WormMine: Gene WBGene00003345

• WormBase Gene ID: WBGene00003345
• Gene Name: mir-251
• Sequence Name: F59F3.7
• Brief Description: mir-251 encodes a microRNA, a small non-protein coding RNA and is conserved in the nematode C. brigssae; mir-251 is weakly expressed from the L1 larval stage into the adult stage 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-251 is unknown.
• Organism: Caenorhabditis elegans
• Automated Description: Is affected by several genes including prg-1; hrpk-1; and alg-1 based on RNA-seq studies.
• Biotype: SO:0001265
• Genetic Position: X :2.84229 ±0.00537
• Length (nt): 97

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003345

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F59F3.7a	F59F3.7a	22	X: 11004746-11004767

Other

0 CDSs

3 RNAi Result

• WBRNAi00049215
• WBRNAi00016131
• WBRNAi00091095

7 Allele

• gk964260
• gk964029
• gk962707
• gk964028
• gk963810
• gk586768
• n4606

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003345
• Start: 11004728
• End: 11004824
• Strand: 1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_11004825..11004983
• Length (nt): 159
• Chromosome Location: X: 11004825-11004983
• Organism: Caenorhabditis elegans

12 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 exhibit changes in expression during adulthood (p-value < = 0.05).	Authors searched for targets with seed matches of perfect Watson-Crick base-pair complementarity to positions two-eight of the miRNAs (counting from the 5' end). In order to consider these seed matches as potential target sites, authors required a minimal cut-off for binding specificity of the remainder of the miRNA to the target. Recent evidence suggests that this is not required for function in humans, but 3' binding does occur in studies of C. elegans. Authors used the scoring algorithm from Robins et al. (2005). The binding cut-off is determined by creating a second-order Markov model of the background for the 3' UTRs. The cut off was p-value < = 0.05.	WBPaper00028344:adult_expr_change
	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 alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
	miRNA with increased 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_upregulated_embryo
Fungus: C. albicans	miRNAs that showed significantly increased expression after 4 hours of infection by fungus C.albicans at 25 C, comparing to control animals infected with heat killed C.albicans.	Fold change > 2.	WBPaper00050386:C.albicans_4h_upregulated
	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
	miRNA with increased 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_upregulated_adult
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_upregulated
	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

4 Expression Patterns

• Primary Identifier: Expr8431
• Pattern: Expression seen from late embryos to adulthood. Expressed in pharyngeal muscles

• Primary Identifier: Expr13550
• Pattern: Pharynx

• Primary Identifier: Expr10923

• Primary Identifier: Expr2476
• Pattern: Faint 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: WBGene00003345
• Start: 11004728
• End: 11004824
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 97

1 Sequence Ontology Term