WormMine: Gene WBGene00020091

• WormBase Gene ID: WBGene00020091
• Gene Name: rnp-8
• Sequence Name: R119.7
• Organism: Caenorhabditis elegans
• Automated Description: Enables enzyme binding activity; poly(G) binding activity; and polynucleotide adenylyltransferase activator activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Located in protein-containing complex. Expressed in germ line and oocyte.
• Biotype: SO:0001217
• Genetic Position: I :-19.0609 ±0.002776
• Length (nt): 4070

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00020091

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R119.7a.1	R119.7a.1	2400	I: 364510-368579
Transcript:R119.7b.1	R119.7b.1	2156	I: 364517-368295
Transcript:R119.7b.2	R119.7b.2	1940	I: 364734-368287
Transcript:R119.7b.3	R119.7b.3	1105	I: 366643-368283

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R119.7a	R119.7a	1752	I: 364519-364679
CDS:R119.7b	R119.7b	555	I: 366850-367209

10 RNAi Result

• WBRNAi00001039
• WBRNAi00007259
• WBRNAi00051755
• WBRNAi00102116
• WBRNAi00004076
• WBRNAi00008174
• WBRNAi00069466
• WBRNAi00022540
• WBRNAi00022692
• WBRNAi00034845

87 Allele

• gk963902
• gk963701
• q784
• WBVar00245946
• WBVar01711306
• otn9
• WBVar02028066
• WBVar02071511
• tm2435
• WBVar00147268
• WBVar00147267
• WBVar00147266
• WBVar00147265
• WBVar00147263
• WBVar00147262
• WBVar00147261
• WBVar00147269
• WBVar00147270
• WBVar01661491
• WBVar01403300
• WBVar01403311
• gk100747
• gk100751
• gk100750
• gk100749
• gk100748
• gk100744
• gk100743
• gk100742
• gk100741

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00020091
• Start: 364510
• End: 368579
• 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

158 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 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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	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 day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	Transcripts that showed significantly increased expression in isp-1(qm150) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:isp-1(qm150)_upregulated
	Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:nuo-6(qm200)_upregulated
	Transcripts that showed significantly increased expression in mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4318)_upregulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated

10 Expression Patterns

• Primary Identifier: Expr8615
• Remark: Picture: Figure 3B, 3C.
• Pattern: The rnp-8L and/or rnp-8S mRNAs were present in embryos, were rare in L1 and L2 larvae, and were abundant in later-stage larvae and in adults; moreover, both transcripts were greatly diminished in mutants lacking a germline .

• Primary Identifier: Expr8617
• Remark: Picture: 3G.
• Pattern: anti-RNP-8 recognized protein in wild-type, but not in mutant germlines. On western blots, RNP-8L was barely detectable in embryos, increasingly detectable in larvae, and abundant in adult hermaphrodites. Moreover, RNP-8L protein was absent from mutants with no germline.

• Primary Identifier: Expr8616
• Remark: Picture: Figure 3D to 3F.
• Pattern: rnp-8L was detectable, but low, in the mitotic region and transition zone, which contains early meiotic prophase germ cells, and it was abundant in the pachytene region and developing oocytes, as assessed with an antisense-strand probe, but not with a sense-strand control probe. The antisense-strand probe was directed against sequence within the q784 deletion and, as a result, did not hybridize to RNA in rnp-8(q784) germlines.

• Primary Identifier: Expr8618
• Remark: Picture: 3H to 3M.
• Subcellular Localization: Immunostaining revealed that RNP-8L protein is predominantly cytoplasmic, colocalizes with the PGL-1 germ granule marker, and is abundant in the proximal pachytene region and developing oocytes. RNP-8L was detectable in males, but much less abundant than in hermaphrodites. As assessed by immunocytochemistry of male germlines, RNP-8L was limited to the mitotic region, transition zone, and distal pachytene region; it was absent from proximal pachytene cells, spermatocytes, and mature sperm. RNP-8L was similar in both hermaphrodite and male distal germlines, both with respect to its low level and its distribution in cytoplasmic granules. As assessed by western blot, RNP-8L was also low in mutant adult hermaphrodites that made only sperm and no oocytes. Abundant RNP-8L seem to be associated with oogenesis.

• Primary Identifier: Expr1038730
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1155420
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr11617
• Pattern: RNP-8 protein was abundant in most oocytes but disappeared from the last oocyte, which had been triggered to mature just before fertilization.

• Primary Identifier: Expr2015397
• 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: Expr1028515
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2033631
• 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).

13 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00020091
• Start: 364510
• End: 368579
• Strand: 1

13 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	RNP-8-associated transcripts, based on microarray experiments.	Two-class unpaired SAM (median-centered).	WBPaper00037611:RNP-8-associated

1 Sequence

• Length: 4070

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00022645
• WBStrain00022641

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_363902..364509
• Length (nt): 608
• Chromosome Location: I: 363902-364509
• Organism: Caenorhabditis elegans