WormMine: Gene WBGene00007352

• WormBase Gene ID: WBGene00007352
• Gene Name: cdc-48.1
• Sequence Name: C06A1.1
• Brief Description: cdc-48.1 encodes a type II AAA ATPase, homologous to yeast Cdc48 and mammalian p97/VCP, that functions as a ubiquitin-selective chaperone; cdc-48.1 acts redundantly with cdc-48.2 and in conjunction with ufd-1 and npl-4 in endoplasmic reticulum-associated protein degradation (ERAD); in addition, CDC-48.1, UFD-2 and chn-1 function together to regulate myosin assembly and muscle formation via the UNC-45 myosin chaperone, and CDC-48.1 and ATX-3 function together in determination of adult lifespan via interaction with the DAF-2-mediated insulin signaling pathway; cdc-48.1 and cdc-48.2 also interact to provide an essential function during embryonic development; CDC-48.1 exhibits ATPase activity in vitro, and in yeast two-hybrid assays, CDC-48.1 interacts with itself, CDC-48.2, ATX-3, UFD-1, and UBXN-1, consistent with studies in yeast and mammals that show CDC48 homologs form homohexameric complexes that interact with adaptor proteins homologous to UFD-1 and UBXN-1.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ATP hydrolysis activity and identical protein binding activity. Involved in several processes, including ERAD pathway; determination of adult lifespan; and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in nucleoplasm and perinuclear region of cytoplasm. Part of VCP-NPL4-UFD1 AAA ATPase complex. Expressed in several structures, including body wall musculature; germ line; and gonad. Used to study amyotrophic lateral sclerosis. Human ortholog(s) of this gene implicated in several diseases, including Charcot-Marie-Tooth disease type 2Y; frontotemporal dementia and/or amyotrophic lateral sclerosis 6; and inclusion body myopathy with early-onset Paget disease of bone with or without frontotemporal dementia 1. Is an ortholog of human VCP (valosin containing protein).
• Biotype: SO:0001217
• Genetic Position: II :3.08111 ±0.00418
• Length (nt): 3372

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00007352

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C06A1.1.1	C06A1.1.1	2744	II: 10560036-10563407

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C06A1.1	C06A1.1	2430	II: 10560333-10560468

40 RNAi Result

• WBRNAi00095487
• WBRNAi00039806
• WBRNAi00066744
• WBRNAi00078676
• WBRNAi00093155
• WBRNAi00094121
• WBRNAi00093395
• WBRNAi00093481
• WBRNAi00093505
• WBRNAi00064984
• WBRNAi00093396
• WBRNAi00093473
• WBRNAi00093523
• WBRNAi00075641
• WBRNAi00061374
• WBRNAi00093145
• WBRNAi00093142
• WBRNAi00093209
• WBRNAi00093213
• WBRNAi00093489
• WBRNAi00093497
• WBRNAi00113069
• WBRNAi00113298
• WBRNAi00076087
• WBRNAi00028525
• WBRNAi00000151
• WBRNAi00075639
• WBRNAi00078151
• WBRNAi00061375
• WBRNAi00079984

40 Allele

• gk963801
• gk963053
• gk962682
• gk964100
• gk961350
• tm544
• WBVar00175190
• gk153166
• WBVar00105484
• gk916311
• gk153168
• gk153167
• gk153164
• gk153165
• WBVar00175189
• gk956507
• gk320734
• gk555525
• gk931478
• gk798532
• gk932516
• gk544346
• gk937913
• gk794605
• gk893133
• gk779615
• gk609626
• gk846026
• gk507859
• gk753744

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00007352
• Start: 10560036
• End: 10563407
• 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_10557645..10560035
• Length (nt): 2391
• Chromosome Location: II: 10557645-10560035
• Organism: Caenorhabditis elegans

168 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 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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	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
	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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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 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 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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
	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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point on the non pathogenic strain Bt407 compared to E. coli OP50.	Cuffdiff	WBPaper00060358:B.thuringiensis_non-pathogen_regulated_elt-2(RNAi)
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
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated

15 Expression Patterns

• Primary Identifier: Expr4372
• Pattern: CDC-48.1 was expressed ubiquitously during all developmental stages and the level of cdc-48.1 mRNA increased as worms grow.

• Primary Identifier: Expr4370
• Remark: Note that genes on extrachromosomal arrays in transgenic worms are usually not expressed in gonads because of strong silencing effects.
• Pattern: CDC-48.1::GFP was expressed from embryos through to adult worms and predominantly in spermatocytes at L4 larvae stage, and in spermathecae at adult stage.

• Primary Identifier: Expr4368
• Pattern: Exclusively localized in germ cells. No significant signals were detected when sense probes were used.

• Primary Identifier: Expr4366
• Pattern: Highly transcribed at embryonic stage. Although the level of mRNA decreased at L1 larva stage, thereafter, mRNA increased as worms grow. The amount of cdc-48.1 mRNA was about twofold of that of cdc-48.2 mRNA in adults.

• Primary Identifier: Expr4569
• Pattern: CDC-48.1::GFP and CDC-48.2::GFP fusion proteins displayed similar expression in body-wall muscle cells.

• Primary Identifier: Expr2009786
• 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: Expr1033168
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8953
• Remark: Picture: Fig. 1A, Fig. S1, and Movie S1.
• Subcellular Localization: YFP::CDC-48 accumulated in the nucleus after its reformation.

• Primary Identifier: Expr10162
• Pattern: The expression pattern of FLAG::CDC-48.1 was observed in the early L4 stage, during which sperm are produced. FLAG::CDC- 48.1 was expressed from the bend to the proximal gonad, although it was predominantly expressed at the pachytene stage and in spermatocytes. FLAG::CDC-48.1 was not localized in sperm. It should also be noted that FLAG::CDC-48.1 was expressed in the distal tip cell in the mitotic region.

• Primary Identifier: Expr15942
• Pattern: CDC-48.1∷GFP was ubiquitously expressed, predominantly in spermathecae at adult stage and in embryos.

• Primary Identifier: Expr2980
• Pattern: In adult worms C06A1.1 was expressed ubiquitously.

• Primary Identifier: Expr2028026
• 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: Expr1024297
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr10161
• Subcellular Localization: FLAG::CDC-48.1 was expressed in meiotic germ cells at the late pachytene, diplotene, and diakinesis stages and was localized in both the nucleoplasm and cytoplasm. CDC-48.1 was predominantly localized in the nucleus, but is not tightly incorporated inside the chromatids in late diakinesis (maturated oocytes).

• Primary Identifier: Expr1143887
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

39 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00007352
• Start: 10560036
• End: 10563407
• Strand: -1

39 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3372

1 Sequence Ontology Term