WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

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; positive regulation of mitotic cell cycle, embryonic; 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)  ? 3377
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Lists
This Gene is in one list:
metrics_list_union (10192)

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00007352

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:C06A1.1.1 C06A1.1.1 2749   II: 10560031-10563407
 

Other

1 CDSs

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

40 RNAi Result

WormBase ID
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

Public Name
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 Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00007352 10560031 10563407 -1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrII_10557645..10560030   2386 II: 10557645-10560030 Caenorhabditis elegans

189 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
  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
  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 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: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to HYS. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:FUR_vs_HYS_upregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly decreased expression after 24 hours of infection by Pseudomonas donghuensis HYS, comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:HYS_vs_OP50_downregulated
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 detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_expressed
  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
Bacteria infection: Staphylococcus aureus Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals colonized by microbiota but not infected by pathogen. DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05. WBPaper00067479:Microbiota-Pathogen_vs_Microbiota_downregulated
  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

16 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr4372 CDC-48.1 was expressed ubiquitously during all developmental stages and the level of cdc-48.1 mRNA increased as worms grow.  
Note that genes on extrachromosomal arrays in transgenic worms are usually not expressed in gonads because of strong silencing effects.   Expr4370 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.  
    Expr4368 Exclusively localized in germ cells. No significant signals were detected when sense probes were used.  
    Expr4366 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.  
    Expr4569 CDC-48.1::GFP and CDC-48.2::GFP fusion proteins displayed similar expression in body-wall muscle cells.  
    Expr2009786 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).  
    Expr1033168 Tiling arrays expression graphs  
Picture: Fig. 1A, Fig. S1, and Movie S1.   Expr8953   YFP::CDC-48 accumulated in the nucleus after its reformation.
    Expr10162 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.  
    Expr15942 CDC-48.1∷GFP was ubiquitously expressed, predominantly in spermathecae at adult stage and in embryos.  
    Expr2980 In adult worms C06A1.1 was expressed ubiquitously.  
    Expr2028026 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).  
    Expr1024297 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr10161   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).
    Expr1143887 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2044763 Translational efficiency and RNA abundance/Ribosome occupancy across early embryonic stages (1-cell to 8-cell). For each developmental stage, translational efficiency was calculated as the ratio between ribosome footprint reads and mRNA abundance after normalization. A detailed description of the experimental methods and analysis can be found in: Shukla Y, Ghatpande V, Hu CF, Dickinson DJ, Cenik C. Landscape and regulation of mRNA translation in the early C. elegans embryo. Cell Rep. 2025 June 24;44(6):115778. doi: 10.1016/j.celrep.2025.115778. PMID: 40450690  

49 GO Annotation

Annotation Extension Qualifier
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7 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00007352 10560031 10563407 -1

49 Ontology Annotations

Annotation Extension Qualifier
  enables
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0 Regulates Expr Cluster

1 Sequence

Length
3377

1 Sequence Ontology Term

Identifier Name Description
gene  

1 Strains

WormBase ID
WBStrain00007563

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrII_10563408..10564111   704 II: 10563408-10564111 Caenorhabditis elegans