WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219720 Gene Name  linc-2
Sequence Name  ? R144.17 Organism  Caenorhabditis elegans
Automated Description  Enriched in AFD and head mesodermal cell based on RNA-seq studies. Is affected by several genes including cua-1; etr-1; and spr-1 based on RNA-seq studies. Is affected by Tunicamycin based on RNA-seq studies. Biotype  SO:0001641
Genetic Position  III :-2.21468± Length (nt)  ? 127
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219720

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:R144.17 R144.17 127   III: 5024881-5025007
 

Other

0 CDSs

0 RNAi Result

7 Allele

Public Name
gk964504
gk964503
WBVar01408558
WBVar01644445
gk331362
gk823294
WBVar01995128

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219720 5024881 5025007 1

2 Data Sets

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

0 Downstream Intergenic Region

18 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:sin-3(tm1276)_upregulated
  Transcripts that showed signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. FDR < 0.05, fold change > 2 WBPaper00067368:pabp-2(RNAi)_upregulated_N2
  Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. DESeq2, fold change > 2, adjusted p-value < 0.01 WBPaper00058598:sin-3(tm1276)_downregulated
  Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. Log2 Fold change > 2 or <-1, p-value < 0.05. WBPaper00053599:female_vs_male_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 set-2(zr2012) animals at embryo stage, comparing to in N2 animals. DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. WBPaper00060014:set-2(zr2012)_upregulated
  Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:spr-1(ok2144)_upregulated
  Transcripts that showed significantly lower expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). DESeq2, fold change >= 2, FDR <= 0.01. WBPaper00056826:hmc_biased
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:AFD_enriched
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 that showed significantly increased expression in let-418(n3536) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:let-418(n3536)_upregulated
  Transcripts that showed signifcantly decreased expression in ubr-5(miy31);pabp-2(RNAi) comparing to in pabp-2(RNAi) animals. FDR < 0.05, fold change > 2 WBPaper00067368:ubr-5(miy31)_downregulated_pabp-2(RNAi)
  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 decreased expression in adr-1(tm668) comparing to in N2 at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066511:adr-1(tm668)_downregulated
  Transcripts that showed significantly decreased expression in cua-1(knu790) comparing to in N2. FDR < 0.05 and fold change > 2. WBPaper00066160:cua-1(knu790)_downregulated
  ncRNAs with significantly increased expression in cep-1(gk138) than in N2 under normal conditions, according to RNAseq. ncRNAs with more than 2 fold difference in expression are considered differentially expressed WBPaper00045380:cep-1(gk138)_upregulated_normal
  Transcripts that showed significantly increased expression after 4 hours of treatment by 50 ub per ml tunicamycin at L4 larva stage in wild type animals. Fold change > 1.75 WBPaper00045971:tunicamycin_upregulated_control

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00219720 5024881 5025007 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
127

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_5024065..5024880   816 III: 5024065-5024880 Caenorhabditis elegans