WormMine: Gene WBGene00004378

• WormBase Gene ID: WBGene00004378
• Gene Name: rme-8
• Sequence Name: F18C12.2
• Brief Description: rme-8 encodes a DNA J domain-containing protein; rme-8 is required for both receptor-mediated endocytosis and pinocytosis (fluid-phase endocytosis) in coelomocytes and other cell types; specifically, RME-8 binds SNX-1, a component of the core retromer complex, in vitro and, along with SNX-1 and HSP-1, regulates endosomal clathrin and retromer-mediated endosome to Golgi retrograde transport; rme-8 is also generally required for development and viability; RME-8 is expressed in several different tissues, including the intestine, coelomocytes, and hypodermis, and abundant on endosomes, localizing to early, recycling, and late endosomes; RME-8 and SNX-1 co-localize on endosomes.
• Organism: Caenorhabditis elegans
• Automated Description: Enables identical protein binding activity. Involved in several processes, including mechanosensory behavior; positive regulation of nematode male tail tip morphogenesis; and vesicle-mediated transport. Located in endosome. Expressed in coelomocyte; hypodermal cell; muscle cell; oocyte; and uterus. Human ortholog(s) of this gene implicated in Parkinson's disease. Is an ortholog of human DNAJC13 (DnaJ heat shock protein family (Hsp40) member C13).
• Biotype: SO:0001217
• Genetic Position: I :2.48758 ±0.017097
• Length (nt): 12035

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004378

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F18C12.2b.1	F18C12.2b.1	7363	I: 8083576-8095610
Transcript:F18C12.2a.1	F18C12.2a.1	7378	I: 8083583-8095608

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F18C12.2b	F18C12.2b	6816	I: 8083630-8083700
CDS:F18C12.2a	F18C12.2a	6840	I: 8083630-8083700

23 RNAi Result

• WBRNAi00000028
• WBRNAi00077293
• WBRNAi00025133
• WBRNAi00025134
• WBRNAi00077306
• WBRNAi00106346
• WBRNAi00066840
• WBRNAi00085601
• WBRNAi00003407
• WBRNAi00025136
• WBRNAi00071845
• WBRNAi00064958
• WBRNAi00044931
• WBRNAi00081350
• WBRNAi00087682
• WBRNAi00071029
• WBRNAi00001898
• WBRNAi00070918
• WBRNAi00114600
• WBRNAi00025135
• WBRNAi00025137
• WBRNAi00110571
• WBRNAi00102048

120 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• otn9342
• gk962622
• WBVar01432246
• WBVar01432245
• snx3786
• ar486
• gk337415
• gk919549
• WBVar01420667
• gk331266
• gk857817
• WBVar01782772
• WBVar01911832
• gk862376
• gk395399
• gk588557
• gk636007
• gk350659
• gk873838
• gk538431
• gk344930
• gk344931
• gk718272
• gk405386
• gk323166

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004378
• Start: 8083576
• End: 8095610
• 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_chrI_8095611..8095739
• Length (nt): 129
• Chromosome Location: I: 8095611-8095739
• Organism: Caenorhabditis elegans

127 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_developing
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
Bacteria: B.thuringiensis	Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
	Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria.	Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.	WBPaper00065732:Cry5Ba_upregulated_N2
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (FLT) starting at L1 lava stage.	DESeq	WBPaper00053302:alovudine_24h_regulated
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated
	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:AVA-neuron_L1-larva_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:GABAergic-motor-neurons_L1-larva_expressed

8 Expression Patterns

• Primary Identifier: Expr4750
• Subcellular Localization: RME-8::GFP localized near the apical surface in embryonic intestinal cells.

• Primary Identifier: Expr2399
• Remark: Similar expression patterns and subcellular localizations were observed by both antibody staining and RME-8::GFP reporter expression, except that RME-8::GFP was not expressed in the germline, most likely because of a general silencing of transgenes in the C. elegans germline. These observations suggest that this RME-8::GFP fusion is an accurate reporter of endogenous RME-8 expression and subcellular localization.
• Pattern: RME-8 expression in other cell types was examined by whole mount immunostaining. RME-8 is expressed in almost all cells. RME-8 was highly expressed in the lateral hypodermis, muscle, and the developing germ cells in larvae. RME-8 staining was extremely abundant in the developing uterus of L4 worms. RME-8 expression was examined in dissected adult ovaries by immunofluorescence. RME-8 was highly expressed in oocytes.
• Subcellular Localization: Immunofluorescence: RME-8 staining was concentrated in the cortex of oocytes beneath the plasma membrane. At high magnification, RME-8 staining was localized to punctate structures that were 0.20.4 um in diameter. RME-8 staining in the rme-8(b1023) missense mutants was diminished and mostly diffuse in the oocyte cytoplasm with little localization to cortical punctate structures . Similar mislocalization was also observed in other cell types in the mutant worms. Similar expression patterns of RME-8 in somatic cells were observed with the RME-8::GFP reporter. In most cells, RME-8::GFP-labeled small puncta with sizes similar to the puncta stained with RME-8 antibodies. In live coelomocytes, RME-8::GFP labeled the limiting membranes of larger vesicles, with diameters ranging from 0.5 to 4.0 um. By serial thin-section confocal microscopy, these vesicles appeared to be round regardless of their sizes, but after fixation, these RME-8::GFP-labeled vesicles appeared smaller, as if they had collapsed. Whole mount immunostaining: in all the cells examined, RME-8 staining was localized to cytoplasmic punctate structures similar to those seen in the oocytes.

• Primary Identifier: Expr1032190
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr11494
• Subcellular Localization: RME-8::GFP is localized in small round structures (which we interpret as vesicles) that form at the apical surfaces of the detaching tail tip cells and are concentrated at the cell surfaces during retraction.

• Primary Identifier: Expr2015378
• 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: Expr2033612
• 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: Expr1148897
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1016791
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

20 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004378
• Start: 8083576
• End: 8095610
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12035

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00005824
• WBStrain00005826

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_8081672..8083575
• Length (nt): 1904
• Chromosome Location: I: 8081672-8083575
• Organism: Caenorhabditis elegans