WormMine: Gene WBGene00003315

• WormBase Gene ID: WBGene00003315
• Gene Name: mir-87
• Sequence Name: F10C2.8
• Brief Description: mir-87 encodes a microRNA (miRNA), a small noncoding RNA that is likely involved in post-transcriptional regulation of gene expression; miR-87 is expressed at high levels at all developmental stages and in glp-4 mutant hermaphrodites lacking a germline, but appears to be most abundant during the L1 larval stage; miR-87 has apparent orthologs in C. briggsae, Drosophila melanogaster, and humans; the targets of miR-87 are not yet known.
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in neurons based on RNA-seq studies. Is affected by several genes including prg-1; alg-1; and alg-2 based on RNA-seq studies.
• Biotype: SO:0001265
• Genetic Position: V :3.61247 ±0.001653
• Length (nt): 94

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003315

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F10C2.8b	F10C2.8b	22	V: 12038700-12038721
Transcript:F10C2.8a	F10C2.8a	24	V: 12038742-12038765

Other

0 CDSs

0 RNAi Result

7 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk963618
• n4104
• n4123

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003315
• Start: 12038688
• End: 12038781
• Strand: -1

2 Data Sets

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

0 Downstream Intergenic Region

23 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
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 decreased expression in VC1743[mett-10(ok2204)] comparing to in N2 when animals grow on standard (OP50) plates.	DESeq2, p-value < 0.05, fold change > 2.	WBPaper00061357:mett-10(ok2204)_downregulated_OP50
	miRNA with decreased expression in N2 1-day post L4 adult hermaphrodite comparing to in N2 L4 larva.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_N2_adult_vs_L4_downregulated_adult
	Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in hypodermis.	Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2.	WBPaper00066447:Day8_vs_Day1_upregulated_hypodermis
	MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(ram2)_downregulated_miRNA
	miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.	A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.	WBPaper00046156:eat-2(ad1116)_Day1_upregulated
	MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_downregulated_miRNA
	MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-2(ok304)_downregulated_miRNA
	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
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_adult
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_embryo
	MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L1
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L2
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L3
	miRNA with decreased expression in prg-1(wm161) comparing to in N2.	DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively.	WBPaper00045316:miRNA_prg-1_downregulated_L4
Heat Shock: 35C 4 hours at L4 larva stage.	Micro RNAs that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_miRNA
	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
Bacteria infection: Pseudomonas aeruginosa PA14	miRNAs up regulated by Pseudomonas aeruginosa infection.	N.A.	WBPaper00046303:P.aeruginosa_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

3 Expression Patterns

• Primary Identifier: Expr12852
• Pattern: Ubiquitous expression, strong expression in hypodermis, less expression in seam cells, anterior and posterior bulb of pharynx and nerve cord; expressed at all stages, highest expression in L4s and lowest expression in L2.

• Primary Identifier: Expr10943

• Primary Identifier: Expr2501
• Pattern: Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003315
• Start: 12038688
• End: 12038781
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 94

1 Sequence Ontology Term