WormMine: Gene WBGene00003760

• WormBase Gene ID: WBGene00003760
• Gene Name: nlp-22
• Sequence Name: T24D8.3
• Organism: Caenorhabditis elegans
• Automated Description: Involved in embryo development and positive regulation of error-prone translesion synthesis. Expressed in RIAL; RIAR; head; and ventral nerve cord.
• Biotype: SO:0001217
• Genetic Position: X :-15.6391±
• Length (nt): 731

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003760

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T24D8.3.1	T24D8.3.1	334	X: 2341359-2342089

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T24D8.3	T24D8.3	309	X: 2341359-2341583

4 RNAi Result

• WBRNAi00054058
• WBRNAi00019156
• WBRNAi00103798
• WBRNAi00103797

19 Allele

• gk963725
• tm11089
• WBVar01979697
• tm6543
• tm5931
• gk748443
• gk509904
• gk832446
• WBVar01987349
• gk357025
• gk454091
• gk669741
• gk273335
• gk273334
• tm6351
• tm5832
• tm6391
• WBVar01619379
• WBVar01911306

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003760
• Start: 2341359
• End: 2342089
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

0 Downstream Intergenic Region

20 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:sre-33-ZK1025.1_8337
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	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
Bacteria infection: Photorhabdus luminescens	Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Photorhabdus_luminescens_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
	Genes with significantly increased expression in eat-2(ad465) treated with 2% DMSO for 72 hours, comparing to in N2 treated with 2% DMSO for 72 hours.	Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes.	WBPaper00048989:eat-2(ad465)_upregulated_in-DMSO
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
	Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.	Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction.	WBPaper00040560:hpl-2_embryo_downregulated
	Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_daf-16
	Genes found to be regulated in N2 by resveratrol treatment with p < 0.01.	N.A.	WBPaper00026929:Resveratrol_regulated_N2
	Transcripts expressed in male tail, according to RNA tomography.	RNA tomography	WBPaper00055648:male-tail_expressed
Bacteria infection: Photorhabdus luminescens	Genes with decreased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_downregulated_RNAseq
Bacteria infection: Serratia marcescens	Genes with decreased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_downregulated_RNAseq
Bacteria infection: Enterococcus faecalis	Genes with decreased 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_downregulated_RNAseq
	Transcripts uniquely expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_enriched
	Genes with differential expression under 0.5mg/l Diazinon (DZN) treatment at 24 centigrade.	To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade.	WBPaper00040210:Diazinon_24C_regulated
	mRNAs that showed decreased expression after 100ug\/L microcystin-LR exposure.	Differentially expressed genes (DEGs) were identified with a random-variance t-test and an SAM (Significance Analysis of Microarrays) test. Gene expression differences were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3 and the fold-change compared to control at least <= 0.67 or >= 1.5.	WBPaper00045807:microcystin-LR_downregulated
	Transcripts that showed significantly increased expression in ceh-14(ch3) comparing to in N2 at L4 larva stage.	DESeq2(1.36.0), fold change > 2, FDR < 0.05.	WBPaper00066004:ceh-14(ch3)_upregulated

6 Expression Patterns

• Primary Identifier: Expr11400
• Reporter Gene: [pnlp-22::GFP] transcriptional fusion and [Pnlp-22::nlp-22:gfp; Pmyo-2::mCherry; unc-119(+)] translational fusion. The transcriptional reporter for nlp-22 (Pnlp-22:Intron:gfp) was made by fusing the promoter of nlp-22 (-450 to +3) to the coding sequence of GFP, amplified from pPD95.75 and replacing one of the synthetic introns of gfp with the intron of nlp-22( +85 to +481).
• Pattern: NLP-22 is selectively expressed, in a single-neuron pair, the RIAs. NLP-22 is predicted to be secreted. When GFP was fused to the C-terminus of the NLP-22 preproprotein, green fluorescence was observed in several neurons in the head as well as in the ventral nerve cord, supporting the notion that NLP-22 is a secreted peptide. mRNA abundance of the gene nlp-22 was higher in the L4 stage than in lethargus. Using qRT-PCR, we confirmed that nlp-22 mRNA expression cycles with a constant phase relationship to lethargus. nlp-22 mRNA peaked midway through the active larval stages, decreased during each lethargus stage, and was absent in adults.

• Primary Identifier: Expr1024260
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1157600
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1715
• Remark: Transgenic lines were generated by coinjection of the nlp::gfp construct (5070 ng/ul) and lin-15 rescue construct (pJM24,100 ng/ul) into lin-15(n765ts) animals. At least two independent transgenic lines were analyzed for each nlp gene; 510 animals were scored per line. 1,1'-Dioctadecyl-3,3,3',3 -tetramethylindodicarbocyanine perchlorate (Molecular Probes) was used to stain amphid and phasmid neurons to facilitate identification.
• Pattern: No expression observed.

• Primary Identifier: Expr2032527
• 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: Expr2014287
• 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).

4 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003760
• Start: 2341359
• End: 2342089
• Strand: -1

4 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 731

1 Sequence Ontology Term