifier: Expr11753
• Remark: genomic

• Primary Identifier: Expr13039

• Primary Identifier: Expr3169
• Pattern: Expressed in ADF, ADL, ASH, ASI, ASJ, ASK, PHA, PHB.

• Primary Identifier: Expr3185
• Pattern: Expressed in ADF, ADL, ASE, ASG, ASH, ASI, ASJ, ASK, PHA, PHB, URX, labial neurons.

• Primary Identifier: Expr15558

• Primary Identifier: Expr15571

7 Life Stages

Remark	Definition	Other Name	Public Name	Primary Identifier
	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 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 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

6 Parents

Definition	Name	Synonym	Primary Identifier
neuron with its cell body situated in the head, excluding the pharynx.	head neuron		WBbt:0006751
embryonic cell	ABpraapappp		WBbt:0005862
cell that exists in and is part of an embryo.	embryonic cell		WBbt:0007028
Neuron class of two ciliated neurons that are part of the amphid sensilla; the endings are in the amphid channel, which is open to the outside.	ASI		WBbt:0005666
neuron type, cell body located in right lateral ganglion.	lateral ganglion right neuron		WBbt:0005100
	amphid right sensillum		WBbt:0005392