WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00077465 Gene Name  rrn-4.2
Sequence Name  ? ZK218.16 Brief Description  rrn-4.2 (ZK218.16) encodes a 5s ribosomal RNA (rRNA), a component of the large ribosomal subunit and synthesised by RNA polymerase III; As this forms a major component of the ribosome, it is essential for all protein synthesis in the cell.
Organism  Caenorhabditis elegans Automated Description  Enriched in ut4 based on single-cell RNA-seq studies. Is affected by several genes including swsn-2.2; etr-1; and hpl-2 based on RNA-seq studies.
Biotype  SO:0001637 Genetic Position  V :12.8004±
Length (nt)  ? 119
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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
WBGene00077465

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:ZK218.16 ZK218.16 119   V: 17115903-17116021
 

Other

0 CDSs

0 RNAi Result

22 Allele

Public Name
gk963271
gk963489
gk963304
WBVar02123303
gk964050
gk963587
gk963588
WBVar02124497
WBVar02124059
WBVar02124270
WBVar02122864
gk964305
WBVar02121796
WBVar02123142
WBVar02124430
WBVar02122255
gk962630
tm1324
ttTi1182
ttTi2609
ttTi2610
WBVar00273063

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00077465 17115903 17116021 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_chrV_17116022..17116335   314 V: 17116022-17116335 Caenorhabditis elegans

12 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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 depleted in purified oocyte P bodies comparing to in the whole animal. DESeq2, FDR < 0.05, fold change > 2. WBPaper00065975:P-body_vs_WholeAnimal_depleted
  Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. WBPaper00054493:hpl-2(tm1489)_downregulated
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
  Transcripts that showed significantly increased expression in swsn-2.2(RNAi) comparing to in control animals. Cuffdiff was used to identify differentially expressed genes. WBPaper00049018:swsn-2.2(RNAi)_upregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased 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_upregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly decreased 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_downregulated
  Transcripts of noncoding genes that showed significantly increased 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_enriched_noncoding-RNA
  Transcripts that showed significantly increased expression in ham-3(RNAi) comparing to in control animals. Cuffdiff was used to identify differentially expressed genes. WBPaper00049018:ham-3(RNAi)_upregulated
  Transcripts interacting with LAG-1 at L4 larva stage in germline ChIP-Seq analysis. edgeR fold change >= 2, FDR <= 0.05. WBPaper00059440:LAG-1_interacting_germline
  Transcripts interacting with LAG-1 at L4 larva stage in whole animal ChIP-Seq analysis. edgeR fold change >= 2, FDR <= 0.05. WBPaper00059440:LAG-1_interacting_WholeAnimal
  Single-cell RNA-Seq cell group 13_1 expressed in epithelium. scVI 0.6.0 WBPaper00065841:13_1

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00077465 17115903 17116021 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
119

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_chrV_17115630..17115902   273 V: 17115630-17115902 Caenorhabditis elegans