WormMine: Gene WBGene00001251

• WormBase Gene ID: WBGene00001251
• Gene Name: elt-3
• Sequence Name: K02B9.4
• Brief Description: elt-3 gene encodes a GATA transcription factor; during embryogenesis, ELT-3 appears to act downstream of ELT-1, also a GATA transcription factor, in a redundant pathway controlling hypodermal cell differentiation; ELT-3 is also required for positive regulation of transcription of nlp-29, which encodes an antimicrobial peptide, in response to fungal infection and gpdh-1 in response to salt stress; in addition, ELT-3 may also play a role in regulating adult lifespan; ELT-3 is expressed in all of the major hypodermal cells except the lateral seam cells and localizes to the nucleus; elt-3 expression in the hypodermis is positively regulated by ELT-1 and negatively regulated by ELT-5 and ELT-6.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in several processes, including determination of adult lifespan; positive regulation of transcription by RNA polymerase II; and response to stress. Located in nucleus. Expressed in several structures, including Caaaaa; Caaaap; hermaphrodite distal tip cell; hypodermal cell; and rectum.
• Biotype: SO:0001217
• Genetic Position: X :15.5355 ±0.088614
• Length (nt): 6343

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001251

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K02B9.4a.2	K02B9.4a.2	1464	X: 13934874-13941216
Transcript:K02B9.4b.1	K02B9.4b.1	954	X: 13934883-13940715
Transcript:K02B9.4a.3	K02B9.4a.3	1390	X: 13934996-13941216
Transcript:K02B9.4a.1	K02B9.4a.1	1265	X: 13938743-13941216
Transcript:K02B9.4c.1	K02B9.4c.1	627	X: 13939340-13940715
Transcript:K02B9.4d.1	K02B9.4d.1	510	X: 13939726-13940715

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K02B9.4b	K02B9.4b	954	X: 13934883-13934949
CDS:K02B9.4a	K02B9.4a	681	X: 13938826-13938868
CDS:K02B9.4c	K02B9.4c	627	X: 13939340-13939431
CDS:K02B9.4d	K02B9.4d	510	X: 13939726-13939824

49 RNAi Result

• WBRNAi00049681
• WBRNAi00016440
• WBRNAi00027885
• WBRNAi00075701
• WBRNAi00077525
• WBRNAi00093276
• WBRNAi00077704
• WBRNAi00077708
• WBRNAi00112738
• WBRNAi00077696
• WBRNAi00069534
• WBRNAi00069536
• WBRNAi00069535
• WBRNAi00069538
• WBRNAi00069537
• WBRNAi00069539
• WBRNAi00069542
• WBRNAi00069541
• WBRNAi00069544
• WBRNAi00069543
• WBRNAi00069546
• WBRNAi00069545
• WBRNAi00069532
• WBRNAi00069531
• WBRNAi00069533
• WBRNAi00069540
• WBRNAi00077766
• WBRNAi00112739
• WBRNAi00112741
• WBRNAi00077526

114 Allele

• gk964260
• gk964029
• gk962707
• gk964028
• gk963810
• gk963581
• WBVar01602405
• gk299826
• gk299823
• gk299824
• gk299825
• gk299829
• gk299830
• gk299831
• gk299832
• gk299827
• gk299828
• gk299833
• gk299834
• gk299835
• gk299836
• gk299840
• gk299837
• gk299838
• gk299839
• WBVar01544713
• WBVar01822665
• WBVar01822664
• gk917688
• WBVar01552507

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001251
• Start: 13934874
• End: 13941216
• 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_chrX_13941217..13945709
• Length (nt): 4493
• Chromosome Location: X: 13941217-13945709
• Organism: Caenorhabditis elegans

140 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
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
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
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
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 mdt-15(mg584gf) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:mdt-15(mg584)_downregulated
	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 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
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	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
	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 decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated

13 Expression Patterns

• Primary Identifier: Expr1030793
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7313
• Pattern: Click the movie links below for interactive 4D movies of a fluorescence reporter. http://glowormnotes.blogspot.com/2009/11/elt-3yfp-transcriptional-fusion.html

• Primary Identifier: Expr7603
• Remark: Clone: pUL#JRH/AD1
• Pattern: Strong, constitutive expression, from mid embryo to early larval stages, but heavily mosaic. Then much stronger and specific expression appears in the distal tip cells, persisting to adult.

• Primary Identifier: Expr8234
• Remark: Picture: Figures 1D and 1E.
• Pattern: In the head, elt-3 GFP expression decreases with age in the hypodermal cells and the pharyngeal-intestinal valve cells, eventually showing little or no expression in old worms. In the trunk, elt-3 expression is mostly derived from the hypodermal cells and the intestinal cells, and expression in this region decreases quickly between day 3 and day 5 of adulthood. The elt-3 GFP reporter did not change expression in the intestinal-rectal valve cells located in the tail of the worm. In summary, these results show that age-related changes in elt-3 expression are complex, as different tissues show different kinetics of age regulation and some tissues show no age regulation at all.

• Primary Identifier: Expr517
• Remark: Transgenic Marker: rol-6(su1006).
• Pattern: At approximately 260 min after the first cleavage, reporter gene expression is now also detected in nuclei on the dorsal surface of the embryo, corresponding to the position of the major hypodermal cells, and in six nuclei on each ventrolateral aspect of the embryo, corresponding to the position of the ventral hypodermal cells (P cells). Expression was first seen in granddaughters of C.paa and C.aaa about 240 min. after first cleavage. About 260 min. after first cleavage, expression was seen in dorsal and ventral hypodermal cells. Between comma-stage and 3-fold stage, expression was seen in dorsal and ventral hypodermal cells, and in tail and head hypodermis. After the 3-fold stage, expression becomes reduced, but is maintained a low levels in larvae and adults. After the 3-fold stage through adulthood, a digestive-tract component is expressed: probably vpi3D and vpi3V in the pharyngeal intestinal valve, virL and virR in intestinal rectal valve, and rect D, rect VL, rect VR.

• Primary Identifier: Expr11554
• Pattern: Expressed in hypodermis, head and tail neurons.

• Primary Identifier: Expr16192
• Pattern: elt-3 expression is intense in the hypodermis but is undetectable in the extruded intestine.

• Primary Identifier: Expr1200167
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2011294
• 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: Expr1153404
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1014013
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029530
• 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: Expr769
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Northern analysis showed strong expression in embryo, much higher level in embryo than in mixed stages or L4. RT-PCR to postembryonic stage animals showed expression in L1, L2, L3, L4 and adults.

32 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001251
• Start: 13934874
• End: 13941216
• Strand: 1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6343

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00022239
• WBStrain00034019
• WBStrain00034021
• WBStrain00035539
• WBStrain00035540

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_13932036..13934873
• Length (nt): 2838
• Chromosome Location: X: 13932036-13934873
• Organism: Caenorhabditis elegans