WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219295 Gene Name  C34C12.12
Sequence Name  ? C34C12.12 Organism  Caenorhabditis elegans
Automated Description  Enriched in ABaraapapaa; ABaraapppaa; and neurons based on single-cell RNA-seq and RNA-seq studies. Is affected by several genes including mut-16; hrde-1; and hpx-2 based on RNA-seq studies. Is affected by four chemicals including metformin; Sirolimus; and Doxycycline based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1067
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219295

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:C34C12.12.1 C34C12.12.1 587   III: 3453194-3454260
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:C34C12.12 C34C12.12 153   III: 3453300-3453332

2 RNAi Result

WormBase ID
WBRNAi00014683
WBRNAi00021206

22 Allele

Public Name
gk962532
gk964281
WBVar01261903
WBVar01541631
WBVar01541632
gk170823
WBVar01408305
WBVar01643888
WBVar01656170
otn2913
WBVar00562707
WBVar01444962
WBVar02074191
WBVar01656169
gk794099
gk740767
gk372694
gk614888
WBVar01566184
gk748004
gk772424
gk385780

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219295 3453194 3454260 1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

26 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. DESEQ2, fold change > 2 and FDR < 0.01. WBPaper00062103:neuron_enriched
  Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. Fold change > 2, FDR < 0.01. WBPaper00065993:glp-1(e2141)_upregulated
  Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Metformin_upregulated
Heat shock: 35C for 1 hour. Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour. The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
  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 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 increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
  Transcripts expressed in vulva. FPKM >= 1. WBPaper00064122:vulva_transcriptome
  Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. WBPaper00061479:hda-1(ne4752)_upregulated
  Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals. DESeq2 v. 1.22.2, adjusted p-value <= 0.05. WBPaper00059605:mut-16(pk710)_upregulated
  Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:eat-2(ad1116)_downregulated
  Transcripts that showed significantly increased 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_upregulated_glp-1(e2141)
Temprature shift to 28C for 24 hours. Transcripts that showed significantly increased 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_upregulated
  Transcripts that showed significantly increased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. edgeR (version 3.24.3), fold change > 4, FDR < 0.01. WBPaper00062456:doxycycline_upregulated_N2_transcript
  Transcripts that showed significantly increased expression in lin-52(n771) comparing to in N2 animals at L1 larva stage. DESeq2 WBPaper00065149:lin-52(n771)_upregulated
moderate static magnetic field Transcripts that showed significantly increased expression after exposure to moderate static magnetic field. N.A. WBPaper00064509:static-magnetic-field_upregulated
  Transcripts the showed altered expression after auxin induced sacy-1 depletion (24 hours of 2mM auxin treatment at 20C starting from young adult hermaphrodite stage). DESeq2 WBPaper00059334:sacy-1(depletion)_regulated
  Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis. N.A. WBPaper00059471:EGL-43_interacting
  Transcripts that showed significantly increased expression in hrde-1(tm1200) in gonads dissected from 1-day old adult animals. Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. WBPaper00061479:hrde-1(tm1200)_upregulated
  Transcripts that showed significantly increased expression in adr-1(tm668) comparing to in N2. DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. WBPaper00055226:adr-1(tm668)_upregulated
  Transcripts that showed significantly increased expression in tetraploid N2 animals after exposure to 5uM cisplatin for 72 hours at 15C from L1 to L4 larve stage. DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. WBPaper00066110:Cisplatin_upregulated_tetraploid
  Top 300 transcripts enriched in ABaraapapaa, ABaraapppaa according to single cell RNAseq. Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. WBPaper00061340:NSM_parent
  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
  Transcripts that showed signicantly increased expression in unc-25(e156) comparing to in N2 animals. DESeq R package (1.18.0), fold change > 2, FDR < 0.05. WBPaper00065734:unc-25(e156)_upregulated
  Transcripts that showed increased expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, and their mRNAs co-purify with SMG-2. edgeR WBPaper00053308:SMG-2_associated_NMD(-)_upregulated_ClassI
  Transcripts that showed significantly decreased expression in hpx-2(dg047) comparing to N2 after animals were exposed to E.Coli OP50 for 16 hours. Cuffcompare and Cuffdiff WBPaper00056090:hpx-2(dg047)_downregulated_E.Coli

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2001378 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).  
    Expr1145858 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2019602 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).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00219295 3453194 3454260 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1067

1 Sequence Ontology Term