WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00002981 Gene Name  lgg-2
Sequence Name  ? ZK593.6 Brief Description  lgg-2 encodes an ortholog of the autophagic budding yeast protein Atg8p;LGG-2 is also homologous the light chain 3 (LC3) subunit of themicrotubule-associated proteins 1A and 1B (MAP1A and MAP1B); LGG-2 is predicted to associate with MAP1A and MAP1B and with microtubules and toperhaps play a role in regulating the microtubule-binding activity ofMAP1A and MAP1B; LGG-2 has no obvious function in RNAi assays, and isnot required for either dauer formation or extended lifespan.
Organism  Caenorhabditis elegans Automated Description  Predicted to enable microtubule binding activity; phosphatidylethanolamine binding activity; and ubiquitin protein ligase binding activity. Involved in cellular response to toxic substance; defense response to other organism; and positive regulation of autophagosome maturation. Acts upstream of or within with a positive effect on plasma membrane repair. Located in autophagosome membrane. Expressed in hypodermis; muscle cell; pharynx; spermatheca; and vulva. Human ortholog(s) of this gene implicated in glioblastoma; hypertrophic cardiomyopathy; and liver cirrhosis. Is an ortholog of human MAP1LC3A (microtubule associated protein 1 light chain 3 alpha); MAP1LC3B (microtubule associated protein 1 light chain 3 beta); and MAP1LC3B2 (microtubule associated protein 1 light chain 3 beta 2).
Biotype  SO:0001217 Genetic Position  IV :4.75551 ±0.001217
Length (nt)  ? 1708
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00002981

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:ZK593.6a.1 ZK593.6a.1 1039   IV: 10934196-10935903
Transcript:ZK593.6b.1 ZK593.6b.1 225   IV: 10934764-10935039
 

Other

2 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:ZK593.6a ZK593.6a 429   IV: 10934764-10934917
CDS:ZK593.6b ZK593.6b 225   IV: 10934764-10934917

21 RNAi Result

WormBase ID
WBRNAi00083909
WBRNAi00083908
WBRNAi00083906
WBRNAi00083905
WBRNAi00059527
WBRNAi00083912
WBRNAi00083911
WBRNAi00022071
WBRNAi00076888
WBRNAi00091343
WBRNAi00033329
WBRNAi00080581
WBRNAi00092336
WBRNAi00092335
WBRNAi00114411
WBRNAi00083914
WBRNAi00114415
WBRNAi00083915
WBRNAi00114677
WBRNAi00106785
WBRNAi00080468

37 Allele

Public Name
gk964278
gk964078
gk964500
gk962765
gk963382
gk963341
gk963678
WBVar02124206
WBVar02058848
gk514621
gk211737
WBVar01731029
WBVar01731030
gk211735
gk211736
tm5755
WBVar01731031
WBVar01731032
tm6474
WBVar01857590
bp556
WBVar01857591
bp595
tm6544
WBVar00191911
WBVar01857589
gk891761
gk506583
gk662839
gk548652

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00002981 10934196 10935903 -1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIV_10934190..10934195   6 IV: 10934190-10934195 Caenorhabditis elegans

163 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
  Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_expressed
adult vs dauer larva Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. N.A. WBPaper00050488:adult_vs_dauer_regulated_N2_20C
Osmotic stress Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present DESeq(version 1.10.1), FDR < 0.05. WBPaper00050726:OsmoticStress_regulated_Food
  Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:arcade_intestinal-valve_expressed
  Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:body-muscle_expressed
  Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:GABAergic-neuron_expressed
  Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:hypodermis_expressed
  Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:intestine_expressed
  Maternal class (M): genes that are called present in at least one of the three PC6 replicates. A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. [cgc5767]:expression_class_M
  Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:NMDA-neuron_expressed
  Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:pharynx_expressed
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:seam_expressed
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
  Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. DEseq 1.18.0, adjusted p-value < 0.05. WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). DEseq 1.18.0, adjusted p-value < 0.05. WBPaper00056471:S.aureus-4h_upregulated_N2
  Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_downregulated
Heat Shock: 35C 4 hours at L4 larva stage. Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours DESeq2 WBPaper00057154:HeatShock_downregulated_mRNA
  Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. DESeq WBPaper00053302:stavudine_24h_regulated
25C vs. 20C Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:25C_vs_20C_upregulated
  Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. CuffDiff, fold change > 2. WBPaper00065096:Day10_vs_Day1_upregulated
  Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. Cufflinks WBPaper00065120:body-muscle-transcriptome
  Transcripts that showed significantly increased expression in xrep-4(lax137). DESeq2. Genes were selected if their p value < 0.01. WBPaper00066062:xrep-4(lax137)_upregulated
  Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. WBPaper00053810:daf-2(e1370)_upregulated
  Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2. Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. WBPaper00053810:nuo-6(qm200)_upregulated
  Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:dopaminergic-neurons_L3-L4-larva_expressed
Bacteria infection: Staphylococcus aureus mRNAs that showed increased expression 8 hours after N2 animals were infected by S. aureus. DESeq, p <= 0.05 WBPaper00045314:S.aureus-induced_N2

8 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1031381 Tiling arrays expression graphs  
    Expr1162945 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr1019064 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
Picture: Fig 2.   Expr9088 Expression of GFP::LGG-2 and GFP::LGG-1 is first detected early during embryogenesis (before the 50 cell stage) with both a punctate and a diffuse cytoplasmic staining. At the beginning of organogenesis the number of puncta diminishes and the signal becomes mainly restricted to the pharynx, intestine and hypodermis. After hatching and during larval development GFP::LGG-1 expression has been reported as a diffuse signal predominantly in the lateral hypodermal seam cells and in the pharynx. Similarly, the expression of GFP::LGG-2 is high in the seam cells and pharynx and also in the nervous system, especially in some head and tail neurons and the neuron cell bodies in the ventral nerve cord. Its expression is mainly diffuse in the cytoplasm but a few dots are often detected in neuron cell bodies and seam cells. In adults, the tissue distribution of GFP::LGG-2 and GFP::LGG-1 remains diffuse but becomes more ubiquitous in particular the signal is detected in the whole hypodermis, the muscles, the vulva and the spermatheca. Together these data show that lgg-1 and lgg-2 present widely overlapping expression patterns and suggests the presence of numerous autophagosomal structures during embryogenesis. Punctate and diffuse cytoplasmic stainings were observed in early embryos.In larva stages, its expression is mainly diffuse in the cytoplasm but a few dots are often detected in neuron cell bodies and seam cells.
    Expr2013143 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).  
    Expr12743 Autophagy-related proteins, LGG-1, LGG-2, and BEC-1::GFP are expressed in a subset of cells within germline tumors.  
    Expr2031375 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).  
    Expr11489   LGG-2 is mainly associated with 250 nm diameter vesicular structures with a double membrane and cytoplasmic material content. These results are adirect evidence that LGG-2 labels autophagosomal membranes. Less frequently, flat or unclosed structures were labeled by LGG-2, suggesting that the protein is associated early during the elongation of autophagosome.

26 GO Annotation

Annotation Extension Qualifier
  enables
  enables
happens_during(GO:0097237) acts_upstream_of_or_within_positive_effect
  enables
  involved_in
  involved_in
  involved_in
  involved_in
  enables
  involved_in
  enables
  enables
  located_in
  located_in
  located_in
  located_in
happens_during(GO:0097237) involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in

11 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
orthologue

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00002981 10934196 10935903 -1

26 Ontology Annotations

Annotation Extension Qualifier
  enables
  enables
happens_during(GO:0097237) acts_upstream_of_or_within_positive_effect
  enables
  involved_in
  involved_in
  involved_in
  involved_in
  enables
  involved_in
  enables
  enables
  located_in
  located_in
  located_in
  located_in
happens_during(GO:0097237) involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in

0 Regulates Expr Cluster

1 Sequence

Length
1708

1 Sequence Ontology Term