WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219293 Gene Name  B0334.20
Sequence Name  ? B0334.20 Organism  Caenorhabditis elegans
Automated Description  Enriched in intestine based on microarray studies. Is affected by several genes including sir-2.1; adr-1; and pals-22 based on RNA-seq and microarray studies. Is affected by resveratrol based on microarray studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 817
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219293

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:B0334.20.1 B0334.20.1 201   II: 11499643-11500459
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:B0334.20 B0334.20 201   II: 11499643-11499783

1 RNAi Result

WormBase ID
WBRNAi00009707

16 Allele

Public Name
gk963801
gk963053
gk962684
gk963539
gk963482
WBVar01851320
WBVar00229640
gk155276
gk155275
gk617766
gk718975
h8914
WBVar01666609
gk876694
gk415946
ttTi13064

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219293 11499643 11500459 -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_chrII_11499626..11499642   17 II: 11499626-11499642 Caenorhabditis elegans

12 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
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)
  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
  Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. N.A. WBPaper00026929:Resveratrol_regulated_daf-16
  Genes enriched in intestine. To identify genes that are significantly enriched by mRNA tagging, we first normalized the total amount of Cy3 and Cy5 signal to each other in each hybridization. We measured the ratio of the signals from the co-immunoprecipitated mRNA (Cy5) to total RNA in the cell extract (Cy3), and calculated the percentile rank for each gene relative to all genes in each hybridization. The mean percentile rank was determined from eight repeats of the mRNA-tagging experiment. Student's t-test was used to determine which genes showed a mean enrichment significantly greater than the median enrichment for all genes (P<0.001). WBPaper00026980:intestine_enriched
Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum Transcripts that showed significantly decreased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. GFold3, logFC < -1 or > 1. WBPaper00066703:L.plantarum-pdxH_downregulated
Fungi: Myzocytiopsis humicola extract Transcripts that showed significantly decreased expression in N2 L4 larva animals after 4 hours of exposure to oomycete Myzocytiopsis humicola extract. Differentially expressed genes as determined by Kallisto and Sleuth (pval < 0.01, qval < 0.1, fold change > 2). WBPaper00065995:M.humicola-extract_downregulated_N2
  Transcripts that showed significantly increased expression in pals-22(jy3) comparing to in N2 animals. limma-voom, fold change > 2, FDR < 0.05 WBPaper00064532:pals-22(jy3)_upregulated
  Transcripts that showed significantly increased expression in pals-25(icb98) comparing to in N2 animals. limma-voom, fold change > 2, FDR < 0.05 WBPaper00064532:pals-25(icb98)_upregulated
  Transcipts that showed significantly increased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 15C. DESeq2 v1.31.16, fold change > 2, FDR < 0.05 WBPaper00068082:octr-1(ok371)_upregulated_old_15C
  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
  Genome-wide analysis of developmental and sex-regulated gene expression profile. self-organizing map cgc4489_group_3
Virus infection: Orsay virus infection at 1-day post L4 adult hermaphrodite for three days. Genes that showed significantly increased expression after infected by 20ul Orsay virus filtrate per 50-mm plate for 3 days starting from 16 hours after L4 larva stage. Differentially regulated genes in any condition were identified by using t test, P < 0.01, and a twofold difference upon infection. WBPaper00053020:OrsayVirus-infection_upregulated_microarray

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1143112 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2000141 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).  
    Expr2018359 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
WBGene00219293 11499643 11500459 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
817

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_chrII_11500460..11508749   8290 II: 11500460-11508749 Caenorhabditis elegans