WormMine: Gene WBGene00002297

• WormBase Gene ID: WBGene00002297
• Gene Name: ect-2
• Sequence Name: T19E10.1
• Brief Description: ect-2 encodes, by alternative splicing, two isoforms of a putative RHO guanine nucleotide exchange factor (RhoGEF) required for cytokinesis of early embryos and epidermal P cells, as well as cell polarity of early embryos and migration of epidermal P cells; ECT-2 is thus required for normal vulval differentiation and locomotion, along with fertility and embryonic viability; ECT-2 also activates LET-60/RAS signalling during vulval development, requiring RHO-1 to do so; ECT-2 is orthologous to the proto-oncogene ECT2 (OMIM:600586) and Drosophila PEBBLE; ECT-2 has two BRCT domains and a RhoGEF domain; ect-2 is expressed ubiquitously during embryogenesis, but restricted to Q cells in early L1 larvae; ect-2's expression then broadens to P-cell derivatives and distal tip cells, vulval precursor cells and their derivatives, and some adult neurons; ECT-2 is symmetrically distributed in unfertilized oocytes, but then temporarily becomes asymmetrically depleted around the centrosomal protein SPD-5, and is required for initial anteroposterior polarization of the newly fertilized embryo; anterior localization of PAR-6 in newly fertilized embryos requires ECT-2, which colocalizes with the nonmuscle myosin NMY-2 in the early embryonic cell cortex; the boundary of anterior versus posterior domains in the early embryo depends on the antagonistic activities of ECT-2 versus RGA-3/4; a hypomorphic ect-2 mutation suppresses the multivulva phenotype of lin-32, whereas a gain-of-function ect-2 mutation hyperinduces vulval development; ECT-2 is expressed in embryonic and P cells.
• Organism: Caenorhabditis elegans
• Automated Description: Enables guanyl-nucleotide exchange factor activity. Involved in several processes, including asymmetric protein localization involved in cell fate determination; mitotic cytokinesis; and regulation of actin filament-based process. Located in cell cortex. Expressed in several structures, including P1.p; germ line; hermaphrodite gonad; neuroblasts; and somatic gonad precursor. Is an ortholog of human ECT2 (epithelial cell transforming 2).
• Biotype: SO:0001217
• Genetic Position: II :3.12567 ±0.000108
• Length (nt): 5576

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002297

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T19E10.1a.2	T19E10.1a.2	3383	II: 10778387-10783962
Transcript:T19E10.1a.1	T19E10.1a.1	3352	II: 10778389-10783289
Transcript:T19E10.1b.1	T19E10.1b.1	3380	II: 10778389-10783293

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T19E10.1a	T19E10.1a	2775	II: 10778942-10779092
CDS:T19E10.1b	T19E10.1b	2799	II: 10778942-10779092

27 RNAi Result

• WBRNAi00107899
• WBRNAi00107895
• WBRNAi00107876
• WBRNAi00107874
• WBRNAi00064008
• WBRNAi00064009
• WBRNAi00064010
• WBRNAi00053549
• WBRNAi00064007
• WBRNAi00009185
• WBRNAi00085449
• WBRNAi00035675
• WBRNAi00071695
• WBRNAi00065682
• WBRNAi00065684
• WBRNAi00065659
• WBRNAi00117498
• WBRNAi00117497
• WBRNAi00071217
• WBRNAi00080552
• WBRNAi00053550
• WBRNAi00026318
• WBRNAi00065656
• WBRNAi00065660
• WBRNAi00065663
• WBRNAi00080211
• WBRNAi00107665

104 Allele

• gk963801
• gk963053
• otn10893
• otn9582
• gk962682
• gk963357
• gk963356
• otn12955
• otn12003
• WBVar01439658
• WBVar01546852
• WBVar01546853
• WBVar01546854
• WBVar01376109
• otn280
• otn2801
• otn1443
• gk153672
• gk153674
• gk153673
• gk153680
• gk153679
• gk153682
• gk153681
• gk153676
• gk153675
• zh8
• gk153678
• gk153677
• WBVar00228626

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002297
• Start: 10778387
• End: 10783962
• 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_10778127..10778386
• Length (nt): 260
• Chromosome Location: II: 10778127-10778386
• Organism: Caenorhabditis elegans

155 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	Transcripts of coding genes that showed significantly decreased 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_depleted_coding-RNA
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_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 decreased 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_downregulated_daf-16(mu86);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)
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	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 that showed significantly decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed
	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 altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	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_S.aureus
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) 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_elt-2(RNAi)
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)

12 Expression Patterns

• Primary Identifier: Expr4993
• Remark: Picture: Fig 4A, 4B.
• Subcellular Localization: Cortical segregation of YFP-ECT-2 was shown.

• Primary Identifier: Expr4277
• Subcellular Localization: Before polarization, GFP-ECT-2 was distributed uniformly throughout the cortex. After the onset of posterior cortical smoothing (when polarization was initiated), the GFP-ECT-2 signal was locally decreased at the cortex nearest the sperm pronuclei, where the centrosomes are located. As posterior cortical smoothing progressed in phase I, the cortical region that was depleted of GFP-ECT-2 expanded anteriorly and as the pronuclei migrated, GFP-ECT-2 signals were gradually recovered at the posterior cortical region. This exclusion of GFP-ECT-2 was not caused by an artifact of association of the sperm pronuclei with the cortex as the plasma membrane marker GFP-PHPLC1delta1 did not exhibit local exclusion during this stage.

• Primary Identifier: Expr1031346
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7865
• Remark: Picture: Figure 2A to 2D.
• Pattern: GFP expression was detected from embryogenesis to adulthood. In embryogenesis, almost all cells, other than those in the gut lineage, showed GFP expression. Before P-cell migration in the L1 stage, expression was detected only in Q cells. After P-cell migration and division, expression was seen in the P-cell derivatives and distal tip cells. In L3, GFP expression was present only in the vulval precursor cells and their derivatives. In L4 and adulthood, GFP fluorescence was detected only in some neuronal cells.

• Primary Identifier: Expr8760
• Remark: No detailed description on expression pattern in other tissue or life stages.. Picture: Fig 1K, Fig 3.
• Pattern: Expressed in Z1/Z4 at L1 stage. Expressed in spermathecal/sheath lineage, VU/DU, AC and DTC at L3 stage. Expressed in uterine epithelium and spermathecal epithelium at L4 stage.

• Primary Identifier: Expr13414
• Pattern: ECT-2::GFP localizes throughout the germline from the mitotically dividing nuclei at the premeiotic tip, where it is enriched at the germ cell membrane, to the end of diakinesis, where it exhibits a stronger nuclear signal.

• Primary Identifier: Expr13045
• Pattern: Similar to myosin, ECT-2 is expressed in neuroblasts and epidermal cells and localizes to the junction-free edges of the lateral epidermal cells around the ventral pocket during ventral enclosure. However, unlike myosin, ECT-2 is more uniformly distributed around the cell boundaries.

• Primary Identifier: Expr2011174
• 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: Expr10632
• Subcellular Localization: ECT-2-GFP expressed from its own regulatory elements was markedly enriched at the cortex of blastomeres, and was present at both contacted and contact-free surfaces.

• Primary Identifier: Expr2029410
• 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: Expr1157115
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1016922
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

19 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002297
• Start: 10778387
• End: 10783962
• Strand: -1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5576

1 Sequence Ontology Term