WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00206533 Gene Name  C30A5.16
Sequence Name  ? C30A5.16 Organism  Caenorhabditis elegans
Automated Description  Enriched in ABarppaapp; ABarpppapp; and neurons based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including mter-4; etr-1; and zip-3 based on RNA-seq studies. Is affected by Zidovudine and Doxorubicin based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1124
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00206533

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:C30A5.16.1 C30A5.16.1 314   III: 8218219-8219342
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:C30A5.16 C30A5.16 159   III: 8218352-8218391

0 RNAi Result

18 Allele

Public Name
gk964518
gk963887
gk962865
WBVar01541859
ttTi12716
WBVar01628944
gk179753
gk179754
WBVar00065109
WBVar00067813
gk669930
gk866792
gk775980
gk892742
gk439583
gk826414
gk464062
gk327880

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00206533 8218219 8219342 1

2 Data Sets

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

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_8219343..8222225   2883 III: 8219343-8222225 Caenorhabditis elegans

37 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
  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
  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 in exos-8(RNAi) animals. fold change > 2, FDR < 0.05 WBPaper00068292:exos-8(RNAi)_upregulated
  Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. WBPaper00062159:hda-2(ok1479)_upregulated
  Transcipts that showed significantly increased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 25C. DESeq2 v1.31.16, fold change > 2, FDR < 0.05 WBPaper00068082:octr-1(ok371)_upregulated_old_25C
  Transcripts that showed significantly increased expression in zip-3(gk3164) comparing to in N2, after exposed to P. aeruginosa for 18 hours. p < 0.05 WBPaper00056326:zip-3(gk3164)_upregulated_P.aeruginosa-infected
  Transcripts that showed significantly increased expression in the F2 (second generation) of ulp-2(tv380) gonad comparing to in N2 gonad. DESeq2, p < 0.05 WBPaper00067685:ulp-2(tv380)_upregulated_F2-gonad
Feeding for 4 hours after L1 arrest. Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 rsks-1(ok1255) animals, comparing to animals continue to starve. DESeq2, FDR < 0.05, fold change > 2. WBPaper00067518:food_downregulated_rsks-1(ok1255)
  Transcripts that showed significantly increased expression in diploid N2 animals after exposure to 5 uM doxorubicin 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:Doxorubicin_upregulated_diploid
  Transcripts that showed significantly decreased expression in mter-4(syb3662 syb3403) comparing to in N2. DESeq2, fold change > 2, FDR < 0.05. WBPaper00061995:mter-4(syb3662syb3403)_downregulated
  Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. DESeq2. FDR < 0.05. WBPaper00060459:bcat-1(RNAi)_upregulated
  Transcripts that showed significantly increased 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)_upregulated
  Transcripts that showed significantly altered expression after 24 hour exposure to zidovudine (AZT) starting at L1 lava stage. DESeq WBPaper00053302:zidovudine_72h_regulated
  Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. Fold change > 2, p-value < 0.05. WBPaper00060661:sensory-neuron_enriched
  Top 300 transcripts enriched in FLPL, FLPR 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:FLP
  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 showed significantly increased expression in PVD neurons isolated from TV22833 wyIs840(ser2prom3::daf-12a(rh273)::gfpnovo2, Pmyo-2::gfp); wyIs592(ser2prom3::myr-gfp), comparing to in PVD neurons isolated from animals that only expressed wyIs592. Cufflinks 2.2.1 WBPaper00058678:DAF-12_upregulated_PVD
  Top 300 transcripts enriched in ABarppaapp, ABarpppapp 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:Neuroblast_ALM_BDU
  Top 300 transcripts enriched in AIML, AIMR 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:AIM
  Transcripts that showed significantly decreased 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)_downregulated
  Single-cell RNA-Seq cell group 65_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:65_0
  Single-cell RNA-Seq cell group 28_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:28_0
  Top 300 transcripts enriched in IL2L, IL2R, IL2DL, IL2DR, IL2VL, IL2VR 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:IL2
  Top 300 transcripts enriched in AIZL, AIZR 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:AIZ
  Single-cell RNA-Seq cell group 53_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:53_0
  Transcripts enriched in HSN according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:HSN_enriched
  Single-cell RNA-Seq cell group 39_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:39_0
  Transcripts enriched in PVR according to single cell RNAseq. Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. WBPaper00061651:PVR_enriched
  Single-cell RNA-Seq cell group 55_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:55_0

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2001239 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).  
    Expr1145539 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2019461 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
WBGene00206533 8218219 8219342 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1124

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_8216571..8218218   1648 III: 8216571-8218218 Caenorhabditis elegans