WormMine: Gene WBGene00022450

• WormBase Gene ID: WBGene00022450
• Gene Name: ubc-26
• Sequence Name: Y110A2AM.3
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable ubiquitin conjugating enzyme activity. Predicted to be involved in ERAD pathway and protein polyubiquitination. Predicted to be located in endoplasmic reticulum and nucleus. Is an ortholog of human UBE2J2 (ubiquitin conjugating enzyme E2 J2).
• Biotype: SO:0001217
• Genetic Position: II :-9.41278 ±0.033837
• Length (nt): 5578

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00022450

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y110A2AM.3a.1	Y110A2AM.3a.1	1563	II: 2894771-2900348
Transcript:Y110A2AM.3b.1	Y110A2AM.3b.1	1359	II: 2894835-2900334
Transcript:Y110A2AM.3a.2	Y110A2AM.3a.2	1408	II: 2894880-2900348
Transcript:Y110A2AM.3b.2	Y110A2AM.3b.2	1265	II: 2894973-2900332

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y110A2AM.3a	Y110A2AM.3a	717	II: 2895597-2895750
CDS:Y110A2AM.3b	Y110A2AM.3b	591	II: 2895643-2895670

1 RNAi Result

• WBRNAi00055307

78 Allele

• gk964317
• gk963801
• otn11906
• otn17634
• WBVar01404468
• otn19362
• snx2127
• snx2126
• snx2128
• snx260
• snx259
• snx258
• gk137166
• ttTi17485
• ttTi17486
• gk137165
• gk137164
• gk137168
• gk137169
• gk137167
• gk137170
• WBVar01339498
• WBVar01339499
• WBVar01339497
• WBVar00100805
• WBVar00215214
• WBVar01404461
• snx3959
• snx3960
• snx3958

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00022450
• Start: 2894771
• End: 2900348
• Strand: -1

4 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_2894396..2894770
• Length (nt): 375
• Chromosome Location: II: 2894396-2894770
• Organism: Caenorhabditis elegans

28 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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 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 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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_N2_mRNA
	Transcripts of coding genes that showed significantly increased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_enriched_coding-RNA
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2.	DESeq2	WBPaper00052884:emb-4(hc60)_upregulated
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:GABAergic-motor-neurons_L1-larva_expressed
	Proteins that showed differential expression in (B) let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge], and in (C) gld-1(op236); let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge]	N.A.	WBPaper00044501:gld-1_let-7_regulated
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated
	Genes that were down regulated as the result of the lmn-1(L535P) mutation.	Differential expression was calculated with cuffdiff, using a count threshold (-c parameter) of at least 15 for statistical significance testing. Significantly differentially expressed genes were defined as ones with at least 1 FPKM level of expression in at least one of the conditions and a q-value less than 0.05.	WBPaper00050182:lmn-1(L535P)_downregulated
	Genes that showed flat mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:flat_dev_expression
	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
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin-Psora_upregulated
	Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in control animals.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:cco-1(RNAi)_upregulated
	Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm.	Fold change > 2, p-value < 0.05.	WBPaper00060661:sensory-neuron_enriched
Temperature shift: 15C vs 20 C.	Transcripts that showed significantly decreased expression in N2 animals treated with empty RNAi vector at 15C comparing to N2 animals treated with empty RNAi vector at 20C.	Statistical comparisons were made by two-tailed t-test, n=3 (each replicate contains 150 extruded germ lines from N2 wild-type worms), P < 0.01 was considered significant.	WBPaper00057288:Cold_downregulated_transcript
	Top 300 transcripts enriched in B cell according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:B
	Transcriptions that showed significantly increased expression in hsf-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:hsf-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in Day 8 adults comparing to in Day 1 adults in neuron cells.	t-test, fold change > 2, p-value < 0.01.	WBPaper00062590:Aging_downregulated_neuron
Stress: Six hours after UV (310 nm, Phillips UV6, Waldmann UV236B)	Proteins significantly (FDR < 5%) decreased in abundance in UV-treated versus untreated xpc-1;csb-1 double mutants	Significantly altered protein quantities were determined by two-sided t tests and correction for multiple testing via estimation of the FDR to 5% with a per mutation-based algorithm (number of permutations = 500, fudge factor s0 = 0.1).	WBPaper00052987:UV_downregulated_xpc-1;csb-1

5 Expression Patterns

• Primary Identifier: Expr2035850
• Pattern: 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).

• Primary Identifier: Expr1012866
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1158845
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1039915
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2017712
• Pattern: 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).

7 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00022450
• Start: 2894771
• End: 2900348
• Strand: -1

7 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5578

1 Sequence Ontology Term