WormMine: Gene WBGene00007799

• WormBase Gene ID: WBGene00007799
• Gene Name: nrx-1
• Sequence Name: C29A12.4
• Brief Description: nrx-1 encodes the C. elegans ortholog of neurexins, presynaptic transmembrane neural adhesion molecules that contain extracellular laminin and EGF domains and play a critical role in synaptic development; genetic analyses suggest that nrx-1 may play a role in regulation of adult lifespan; nrx-1 expression is controlled by daf-2 and daf-16.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in negative regulation of receptor clustering. Located in presynaptic active zone. Expressed in GABAergic neurons; cholinergic neurons; nervous system; and ventral cord neurons. Used to study autism spectrum disorder. Human ortholog(s) of this gene implicated in Pitt-Hopkins-like syndrome 2 and alcohol dependence. Is an ortholog of human NRXN1 (neurexin 1) and NRXN3 (neurexin 3).
• Biotype: SO:0001217
• Genetic Position: V :2.82231 ±0.001163
• Length (nt): 21693

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00007799

Genomics

13 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C29A12.4a.1	C29A12.4a.1	4914	V: 10825011-10846699
Transcript:C29A12.4b.1	C29A12.4b.1	5439	V: 10825014-10846699
Transcript:C29A12.4k.1	C29A12.4k.1	5178	V: 10825024-10846421
Transcript:C29A12.4l.1	C29A12.4l.1	4650	V: 10825024-10846421
Transcript:C29A12.4c.1	C29A12.4c.1	1233	V: 10835626-10846421
Transcript:C29A12.4d.1	C29A12.4d.1	705	V: 10835626-10846421
Transcript:C29A12.4m.1	C29A12.4m.1	1338	V: 10841857-10846699
Transcript:C29A12.4f.1	C29A12.4f.1	1695	V: 10842032-10846703
Transcript:C29A12.4i.1	C29A12.4i.1	303	V: 10842053-10842355
Transcript:C29A12.4g.1	C29A12.4g.1	375	V: 10842053-10842528
Transcript:C29A12.4j.1	C29A12.4j.1	1005	V: 10842053-10846421
Transcript:C29A12.4h.1	C29A12.4h.1	675	V: 10843369-10846421
Transcript:C29A12.4e.1	C29A12.4e.1	414	V: 10845755-10846421

Other

13 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C29A12.4a	C29A12.4a	4623	V: 10825024-10825142
CDS:C29A12.4k	C29A12.4k	5178	V: 10825024-10825142
CDS:C29A12.4c	C29A12.4c	1233	V: 10835626-10835652
CDS:C29A12.4d	C29A12.4d	705	V: 10835626-10835652
CDS:C29A12.4f	C29A12.4f	1392	V: 10842053-10842332
CDS:C29A12.4i	C29A12.4i	303	V: 10842053-10842355
CDS:C29A12.4j	C29A12.4j	1005	V: 10842053-10842332
CDS:C29A12.4h	C29A12.4h	675	V: 10843369-10843519
CDS:C29A12.4e	C29A12.4e	414	V: 10845755-10845784
CDS:C29A12.4b	C29A12.4b	5151	V: 10825024-10825142
CDS:C29A12.4g	C29A12.4g	375	V: 10842053-10842332
CDS:C29A12.4l	C29A12.4l	4650	V: 10825024-10825142
CDS:C29A12.4m	C29A12.4m	864	V: 10842053-10842332

6 RNAi Result

• WBRNAi00041440
• WBRNAi00011320
• WBRNAi00029309
• WBRNAi00099062
• WBRNAi00080988
• WBRNAi00080991

284 Allele

• gk963301
• gk964451
• gk964452
• gk963495
• gk963496
• WBVar02060870
• WBVar02060871
• WBVar02060872
• WBVar02060873
• WBVar02060874
• WBVar02060875
• gk852610
• gk626705
• gk786227
• gk347526
• gk516474
• gk470482
• gk470914
• gk553423
• gk554818
• gk492828
• gk437362
• gk372766
• gk519701
• gk645394
• gk648312
• gk448728
• gk666722
• gk642891
• gk428627

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00007799
• Start: 10825011
• End: 10846703
• 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_chrV_10846704..10847192
• Length (nt): 489
• Chromosome Location: V: 10846704-10847192
• Organism: Caenorhabditis elegans

195 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 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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	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
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
	Genes that showed increased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_upregulated
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_12h_regulated
	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 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 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
	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 wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage.	fold change > 2	WBPaper00058711:wdr-5(ok1417)_upregulated
	Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_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 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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_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

13 Expression Patterns

• Primary Identifier: Expr9158
• Remark: Picture: Fig. 2A.
• Pattern: nrx-1::gfp is expressed broadly throughout the entire nervous system during all larval and adult stages. Co-labeling with reporters that label subpopulation of individual neurons as well as the counting of neurons in several ganglia indicate that all neurons in the nervous system may express NRX-1. The only exception may be the canal-associated neuron CAN. No expression is observed in glia cells. The only cells outside the nervous system in which NRX-1::GFP could be observed are the spermathecal valve cells.
• Subcellular Localization: NRX-1 localizes along the entire length of axonal projection.

• Primary Identifier: Expr1033384
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr10695

• Primary Identifier: Expr12334
• Subcellular Localization: The nrx-1::SL2::GFP transgene showed GFP expression in GABAergic neurons, as well as some other ventral cord motor neurons. Furthermore, a GFP-tagged NRX-1 expressed in GABAergic neurons localized to presynaptic sites.

• Primary Identifier: Expr9159
• Remark: Picture: Fig. 2B.
• Subcellular Localization: Transgenic animals reveal that NRX-1alpha shows a synaptic localization pattern in the nerve ring. Its localization overlaps with that of the presynaptic marker synaptotagmin/SNB-1.

• Primary Identifier: Expr14641
• Pattern: nrx- 1L::GFP is strongly expressed in cholinergic motor neurons.

• Primary Identifier: Expr2014446
• 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: Expr1028791
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1145469
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr14642
• Subcellular Localization: Expression of unc-129::NRX-1L::GFP produces discrete puncta along the dorsal nerve cord where the synaptic outputs of DA/DB neurons are located. NRX-1L::GFP clusters colocalize with clusters of mCherry::RAB-3 fluorescence, providing evidence that NRX-1L is preferentially localized to cholinergic presynaptic sites.

• Primary Identifier: Expr2032687
• 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: Expr13946
• Subcellular Localization: NRX-1-gamma isoform localized specifically to synapses in DA9 and accumulated at the ventral tip of the presynaptic varicosity, where active zone proteins reside, and is concentrated at the active zone, at the ventral tip of the presynaptic varicosity.These results confirm that NRX-1 is a presynaptically localized protein.

• Primary Identifier: Expr13947
• Subcellular Localization: NRX-1-alpha isoform localized specifically to synapses in DA9 and accumulated at the ventral tip of the presynaptic varicosity, where active zone proteins reside, and is concentrated at the active zone, at the ventral tip of the presynaptic varicosity.These results confirm that NRX-1 is a presynaptically localized protein.

3 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00007799
• Start: 10825011
• End: 10846703
• Strand: 1

3 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed significantly increased expression in nrx-1(tm1961) mutants comparing to in N2.	Seqsolve uses Cufflinks/Cuffdiff to quantify and identify transcripts with a significant level of expression between different conditions. p-value < 0,005.	WBPaper00053023:nrx-1(tm1961)_upregulated
	Genes that showed significantly increased expression in nrx-1(tm1961);nlg-1(ok259) mutants comparing to in N2.	Seqsolve uses Cufflinks/Cuffdiff to quantify and identify transcripts with a significant level of expression between different conditions. p-value < 0,005.	WBPaper00053023:nrx-1(tm1961);nlg-1(ok259)_upregulated
	Genes that showed significantly decreased expression in nrx-1(tm1961) mutants comparing to in N2.	Seqsolve uses Cufflinks/Cuffdiff to quantify and identify transcripts with a significant level of expression between different conditions. p-value < 0,005.	WBPaper00053023:nrx-1(tm1961)_downregulated
	Genes that showed significantly decreased expression in nrx-1(tm1961);nlg-1(ok259) mutants comparing to in N2.	Seqsolve uses Cufflinks/Cuffdiff to quantify and identify transcripts with a significant level of expression between different conditions. p-value < 0,005.	WBPaper00053023:nrx-1(tm1961);nlg-1(ok259)_downregulated

1 Sequence

• Length: 21693

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00034059
• WBStrain00035064
• WBStrain00036581

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_10824996..10825010
• Length (nt): 15
• Chromosome Location: V: 10824996-10825010
• Organism: Caenorhabditis elegans