WormMine: Gene WBGene00003354

• WormBase Gene ID: WBGene00003354
• Gene Name: mir-260
• Sequence Name: F39E9.13
• Brief Description: mir-260 encodes a microRNA, a small non-protein coding RNA and is conserved in C. briggsae; mir-260 is primarily embryonic in expression; many of the known microRNAs are involved in post-transcriptional regulation of genes; the precise function of miR-260 is unknown.
• Organism: Caenorhabditis elegans
• Automated Description: Is affected by several genes including swsn-1; stau-1; and atfs-1 based on RNA-seq studies. Is affected by multi-walled carbon nanotube; nicotine; and sodium arsenite based on RNA-seq studies.
• Biotype: SO:0001265
• Genetic Position: II :-6.75387 ±0.020123
• Length (nt): 103

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003354

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F39E9.13b	F39E9.13b	20	II: 3306302-3306321

Other

0 CDSs

2 RNAi Result

• WBRNAi00046780
• WBRNAi00014606

36 Allele

• gk964317
• gk963801
• gk963053
• WBVar02122302
• WBVar02120456
• WBVar02123019
• WBVar02122780
• WBVar02122532
• WBVar02124390
• WBVar02122098
• WBVar02122355
• WBVar02124673
• WBVar02120786
• WBVar02120617
• WBVar02121131
• WBVar02123186
• WBVar02123659
• WBVar02121370
• WBVar02122914
• WBVar02122218
• WBVar02121721
• gk964209
• gk964210
• WBVar02124763
• WBVar02121950
• WBVar02120928
• tm10837
• tm1612
• WBVar02121547
• WBVar00091192

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003354
• Start: 3306234
• End: 3306336
• Strand: 1

2 Data Sets

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

0 Downstream Intergenic Region

17 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_upregulated
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 cat-2(e1112);odIs77 comparing to in odIs77 control animals.	EdgeR, FDR<0.01	WBPaper00060921:cat-2(e1112)_downregulated
	Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms.	DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.)	WBPaper00060764:swsn-1(os22ts)_downregulated
	Transcripts that showed significantly decreased expression in atfs-1(et18) comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(et18)_downregulated
	Transcripts that showed significantly decreased expression in tdc-1(n3419);odIs77 comparing to in odIs77 control animals.	EdgeR, FDR<0.01	WBPaper00060921:tdc-1(n3419)_downregulated
	Genes that showed significantly changed expression in oxidative stressed N2 animals caused by 10mM sodium arsenite (NaAsO2) comparing to in unstressed N2.	R-Bioconductor package.	WBPaper00049266:NaAsO2-Stress_regulated_N2
	Transcripts that showed significantly decreased expression in tph-1(mg280);odIs77 comparing to in odIs77 control animals.	EdgeR, FDR<0.01	WBPaper00060921:tph-1(mg280)_downregulated
	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 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
	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
	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 decreased expression in alg-5(tm1163), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-5(tm1163)_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
	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
	miRNA that showed significantly increased expression in stau-1(tm2266) comparing to in N2.	Differentially expressed genes were identified using edgeR package in R.	WBPaper00049286:stau-1(tm2266)_upregulated

1 Expression Patterns

• Primary Identifier: Expr10967

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003354
• Start: 3306234
• End: 3306336
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 103

1 Sequence Ontology Term