WormMine: Gene WBGene00016354

• WormBase Gene ID: WBGene00016354
• Gene Name: rig-6
• Sequence Name: C33F10.5
• Brief Description: rig-6 encodes a protein with immunoglobulin and fibronectin type III domains and is similar to vertebrate contactins; based upon large-scale RNAi screens, rig-6 activity appears to be required for reproduction and positive regulation of body size; rig-6::gfp reporter fusion are expressed in neurons, particularly the URX ring interneurons.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable cell-cell adhesion mediator activity. Involved in several processes, including axon guidance; negative regulation of defecation rhythm; and regulation of locomotion. Located in axon; neuronal cell body; and synapse. Expressed in several structures, including body wall musculature; neurons; non-striated muscle; rectal epithelium; and spermatheca. Human ortholog(s) of this gene implicated in several diseases, including Compton-North congenital myopathy; familial adult myoclonic epilepsy 5; and high grade glioma. Is an ortholog of human CNTN6 (contactin 6).
• Biotype: SO:0001217
• Genetic Position: II :-3.02721 ±0.005159
• Length (nt): 13936

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00016354

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:C33F10.5d.1	C33F10.5d.1	3716	II: 4798151-4812086
MRNA	Transcript:C33F10.5c.1	C33F10.5c.1	2449	II: 4798152-4801033
NcPrimaryTranscript	Transcript:C33F10.5a	C33F10.5a	2803	II: 4798276-4801844

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C33F10.5d	C33F10.5d	3591	II: 4798276-4798563
CDS:C33F10.5c	C33F10.5c	2325	II: 4798276-4798563

11 RNAi Result

• WBRNAi00111604
• WBRNAi00111603
• WBRNAi00041778
• WBRNAi00041779
• WBRNAi00002147
• WBRNAi00011545
• WBRNAi00011546
• WBRNAi00093006
• WBRNAi00111602
• WBRNAi00085674
• WBRNAi00111601

166 Allele

• gk963801
• gk963053
• h5936
• h4641
• h16116
• gk330480
• gk141625
• WBVar02017887
• WBVar00171766
• WBVar01695503
• WBVar01719627
• gk858442
• WBVar01437617
• WBVar01437616
• WBVar01372244
• WBVar01372255
• WBVar01372233
• WBVar01719626
• WBVar01719628
• WBVar02029209
• gk449
• gk376
• ttTi1499
• WBVar01982432
• gk141627
• gk141621
• gk141622
• gk141623
• gk141624
• gk141617

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00016354
• Start: 4798151
• End: 4812086
• 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

205 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	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
	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
	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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
	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
	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
	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 upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted

9 Expression Patterns

• 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: Expr10584
• Pattern: The prig-6RIG-6::GFP construct drives expression of all RIG-6 isoforms in fusion with GFP, under their endogenous promoter. rig-6 expression is detected during embryogenesis and is maintained throughout adulthood. rig-6 is expressed in I1 and I3 pharyngeal interneurons, NSM motor neurons and other unidentified head neurons. RIG-6::GFP is also localized in the cell bodies and axons of different subtypes of VNC motorneurons, in the HSN and the CAN neurons. Neuronal expression of rig-6 also includes the ALM and PLM touch receptor neurons. Non-neuronal cells expressing rig-6 include somatic muscles and the hypodermis. We also detected rig-6 expression in the developing and adult EC. The prig-6RIG-6::GFP construct drives expression of all RIG-6 isoforms in fusion with GFP, under their endogenous promoter. rig-6 expression is detected during embryogenesis and is maintained throughout adulthood. rig-6 is expressed in I1 and I3 pharyngeal interneurons, NSM motor neurons and other unidentified head neurons. RIG-6::GFP is also localized in the cell bodies and axons of different subtypes of VNC motorneurons, in the HSN and the CAN neurons. Neuronal expression of rig-6 also includes the ALM and PLM touch receptor neurons. Non-neuronal cells expressing rig-6 include somatic muscles and the hypodermis. We also detected rig-6 expression in the developing and adult EC.

• Primary Identifier: Expr16093
• Pattern: rig-6 is broadly expressed in many pharyngeal neurons.

• Primary Identifier: Expr1767
• Remark: Reference: personal communication from Oliver Hobert 2002-12-07.
• Pattern: Neuronal expression in: consistent, strong URXL/R + few inconsistent weak head neurons

• Primary Identifier: Expr1037002
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2015355
• 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: Expr1145797
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2033589
• 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: Expr1025818
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

35 GO Annotation

17 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00016354
• Start: 4798151
• End: 4812086
• Strand: -1

35 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 13936

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00036345
• WBStrain00036110
• WBStrain00036147
• WBStrain00036006
• WBStrain00055147

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_4812087..4812846
• Length (nt): 760
• Chromosome Location: II: 4812087-4812846
• Organism: Caenorhabditis elegans