WormMine: Gene WBGene00003343

• WormBase Gene ID: WBGene00003343
• Gene Name: mir-249
• Sequence Name: Y48D7A.3
• Brief Description: mir-249 encodes a microRNA, a small non-protein coding RNA and has a potential ortholog in the nematode C. brigssae; as mir-249 could not be detected on northern blots, its expression profile is unknown; many of the known microRNAs are involved in post-transcriptional regulation of genes; the precise function of miR-249 is unknown.
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in head neurons and seam cell.
• Biotype: SO:0001265
• Genetic Position: X :-12.6566 ±0.000842
• Length (nt): 97

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003343

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y48D7A.3b	Y48D7A.3b	23	X: 3006454-3006476
Transcript:Y48D7A.3a	Y48D7A.3a	24	X: 3006497-3006520

Other

0 CDSs

1 RNAi Result

• WBRNAi00002229

5 Allele

• gk963725
• WBVar01549428
• n4983
• tm2813
• gk485788

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003343
• Start: 3006440
• End: 3006536
• Strand: -1

2 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_3004762..3006439
• Length (nt): 1678
• Chromosome Location: X: 3004762-3006439
• Organism: Caenorhabditis elegans

21 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
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
	Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2	DESeq2	WBPaper00057162:meg-3_meg-4_upregulated_sRNA
	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
	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
	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
	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
	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
	miRNA with increased 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_upregulated_adult
	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
	Micro RNAs that showed significantly increased expression in hrpk-1(zen17) comparing to in N2 at embryo stage.	DESeq, fold change > 2, p-value <= 0.05.	WBPaper00058673:hrpk-1(zen17)_upregulated_miRNA_embryo
	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 decreased 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_downregulated
	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
Temperature Shift: 35 centigrade for 4 hours.	miRNAs up regulated after 4 hours of exposure to 35C.	miRNAs with > 1.9 fold change in expression were considered differentially expressed.	WBPaper00046567:HeatStress_upregulated
	miRNAs that showed significantly increased 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_upregulated

4 Expression Patterns

• Primary Identifier: Expr8595
• Remark: Picture: Fig 4E, 4F, 4G.
• Pattern: Expression of mir-249::gfp driven by a 6.0-kb upstream region was first observed in most, if not all seam cells in L1 stage worms in both hermaphrodites and males. Some head neurons and P lineage cells also consistently expressed gfp.

• Primary Identifier: Expr10960

• Primary Identifier: Expr10786
• Pattern: The expression of miR-249 is relatively high in early stages, especially from the L1 to L3 stages whereas it becomes decreased in later larval and adult stages.

• Primary Identifier: Expr2593
• Pattern: No expression was detected.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003343
• Start: 3006440
• End: 3006536
• Strand: -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 97

1 Sequence Ontology Term