WormMine: Gene WBGene00004048

• WormBase Gene ID: WBGene00004048
• Gene Name: plx-2
• Sequence Name: K04B12.1
• Brief Description: plx-2 encodes one of two C. elegans plexins, conserved transmembrane proteins that function as semaphorin receptors in both vertebrates and invertebrates; plx-2 activity is essential for proper male tail and epidermal morphogenesis and for normal axon guidance in a select group of neurons, including SDQL; genetic analyses indicate that plx-2 functions with mab-20/semaphorin-2a, efn-4/ephrin-4, and unc-129/TGF-beta to regulate male tail morphogenesis and with mab-20 and lad-2/L1CAM to mediate axon guidance; PLX-2 can bind MAB-20 and this interaction is enhanced in the presence of LAD-2; PLX-2::GFP reporters are expressed in a subset of neurons and epidermal cells, as well as a subset (1, 3, 5, and 7) of male sensory ray cell clusters.
• Organism: Caenorhabditis elegans
• Automated Description: Enables semaphorin receptor activity. Involved in several processes, including axonal fasciculation; nematode larval development; and nematode male tail tip morphogenesis. Located in cell leading edge and cell surface. Expressed in several structures, including P3/4L; P9/10L; P9/10R; neuroblasts; and ray structural cell.
• Biotype: SO:0001217
• Genetic Position: II :22.9962 ±0.007199
• Length (nt): 7037

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004048

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K04B12.1.1	K04B12.1.1	5538	II: 14417855-14424891

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K04B12.1	K04B12.1	5358	II: 14418025-14418228

5 RNAi Result

• WBRNAi00065915
• WBRNAi00000986
• WBRNAi00049879
• WBRNAi00016577
• WBRNAi00117920

139 Allele

• gk963801
• gk963053
• WBVar01320118
• WBVar01320124
• gk962684
• gk904120
• gk662190
• gk717815
• gk601907
• gk789580
• gk589302
• gk368024
• gk515346
• gk868827
• gk650298
• gk654789
• gk759072
• gk599169
• gk599168
• gk766601
• gk766600
• gk728483
• gk516782
• gk521652
• gk499875
• gk353185
• gk808569
• gk900469
• gk617169
• gk338383

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004048
• Start: 14417855
• End: 14424891
• 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_chrII_14413476..14417854
• Length (nt): 4379
• Chromosome Location: II: 14413476-14417854
• Organism: Caenorhabditis elegans

213 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 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
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 that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_upregulated
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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
	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
	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 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 the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	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 altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	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
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
	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
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult

9 Expression Patterns

• Primary Identifier: Expr1031948
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr4682
• Remark: In addition to its widespread neuronal expression, EFN-4::GFP is also expressed in anterior and posterior epidermal cells, including the lateral epidermal cells H0 and QV5, the leading ventral epidermal cells of the anterior, and the posterior three pairs of ventral epidermal cells (P7 - 12).
• Pattern: In early embryos EFN-4::GFP is widely expressed in ventral neuroblasts prior to epidermal enclosure (see Expr2300). In contrast, PLX-2 reporters were expressed in a much smaller number of ventral neuroblasts. Following epidermal enclosure PLX-2::GFP reporters were expressed in neurons and in a subset of posterior lateral and ventral epidermal cells; these were identified as the lateral cell QV5 and the ventral epidermal cells P9-12.

• Primary Identifier: Expr2929
• Reporter Gene: Transgenic animals carrying an integrated array of the transcriptional reporter evIs136[plx-2::gfp] or the translational reporter evIs168[plx-2::GFP] were analyzed. The transcriptional and translational plx-2 GFP reporters are expressed in the same cells including several that undergo guided migrations during development.
• Pattern: plx-2 expression occurs predominantly in the nervous system from embryonic to adult stages. The onset of plx-2 reporter expression coincides with the normal timing of outgrowth or migration (e.g., CAN) of these neurons. Several nonneuronal tissues also express evIs136[plx-2::gfp] and evIs168[plx-2(+)::GFP] including gonadal sheath, vulva precursors, and excretory canal. Of most relevance, expression of both the transcriptional and translational reporters occurs throughout a number of stages of sensory ray morphogenesis in the male tail. Expression of the plx-2 translational reporter evIs168[plx-2::GFP] is observed during ray morphogenesis at the Rn stage in the early L3 larva in R1, 3, 5, and 7. This reporter continues to express faintly in the Rn.a descendents that form rays 1, 3, 5, and 7 of late L3 larvae, which coincides with the period during which lineally related Rn.a descendants sort from neighboring Rn.a descendants to form distinct rays. However, in mid-L4 larvae, expression appears restricted to the ray structural cell (Rnst) for rays 3, 5, 6, and 7, and this expression continues into the late-L4 larval stage. Ray 1 expression of both reporters is undetectable in late L4 larvae.

• Primary Identifier: Expr1153584
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr10005
• Pattern: At the onset of pocket closure, the plx-2 reporter expresses in six blast cells (and sporadically in a seventh) on the surface of the open ventral pocket, five of which, after dividing, form a band of ten PLX-2/plexin expressing plexin band cells that extends across the midline spanning the open pocket. At the onset of pocket closure, the plx-2 reporters express in right and left side analogs of QV5 and P cells P3/4, P5/6, P9/10, P11/12. The reporter also expresses in bridge and scaffold cells, which together comprise a band of PLX-2 and VAB-1 expressing cells that cross the open pocket. Expression in all of these cells continues throughout pocket closure and beyond. Among the P cells, expression is most prominent in P9/10 right (R) and left (L).

• Primary Identifier: Expr1023808
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014968
• 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: Expr1200099
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2033203
• 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).

30 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004048
• Start: 14417855
• End: 14424891
• Strand: -1

30 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7037

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00029149
• WBStrain00029148
• WBStrain00029147
• WBStrain00029146
• WBStrain00030125

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_14424892..14428754
• Length (nt): 3863
• Chromosome Location: II: 14424892-14428754
• Organism: Caenorhabditis elegans