WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219413 Gene Name  Y38F2AL.12
Sequence Name  ? Y38F2AL.12 Organism  Caenorhabditis elegans
Automated Description  Is affected by several genes including swsn-9; mut-16; and fog-2 based on RNA-seq and microarray studies. Is affected by Alovudine and Zidovudine based on RNA-seq studies. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 2260
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219413

Genomics

3 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y38F2AL.12.1 Y38F2AL.12.1 1992   IV: 2316573-2318673
Transcript:Y38F2AL.12.2 Y38F2AL.12.2 892   IV: 2317003-2318675
Transcript:Y38F2AL.12.3 Y38F2AL.12.3 917   IV: 2317797-2318832
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:Y38F2AL.12 Y38F2AL.12 45   IV: 2317858-2317868

0 RNAi Result

61 Allele

Public Name
gk963722
WBVar00569809
gk963025
gk962726
gk964255
gk899484
WBVar01785914
gk195880
gk195881
gk195882
gk195883
gk195884
gk195885
gk195886
gk195887
gk195888
gk615628
gk313559
gk666564
gk468263
gk936168
gk734265
gk440840
gk825347
gk400361
gk603466
gk818110
gk332581
WBVar00185371
WBVar02034339

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219413 2316573 2318832 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_chrIV_2318833..2323270   4438 IV: 2318833-2323270 Caenorhabditis elegans

30 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
  Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals. DESeq2 v. 1.22.2, adjusted p-value <= 0.05. WBPaper00059605:mut-16(pk710)_upregulated
  Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:daf-2(e1370)_upregulated
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
Temprature shift to 28C for 48 hours. Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours. Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. WBPaper00061341:28C_48h_upregulated
  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 plp-1(ok2155) adult animals comparing to in wild type. DESeq2. Genes with at least 2-fold upregulation with a raw P value <= 0.05 only are listed. WBPaper00060526:plp-1(ok2155)_upregulated
Bacteria diet: complex environmental microbiotas Transcripts that showed significantly decreased expression after L1 larva grew on soil microbiota at 25C for 3 days. N.A. WBPaper00056139:soil-microbiota_downregulated
  Transcripts that showed significantly decreased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. WBPaper00066146:germline-inx-14(RNAi)_downregulated_PA14
  Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2. edgeR WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
  Transcripts that showed significantly decreased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. Fold change > 2, FDR < 0.01. WBPaper00065993:glp-1(e2141)_downregulated
  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
  Transcripts with promoter regions binding DREAM protein complex, according to ChIP-seq of E2F-DP (DPL-1 and EFL-1) and MuvB (LIN-9, LIN-37, LIN-52, and LIN-54) of N2 late embryo. N.A. WBPaper00053289:DREAM-target
  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
  Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. WBPaper00045521:Spermatogenic
  Targets of endo-siRNA that showed significantly decreased expression in the whole animal of JH3225[meg-3(tm4259) meg-4(ax2026)] comparing to in N2. DESeq2 1.22.2, fold change > 2, FDR < 0.05 WBPaper00057161:meg-3(tm4259)_meg-4(ax2026)_downregulated_endo-siRNA_targets
  Transcripts that showed significantly altered expression after 24 hour exposure to zidovudine (AZT) starting at L1 lava stage. DESeq WBPaper00053302:zidovudine_72h_regulated
  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 increased expression in nfki-1(cer1) animals at L4 larva stage, comparing to in N2 animals. Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01. WBPaper00060445:nfki-1(cer1)_upregulated_L4
  Transcripts that showed significantly increased expression in ins-11(tm1053) young adult animals comparing to in N2. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18. 75th percentile were defined as down-regulated. WBPaper00053664:ins-11(tm1053)_upregulated
  Transcripts that showed significantly increased expression in gcn-1(nc40) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.05 WBPaper00065578:gcn-1(nc40)_upregulated
  Transcripts that showed significantly changed expression in fog-2(q71) comparing to in N2, at 6-day post-L4 adult hermaphrodite comparing and 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:fog-2(q71)_regulated
  Transcripts that showed significantly increased expression in daf-1(m40);daf-3(mgDf90) comparing to in daf-1(m40) at 1-day post L4 adult hermaphrodite animals. CuffDiff fold change >= 2, q < 0.05. WBPaper00059421:daf-3(mgDf90)_upregulated
  Transcripts that showed significantly increased expression in mip-1(how5) comparing to in control animals. DESeq2, fold change > 2. WBPaper00066038:mip-1(how5)_downregulated
  Transcripts that showed significantly increased expression in simr-1(cmp36), comparing to in N2 animals. DESeq2 v. 1.22.2, adjusted p-value <= 0.05. WBPaper00059605:simr-1(cmp36)_upregulated
  Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (FLT) starting at L1 lava stage. DESeq WBPaper00053302:alovudine_72h_regulated
  Transcripts that showed significantly decreased expression in RA629 swsn-9(ok1354);rdIs49[Cb-unc-119] comparing to in RA577 swsn-9(ok1354); rdIs52 [Pric-19::swsn-9::gfp; Cb-unc-119] (swsn-9 neuronal rescue) animals at young adult worms. DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) WBPaper00060764:swsn-9(ok1354)_downregulated
Bacteria diet: Lb.delbrueckii Transcripts that showed significantly increased expression in animals fed with homofermentative LAB Lb. delbrueckii, comparing to animals fed with OP50 from day 1 to day 5 adult stage. fold change > 2 and p value < 0.05 by Students t- test. WBPaper00065392:Lb.delbrueckii_upregulated

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2025548 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  
    Expr2007314 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00219413 2316573 2318832 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
2260

1 Sequence Ontology Term