WormMine: Gene WBGene00003088

• WormBase Gene ID: WBGene00003088
• Gene Name: lsy-6
• Sequence Name: C32C4.6
• Brief Description: lsy-6 encodes a microRNA and was the first microRNA discovered to have a role in nervous system development in vivo; lsy-6 is involved in the pathway for functional lateralization of the chemosensory ASE neuron; lsy-6 controls the asymmetrical expression of the gcy chemoreceptors, gcy-5 and gcy-7, in ASER and ASEL; genetic epistasis experiments indicate that the transcription of lsy-6 is regulated by lsy-2, a novel C2H2 zinc finger transcription factor; reporter gene fusion studies indicate that lsy-6 is expressed in one pair of tail neurons and seven head neurons including ASEL, but not in ASER.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity. Involved in determination of left/right asymmetry in nervous system and miRNA-mediated post-transcriptional gene silencing. Expressed in ASEL; head neurons; and tail neurons.
• Biotype: SO:0001265
• Genetic Position: V :2.658 ±0.010694
• Length (nt): 73

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003088

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C32C4.6a	C32C4.6a	21	V: 10647237-10647257
Transcript:C32C4.6b	C32C4.6b	22	V: 10647280-10647301

Other

0 CDSs

0 RNAi Result

11 Allele

• gk963301
• gk964451
• gk964452
• gk963495
• gk963496
• gk964351
• gk964304
• ot150
• ot149
• ot71
• ot182

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003088
• Start: 10647232
• End: 10647304
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_10647305..10647560
• Length (nt): 256
• Chromosome Location: V: 10647305-10647560
• Organism: Caenorhabditis elegans

8 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
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
	Micro RNAs that showed significantly decreased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(tm5522)_downregulated_miRNA_L4
	MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_upregulated_miRNA
	MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:Aging_downregulated_miRNA_N2
	MicroRNAs that showed significantly increased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.	Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method.	WBPaper00053318:mir-71(n4115)_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_upregulated_miRNA
	MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated_miRNA

5 Expression Patterns

• Primary Identifier: Marker96
• Remark: Picture: Fig 2A.
• Pattern: Marker for ASEL neuron.

• Primary Identifier: Expr2807
• Remark: No detailed description on expression pattern in other life stages.
• Pattern: Adult transgenic animals expressing this reporter show only limited expression in one pair of tail neurons and in about seven head neurons. Of the head neurons, expression was consistently observed in ASEL but not in ASER in adult animals.

• Primary Identifier: Expr10657
• Pattern: Expression from the lsy-6 fosmid reporter is first observed at the end of gastrulation -around the bean stage- in the mother cell of the ASEL neuron, but not in the mother of ASER. After the ASEL mother cell divides, the lsy-6 reporter continues to be expressed only in ASEL as the ASEL sister cell dies by apoptosis shortly after. Expression of the lsy-6 reporter fosmid in ASEL continues throughout embryonic and larval development and into adulthood.

• Primary Identifier: Expr8410
• Remark: Picture: N.A.
• Pattern: No expression detected.

• Primary Identifier: Expr2808
• Remark: No GO_term assigned.
• Subcellular Localization: Expressed bilaterally in post-mitotic ASEL and ASER.

3 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003088
• Start: 10647232
• End: 10647304
• Strand: 1

3 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 73

1 Sequence Ontology Term

• Name: gene

13 Strains

• WBStrain00029456
• WBStrain00029464
• WBStrain00029347
• WBStrain00029360
• WBStrain00029375
• WBStrain00029376
• WBStrain00029658
• WBStrain00029657
• WBStrain00029655
• WBStrain00029654
• WBStrain00049807
• WBStrain00049809
• WBStrain00050764

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_10647144..10647231
• Length (nt): 88
• Chromosome Location: V: 10647144-10647231
• Organism: Caenorhabditis elegans