WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00014838 Gene Name  cyp-13A9
Sequence Name  ? T10B9.6 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including swsn-1; etr-1; and mrps-5 based on RNA-seq and microarray studies. Is affected by paraquat; bortezomib; and cadmium based on RNA-seq studies. Biotype  SO:0000336
Genetic Position  II :1.71528 ±0.000242 Length (nt)  ? 1788
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00014838

Genomics

0 Transcripts

 

Other

0 CDSs

0 RNAi Result

31 Allele

Public Name
gk963801
gk963053
gk962682
gk963142
WBVar01696216
tm10770
WBVar02075152
WBVar01989274
WBVar01253262
WBVar01310035
WBVar01310039
gk151567
WBVar01310038
WBVar00174797
WBVar00174796
gk737081
WBVar00238497
gk850503
WBVar01243501
gk850502
gk877499
gk525763
gk495884
gk732164
gk773542
gk529120
gk826337
gk879602
gk335059
ok5064

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00014838 9793754 9795541 -1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrII_9793298..9793753   456 II: 9793298-9793753 Caenorhabditis elegans

46 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly decreased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_downregulated_N2
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. Transcripts that showed significantly decreased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. DESeq2, fold change > 2. WBPaper00061081:E.faecalis_downregulated_skpo-1(ok1640)
  Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. WBPaper00048971:daf-16(mgDf50)_downregulated_L1
Bacteria infection: Pseudomonas aeruginosa PA14 Genes that showed decreased expression after 4 hours of infection by P.aeruginosa PA14. P value and fold-change calculations were performed using Partek Genomics Suite (Partek Inc.). A P value of < 0.05 using the FDR linear step-up procedure 55 was considered significant. WBPaper00050096:P.aeruginosa_downregulated
  Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50. Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. WBPaper00059824:rnp-6(dh1127)_regulated_OP50
Bacteria: B.thuringiensis Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
Bacteria ibfection: Pseudomonas aeruginosa PA14 Transcripts that showed significantly decreased expression in N2 animals exposed to PA14, comparing to in N2 animals grown on OP50. fold change > 2, FDR < 0.05 WBPaper00066858:PA14_downregulated_N2
  Transcripts that showed significantly increased expression in lin-29(n333) comparing to in N2 at day 1 adult stage. DESeq2, FDR < 0.01, fold change > 2. WBPaper00066970:lin-29(n333)_upregulated
  Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:daf-2(e1370)_upregulated_neuron
  Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. DESeq2, FDR < 0.05, fold change > 2. WBPaper00066978:daf-16(mu86)_upregulated_neuron
  Transcripts that showed significantly increased expression in sams-3(RNAi) comparing to N2 animals injected with empty vector. Deseq FDR < 0.01, fold change > 2. WBPaper00065005:sams-3(RNAi)_upregulated
  Transcripts that showed significantly increased expression in sams-4(RNAi) comparing to N2 animals injected with empty vector. Deseq FDR < 0.01, fold change > 2. WBPaper00065005:sams-4(RNAi)_upregulated
  Transcripts that showed significantly increased exression in animals exposed to 100uM cadmium for 24 hours. DESeq2 v1.20.0, fold change > 2, FDR < 0.05. WBPaper00065029:cadmium_upregulated
  Transcripts that showed significantly decreased expression in pals-17(syb3980) comparing to in N2 animals at young adult stage. Differential expression analyses were performed using limma-voom in Galaxy, adj p <= 0.05, logFC > 2 WBPaper00065984:pals-17(syb3980)_downregulated
  Transcripts that showed significantly increased expression in rbr-2(tm3141) comparing to in N2 animals. Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05). WBPaper00050080:rbr-2(tm3141)_upregulated
  Transcripts that showed significantly increased expression in MT333 lin-29(n333) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.01. WBPaper00067704:lin-29(n333)_upregulated
  Transcripts that showed significantly increased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage. DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. WBPaper00066110:tetraploid_vs_diploid_upregulated
Wounding: 2 hours after a single stab of a microinjection needle to either anterior or posterior body of lateral hyp7 (avoid the gonad) 24 hr after the L4 stage. Transcripts that showed significantly increased expression 2 hours after animals had a single stab of a microinjection needle to either anterior or posterior body of lateral hyp7 (avoid the gonad) 24 hr after the L4 stage. The cutoff for differential expressed genes (DEGs) were: Benjamini-Hochberg adjustedP-valueless than 0.05 and fold change larger than 1.5. WBPaper00059987:Wounding_upregulated
  Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals. edgeR p-value < 0.01 and fold change > 4. WBPaper00061613:human-amyloid-beta_upregulated
  Transcripts that showed significantly increased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults. Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05. WBPaper00061530:nhr-49(e2144)_upregulated
  Transcripts that showed significantly increased expression in lipl-4 overexpression transgenic lines comparing to wild type control animals. DESeq2 fold change > 2, FDR < 0.05. WBPaper00064156:lipl-4(overexpress)_upregulated
  Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals. Fold change > 4, p-value < 0.01 WBPaper00056330:mrps-5(RNAi)_upregulated
  Transcripts that showed significantly decreased expression in sma-9(ok1628) comparing to in N2. EdgeR fold change > 2, FDR < 0.05. WBPaper00067781:sma-9(ok1628)_downregulated
  Transcripts that showed significantly altered expression at RMG neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. WBPaper00061902:camt-1(ok515)_regulated_RMG
  Transcripts that showed significantly decreased expression in eat-2(ad465) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:eat-2(ad465)_downregulated
  Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals. edgeR p-value < 0.01 and fold change > 4. WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated
  Transcripts that showed significantly decreased 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_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
Diet: supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. Transcripts that showed significantly increased expression in N2 animals fed with OP50 supplemented with milk fat-containing protein powder from L1 to day 2 adult stage. Differential expression analysis between two conditions (three biological replicates per condition) was performed using DESeq2. Genes with p-value < 0.05 and Fold Change > 2 found by DESeq2 were assigned as differentially expressed. WBPaper00067530:Milk-protein_upregulated
  Transcripts that showed significantly increased expression in mdt-15(mg584gf) comparing to in N2 at L4 larva stage. EdgeR, fold change > 2, FDR < 0.001. WBPaper00056290:mdt-15(mg584)_upregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00014838 9793754 9795541 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1788

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrII_9795542..9795755   214 II: 9795542-9795755 Caenorhabditis elegans