WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00271567 Gene Name  T28F4.8
Sequence Name  ? T28F4.8 Organism  Caenorhabditis elegans
Automated Description  Enriched in ADFL based on single-cell RNA-seq studies. Is affected by raga-1; csr-1; and pals-17 based on RNA-seq studies. Is affected by resveratrol based on microarray studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 535
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00271567

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T28F4.8.1 T28F4.8.1 451   I: 7489894-7490428
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:T28F4.8 T28F4.8 192   I: 7489894-7490008

2 RNAi Result

WormBase ID
WBRNAi00004347
WBRNAi00036104

7 Allele

Public Name
gk962858
gk962706
gk963902
gk418465
gk920609
gk520780
gk115081

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00271567 7489894 7490428 1

2 Data Sets

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

0 Downstream Intergenic Region

21 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Single-cell RNA-Seq cell group 84_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:84_0
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly decreased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_downregulated_N2
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly decreased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_downregulated_skpo-1(ok1640)
  Transcripts that showed significantly decreased expression in N2 day 4 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day4_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day5_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day7_vs_Day1_downregulated_Illumina
  Transcripts that showed significantly decreased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. DESeq fold change > 2, FDR < 0.05. WBPaper00067499:Day10_vs_Day1_downregulated_Illumina
Bacteria ibfection: Pseudomonas aeruginosa PA14 Transcripts that showed significantly decreased expression in osm-3(p802) animals exposed to PA14, comparing to in osm-3(p802) animals grown on OP50. fold change > 2, FDR < 0.05 WBPaper00066858:PA14_downregulated_osm-3(p802)
  Genome-wide analysis of developmental and sex-regulated gene expression profile. self-organizing map cgc4489_group_12
Bacteria infection: N.ausubeli Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:JU1400_N.ausubeli_regulated
  Transcripts that showed significantly decreased expression in pals-17(syb3980) comparing to in N2 animals at young adult stage. Differential expression analyses were performed using limma-voom in Galaxy, adj p <= 0.05, logFC > 2 WBPaper00065984:pals-17(syb3980)_downregulated
  Transcripts that showed significantly increased expression in sma-9(ok1628) comparing to in N2. EdgeR fold change > 2, FDR < 0.05. WBPaper00067781:sma-9(ok1628)_upregulated
  Transcripts that showed significantly decreased expression in csr-1a(tor159) comparing to in N2 at 25C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_downregulated_25C
  Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. N.A. WBPaper00026929:Resveratrol_regulated_daf-16
  Proteins detected in intestine from single-worm studies. N.A. WBPaper00066880:intestine_expressed
Bacteria infection: N.ausubeli Transcripts that showed significantly altered expression in C. elegans wild isolate strain N2 infected by N.ausubeli microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:N2_N.ausubeli_regulated
Bacteria infection: Vibrio cholerae A1552, 8 hours at L4 larva stage. Transcripts that showed significantly decreased expression in shk-1(yum1003) animals infected by bacteria strain Vibrio cholerae A1552. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:V.cholerae_downregulated_shk-1(yum1003)
  Transcripts that showed significantly increased expression in VC222[raga-1(ok386)] comparing to in N2 at mid-L4 larva stage. DESeq2, FDR < 0.01, fold change > 2. WBPaper00057196:raga-1(ok386)_upregulated)
Bacteria infection: Vibrio cholerae A1552, 8 hours at L4 larva stage. Transcripts that showed significantly decreased expression in N2 animals infected by bacteria strain Vibrio cholerae A1552. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:V.cholerae_downregulated_N2
Bacteria diet: Comamonas aquatica DA1887 vs. E. coli OP50 Transcripts that showed significantly decreased expression in N2 1-day-old adult animals fed with Comamonas aquatica strain DA1887, comparing to in N2 adult animals fed with E. coli OP50. edgeR, fold change > 2, p-value < 0.05. WBPaper00067248:C.aquatica_downregulated_adult
Bacteria infection: N.ferruginous Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage. FDR < 0.01 WBPaper00065086:JU1400_N.ferruginous_regulated

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2024852 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).  
    Expr2006635 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
WBGene00271567 7489894 7490428 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
535

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

0 Upstream Intergenic Region