WormMine: Gene WBGene00003329

• WormBase Gene ID: WBGene00003329
• Gene Name: mir-236
• Sequence Name: C52E12.7
• Brief Description: mir-236 encodes a microRNA, a small non-protein coding RNA and appears to be conserved in C. briggsae; based on RNA sequence identity, miR-236 belongs to the miR-8 family of microRNAs which includes Drosophila miR-8; human miR-200b also appears to be similar to miR-236; miR-236 is strongly expressed at all stages of development in normal worms and in glp-4(bn2) mutant worms; many of the known microRNAs are involved in post-transcriptional regulation of genes; the precise function of miR-236 is unknown.
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in pharynx.
• Biotype: SO:0001265
• Genetic Position: II :0.316536±
• Length (nt): 98

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003329

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C52E12.7b	C52E12.7b	23	II: 7030195-7030217
Transcript:C52E12.7a	C52E12.7a	24	II: 7030236-7030259

Other

0 CDSs

0 RNAi Result

2 Allele

• gk963801
• gk963053

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003329
• Start: 7030180
• End: 7030277
• Strand: -1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_7030157..7030179
• Length (nt): 23
• Chromosome Location: II: 7030157-7030179
• Organism: Caenorhabditis elegans

19 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	miRNAs that showed increased expression after exposure to graphene oxide (GO)	The dysregulated expression of miRNAs in GO-exposed nematodes was analyzed by DESeq (an R package, a powerful tool to estimate the variance and test for differential expression). The data were extracted as up- or down-regulated miRNAs according to a cutoff of 2 fold change, and were presented in the scatter diagram after normalization.	WBPaper00045209:graphene-oxide_upregulated
	miRNA with decreased expression in N2 L3 larva comparing to in N2 L2 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_L3_vs_L2_downregulated_adult
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 increased 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)_upregulated_miRNA_L4
	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 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
	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
	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
	miRNAs in F1 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation.	Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control.	WBPaper00049006:nicotine_upregulated_F1
	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
	miRNA that showed significantly decreased expression in stau-1(tm2266) comparing to in N2.	Differentially expressed genes were identified using edgeR package in R.	WBPaper00049286:stau-1(tm2266)_downregulated

5 Expression Patterns

• Primary Identifier: Expr13547
• Pattern: Intestine and pharynx

• Primary Identifier: Expr8420
• Pattern: Expressed from mid embryo to adulthood. Expression seen in intestine, rectal glands and dnc.

• Primary Identifier: Expr10949

• Primary Identifier: Expr2509
• Pattern: Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults.

• Primary Identifier: Expr2656
• Pattern: Precursor miRNA: Weak expression in L1. No expression in embryo, L2-L4 and adult. mature miRNA: Strong expression in L1. Intermediate expression in L2 and L3. Weak expression in embryo, L4 and adult.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003329
• Start: 7030180
• End: 7030277
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 98

1 Sequence Ontology Term