WormMine: Gene WBGene00002141

• WormBase Gene ID: WBGene00002141
• Gene Name: inx-19
• Sequence Name: T16H5.1
• Brief Description: inx-19 encodes an innexin, proteins that form gap junction channels; inx-19 functions in parallel with the NSY-4 claudin to specify the AWC chemosensory neuron ON fate; in specifying the AWC on fate, inx-19 appears to function cell autonomously; inx-19 also regulates body size and growth.
• Organism: Caenorhabditis elegans
• Automated Description: Enables calcium channel inhibitor activity; gap junction hemi-channel activity; and protein kinase inhibitor activity. Involved in determination of left/right asymmetry in nervous system and intercellular transport. Located in gap junction and neuronal cell body membrane. Expressed in several structures, including K' cell; head neurons; hermaphrodite distal tip cell; lumbar neurons; and pharyngeal neurons.
• Biotype: SO:0001217
• Genetic Position: I :-8.61155 ±0.034051
• Length (nt): 12721

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002141

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T16H5.1b.1	T16H5.1b.1	1414	I: 2451898-2456465
Transcript:T16H5.1a.1	T16H5.1a.1	1515	I: 2451911-2463461
Transcript:T16H5.1a.2	T16H5.1a.2	1594	I: 2451911-2464618

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T16H5.1b	T16H5.1b	1317	I: 2451974-2452177
CDS:T16H5.1a	T16H5.1a	1365	I: 2451974-2452177

5 RNAi Result

• WBRNAi00053441
• WBRNAi00003437
• WBRNAi00004223
• WBRNAi00002207
• WBRNAi00066440

333 Allele

• gk963902
• gk964159
• gk963630
• WBVar01430642
• WBVar01430640
• WBVar01712648
• WBVar01712649
• WBVar01712646
• WBVar01712647
• WBVar01712653
• WBVar01712651
• WBVar01712652
• WBVar01712650
• WBVar01712633
• WBVar01712634
• WBVar01712631
• WBVar01712632
• WBVar01712639
• WBVar01712637
• WBVar01712638
• WBVar01712635
• WBVar01712636
• WBVar01712644
• WBVar01712645
• WBVar01712642
• WBVar01712643
• WBVar01712640
• WBVar01712641
• WBVar01545889
• WBVar01931615

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002141
• Start: 2451898
• End: 2464618
• 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_chrI_2451367..2451897
• Length (nt): 531
• Chromosome Location: I: 2451367-2451897
• Organism: Caenorhabditis elegans

114 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
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 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 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 significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in ubc-9(ne4833[ubc-9(G56R)] in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:ubc-9(ne4833)_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 srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.	A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR.	WBPaper00045974:NSM_enriched_totalRNA_tiling
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly increased expression in animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103.	ANOVA, p-value < 0.05.	WBPaper00056167:Cry5B_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C.	Transcripts that showed significantly increased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C.	DESeq2, fold change > 2.	WBPaper00061081:E.faecalis_upregulated_skpo-1(ok1640)
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed siginificantly increased expression in nmad-1(ok3133) comparing to in N2 at 25 entigrade.	edgeR, FDR < 0.05, fold change > 2.	WBPaper00056997:nmad-1(ok3133)_upregulated_germline_25C
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_downregulated
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_upregulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_upregulated
	Transcripts that showed significantly increased expression in dpy-7(e88) animals comparing to N2 animals.	Authors considered genes differentially expressed if they had a q-value <= 0.05 and a b-value >= 1 or <= -1.	WBPaper00053771:up_at_dpy-7(e88)
	Transcripts that showed significantly increased expression in nuo-6(qm200);atfs-1(gk3094) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:nuo-6(qm200);atfs-1(gk3094)_upregulated

12 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: Expr4694
• Remark: nsy-5 = T16H5.1.
• Subcellular Localization: Tagged NSY-5::GFP and NSY-5::DsRed fusion proteins that rescued nsy-5 mutants were first detected in embryos in a punctate pattern surrounding the sensory neurons and interneurons that expressed nsy-5::GFP. Individual NSY-5 puncta appeared to reside at the borders between neuronal cell bodies and were largely excluded from axons and dendrites.

• Primary Identifier: Expr4695
• Remark: Type: mammalian cell transfection. nsy-5 = T16H5.1.
• Subcellular Localization: The subcellular localization of NSY-5 was examined in COS cells expressing a heterologous NSY-5::EGFP fusion protein. In isolated COS cells, NSY-5::EGFP was observed mainly in intracellular vesicles. In pairs of COS cells that contacted each other, NSY-5::EGFP clustered at points of cell-cell contact, but only when both cells expressed NSY-5.

• Primary Identifier: Expr1019213
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr15392
• Remark: Promoter 3

• Primary Identifier: Expr15393
• Remark: Promoter 4

• Primary Identifier: Expr10564
• Pattern: nsy-5 is expressed in both AWC neurons and at least 17 pairs of other sensory neurons and interneurons in the head and tail (Chuang et al., 2007). AWBL, AWCL, AWBR and AWCR cells represent four lineage groups within the NSY-5 network and express the co-injection mosaic marker odr-1p::DsRed. Fifteen out of the 34 non-AWC cells expressing nsy-5 are closely related to either AWB by lineage. In addition to what described before ncy-5 was found to be expressed in PHA and PHB neurons.

• Primary Identifier: Expr8687
• Remark: Picture: Fig 3.
• Pattern: Expression in the alimentary canal: Strong and consistent expression in K.a/K' cells. Weak or rare expression in intestine. Expression in the nervous system: AVB, AVK. Expression in the reproductive system: In developing larva stage, expressed in distal tip cells during distal tip cell migration.

• Primary Identifier: Expr11348
• Pattern: inx-19 is expressed in body wall musculature.

• Primary Identifier: Expr2012793
• 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: Expr1157013
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031032
• 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).

21 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002141
• Start: 2451898
• End: 2464618
• Strand: -1

21 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12721

1 Sequence Ontology Term