WormMine: Gene WBGene00219721

• WormBase Gene ID: WBGene00219721
• Gene Name: linc-104
• Sequence Name: T01A4.7
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in GLR; neurons; and spermathecal-uterine valve cell based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including etr-1; spr-5; and unc-39 based on RNA-seq studies.
• Biotype: SO:0001641
• Genetic Position: I :-1.27738±
• Length (nt): 339

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00219721

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T01A4.7	T01A4.7	287	I: 4467346-4467684

Other

0 CDSs

0 RNAi Result

15 Allele

• gk962706
• gk963902
• gk964159
• gk964070
• WBVar00245979
• WBVar00245980
• WBVar01282127
• WBVar01282125
• WBVar02039646
• tm8351
• WBVar01846403
• gk639586
• WBVar00153049
• WBVar00153047
• WBVar00153048

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00219721
• Start: 4467346
• End: 4467684
• Strand: -1

2 Data Sets

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

0 Downstream Intergenic Region

18 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
	Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing.	DESeq2, fold change > 2,, p-value < 0.01	WBPaper00055334:DLC-1_interacting
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure.	Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.	DESeq2, FDR < 0.05	WBPaper00056868:P.aeruginosa_upregulated_smallRNA
	Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_upregulated
	Genes regulated by unc-39(hp701). Authors compared genes enriched in FACS sorted GFP+ cells (RID, ALA, AIY, CAN and a sheath cell) vs. whole animal in WT hpIs202[Pceh-10GFP] (WT enriched sets), and genes enriched in FACS sorted GFP+ cells (ALA, AIY, CAN and a sheath cell) vs. whole animal in unc-39(hp701) hpIs202[Pceh-10GFP] (unc-39 enriched sets) at L2 larva stage. This set of genes are WT enriched but not unc-39 enriched, suggesting they are enriched in RID neurons.	DESeq	WBPaper00050496:unc-39(hp701)_regulated
	Transcripts that showed significantly decreased expression in sams-3(RNAi) comparing to N2 animals injected with empty vector.	Deseq FDR < 0.01, fold change > 2.	WBPaper00065005:sams-3(RNAi)_downregulated
	Transcripts of noncoding genes that showed significantly decreased 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_depleted_noncoding-RNA
	Single-cell RNA-Seq cell group 60_0 expressed in valve.	scVI 0.6.0	WBPaper00065841:60_0
	Transcripts enriched in AVJ according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:AVJ_enriched
	Transcripts that showed significantly decreased expression in spr-5(by101);met-2(n4256) L1 animals comparing to in N2 control.	DeSeq2 (v.2.11.40.2), p < 0.05.	WBPaper00060886:spr-5(by101);met-2(n4256)_downregulated
	Single-cell RNA-Seq cell group 63_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:63_0
	Single-cell RNA-Seq cell group 35_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:35_0
	Genes enriched in RID neurons. Authors compared genes enriched in FACS sorted GFP+ cells (RID, ALA, AIY, CAN and a sheath cell) vs. whole animal in WT hpIs202[Pceh-10GFP] (WT enriched sets), and genes enriched in FACS sorted GFP+ cells (ALA, AIY, CAN and a sheath cell) vs. whole animal in unc-39(hp701) hpIs202[Pceh-10GFP] (unc-39 enriched sets) at L2 larva stage. This set of genes are WT enriched but not unc-39 enriched, suggesting they are enriched in RID neurons.	DESeq	WBPaper00050496:RID_enriched
	Single-cell RNA-Seq cell group 119_0 expressed in mesoderm.	scVI 0.6.0	WBPaper00065841:119_0
	Transcripts enriched in PVN according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:PVN_enriched
	Single-cell RNA-Seq cell group 129_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:129_0
	Transcripts enriched in RID according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:RID_enriched

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00219721
• Start: 4467346
• End: 4467684
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 339

1 Sequence Ontology Term