WormMine: Gene WBGene00003263

• WormBase Gene ID: WBGene00003263
• Gene Name: mir-35
• Sequence Name: Y62F5A.2
• Brief Description: mir-35 encodes a microRNA, a small non-protein coding RNA that belongs to a large group of microRNAs that include the stRNAs, lin-4 and let-7; the mir-35 genomic cluster of microRNAs consists of seven genes, that are similar in sequence, mir-35-mir-41; this group of microRNAs functions redundantly to control embryonic development and is expressed only during embryogenesis and in young adults with eggs.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable mRNA binding activity. Predicted to be involved in RNA destabilization. Expressed in germ line.
• Biotype: SO:0001265
• Genetic Position: II :3.63227 ±0.004834
• Length (nt): 97

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003263

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y62F5A.2a	Y62F5A.2a	23	II: 11537629-11537651
Transcript:Y62F5A.2b	Y62F5A.2b	22	II: 11537668-11537689

Other

0 CDSs

0 RNAi Result

7 Allele

• gk963801
• gk963053
• gk962684
• gk963539
• gk963482
• gk262
• nDf50

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003263
• Start: 11537608
• End: 11537704
• Strand: 1

3 Data Sets

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

0 Downstream Intergenic Region

30 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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
	miRNAs that showed significantly decreased expression in glp-4(bn2) at 26 centigrade, comparing to in N2 animals at 26 centigrade.	DESeq2 q-value < 0.05.	WBPaper00049990:glp-4(bn2)_26C_vs_N2_26C_downregulated
	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
	Micro RNAs that showed significantly higher expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine).	DESeq2 v1.13.8, fold change > 2, FDR < 0.01.	WBPaper00056161:hermaphrodite_enriched_miRNA
	MicroRNAs that showed significantly increased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult.	DESeq, cut-off of 2-fold change.	WBPaper00045019:MWCNT_upregulated
Fasting for 48 hours, from 3 days post L4 to 5 days post L4.	MicroRNAs that showed significantly decreased expression after 48 hours of fasting	p < 0.0002, Fishers exact test.	WBPaper00051247:fasting_downregulated
	MicroRNAs that showed significantly increased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood mir-71(n4115) 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_upregulated_miRNA_mir-71(n4115)
	Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in neuron.	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_neuron
	MicroRNAs that showed significantly increased 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_upregulated_miRNA_N2
	miRNAs that showed significantly decreased expression in glp-4(bn2) at 26 centigrade than in 15 centigrade.	DESeq2 q-value < 0.05.	WBPaper00049990:glp-4(bn2)_26C_vs_15C_downregulated
	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
	miRNAs that showed decreased expression in 8 days 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)_Day8_downregulated
12 hour starvation	miRNA that showed significantly increated expression after 12 hour starvation in L4 larva stage. Fold change was calculated by dividing the higher counts per million by the lower, but adding the sign from the logFC to indicate direction.	Authors only considered miRNA regions with at least 1 reads per-million from one of the libraries. These were tested for differential expression using the edgeR package, setting the common dispersion to 0.1 (since they did not have biological replicates) and normalizing with the TMM method. False Discovery Rates were calculated using the Benjamini & Hochberg procedure.	WBPaper00048790:12h-starvation_upregulated_miRNA
Exposed to 1mg / L PM2.5 from L1 larva to young adult.	MicroRNAs that showed significantly decreased expression after animals were exposed to 1 mg per liter PM2.5 from L1 larva to young adult.	DESeq, cut-off of 2-fold change, p-value < 0.05.	WBPaper00054985:PM2.5_downregulated
	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
	miRNA with increased 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_upregulated_adult
	miRNA with decreased expression in N2 L1 larva comparing to in N2 embryo.	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_L1_vs_embryo_downregulated_adult
	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
	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) L1 larva comparing to in prg-1(wm161) embryo.	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_L1_vs_embryo_downregulated_adult
	miRNA with decreased expression in prg-1(wm161) L3 larva comparing to in prg-1(wm161) 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_prg-1_L3_vs_L2_downregulated_adult
	miRNAs with age dependent abundance in wild type animals.	Details available in Supplementary material of the paper. Diff Exp, is the approximate ratio of expression comparing Young to Old animals (11 day difference in age). The raw p-value is for the null hypothesis that the Diff exp Ratio = 1 (based on robust inference - see supplemental information) and the associated 95% CI of the ratio.	WBPaper00042527:age_dependent_miRNA
	Micro RNAs that showed significantly decreased expression in drsh-1(ok369) comparing to in N2.	Fold change > 1.5.	WBPaper00055896:drsh-1(ok369)_downregulated
	Micro RNAs that showed significantly decreased expression in hrpk-1(zen17) comparing to in N2 at L4 larva stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(zen17)_downregulated_miRNA_L4
	miRNAs that showed significantly decreased expression after 48 hour treatment in 10uM sanguinarine.	Fold change > 2.	WBPaper00055663:sanguinarine_downregulated
	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

4 Expression Patterns

• Primary Identifier: Expr8445
• Pattern: Expressed from early embryo continuing through adulthood. Expression is strong in the earlier stages and becomes weaker in the later stages. Expressed in muscles: vulva, head and rectal muscles. Also, expressed in seam cells, hypodermis, partial intestne and nerves, including dnc, head and tail nerves.

• Primary Identifier: Expr2530
• Pattern: No signal was detected in larval stages (L1, L2, L3, L4) and glp-4(bn2) adults. Intense signals detected in embryos and adults.

• Primary Identifier: Expr10897

• Primary Identifier: Expr1653
• Remark: For this miRNA, longer species with mobilities expected for the respective foldback RNAs also appear to be expressed in the germ line; these longer RNAs were observed in wild-type L4 larvae (which have proliferating germ cells) but not in germ linedeficient mutant animals.
• Pattern: Highly expressed in the embryo and in young adults with eggs, but not at other developmental stages.

2 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003263
• Start: 11537608
• End: 11537704
• Strand: 1

2 Ontology Annotations

6 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Probes that showed significantly increased expression in mir-35-41(nDf50) comparing to in N2 at 20C.	Genes listed exhibited a fold change >= 1.5, with q-value <= 0.5 (Storey multiple testing correction with bootstrapping).	WBPaper00050903:mir-35-41(nDf50)_20C_upregulated
	Probes that showed significantly increased expression in mir-35-41(nDf50) comparing to in N2 at 25C.	Genes listed exhibited a fold change >= 1.5, with q-value <= 0.5 (Storey multiple testing correction with bootstrapping).	WBPaper00050903:mir-35-41(nDf50)_25C_upregulated
	Genes with expression level down regulated in mir-35 mutants comparing with N2.	The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type.	WBPaper00040876:mir-35_downregulated
	Genes with expression level up regulated in mir-35 mutants comparing with N2.	The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type.	WBPaper00040876:mir-35_upregulated
	Probes that showed significantly decreased expression in mir-35-41(nDf50) comparing to in N2 at 25C.	Genes listed exhibited a fold change >= 1.5, with q-value <= 0.5 (Storey multiple testing correction with bootstrapping).	WBPaper00050903:mir-35-41(nDf50)_25C_downregulated
	Probes that showed significantly decreased expression in mir-35-41(nDf50) comparing to in N2 at 20C.	Genes listed exhibited a fold change >= 1.5, with q-value <= 0.5 (Storey multiple testing correction with bootstrapping).	WBPaper00050903:mir-35-41(nDf50)_20C_downregulated

1 Sequence

• Length: 97

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00035835
• WBStrain00051757
• WBStrain00051758
• WBStrain00051755
• WBStrain00054866
• WBStrain00054865
• WBStrain00054864

0 Upstream Intergenic Region