WormMine: Gene WBGene00219649

• WormBase Gene ID: WBGene00219649
• Gene Name: linc-55
• Sequence Name: C10F3.18
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in muscle cell.
• Biotype: SO:0001641
• Genetic Position: V :-0.465312±
• Length (nt): 281

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00219649

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C10F3.18	C10F3.18	281	V: 5994260-5994540

Other

0 CDSs

0 RNAi Result

12 Allele

• gk963301
• gk963591
• gk963553
• gk963042
• gk963041
• gk964259
• gk964351
• gk963850
• WBVar01588349
• gk236341
• gk236340
• gk500759

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00219649
• Start: 5994260
• End: 5994540
• Strand: -1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_5991673..5994259
• Length (nt): 2587
• Chromosome Location: V: 5991673-5994259
• Organism: Caenorhabditis elegans

18 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
	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 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 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 hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in sams-3(RNAi) comparing to N2 animals injected with empty vector.	Deseq FDR < 0.01, fold change > 2.	WBPaper00065005:sams-3(RNAi)_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
	Transcripts that showed significantly increased expression in zcIs13; twnEx320[Punc-119-ds-fzo-1] comparing to in zcIs13[Phsp-6-gfp] animals.	Fold change >= 1.5.	WBPaper00061409:neuronal-fzo-1(RNAi)_upregulated
	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
	Transcripts that showed significantly decreased expression in nfki-1(cer1) animals at L4 larva stage, comparing to in N2 animals.	Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01.	WBPaper00060445:nfki-1(cer1)_downregulated_L4
	Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector.	Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant.	WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
	Transcripts that were enriched in muscle in young adult animals, according to trans-splicing-based RNA tagging (SRT) and RNAseq.	DESeq and Benjamini-Hochberg adjusted p-values were used.	WBPaper00050053:muscle_enriched_Day4
	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
	Single-cell RNA-Seq cell group 68_1 expressed in epithelium.	scVI 0.6.0	WBPaper00065841:68_1
Bacteria: C.neoformans strain H99	Transcripts that showed significantly increased expression after infection by C. neoformans H99.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:C.neoformans_H99_upregulated
	Transcripts that showed significantly decreased expression in ikb-1(nr2027) animals at L4 larva stage, comparing to in N2 animals.	Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01.	WBPaper00060445:ikb-1(nr2027)_downregulated_L4
	Single-cell RNA-Seq cell group 68_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:68_0
	Transcripts that were enriched in muscle in day 12 animals, according to trans-splicing-based RNA tagging (SRT) and RNAseq.	DESeq and Benjamini-Hochberg adjusted p-values were used.	WBPaper00050053:muscle_enriched_Day12

1 Expression Patterns

• Primary Identifier: Expr13250
• Remark: Construct details not specified.
• Pattern: Further validation by fluorescent reporter showed that the three annotated lincRNAs detected by our muscle profiling (linc-5, linc-55 and linc-57) were muscle-enriched.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00219649
• Start: 5994260
• End: 5994540
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 281

1 Sequence Ontology Term