WormMine: Gene WBGene00001182

• WormBase Gene ID: WBGene00001182
• Gene Name: egl-13
• Sequence Name: T22B7.1
• Brief Description: egl-13 encodes a SOX domain transcription factor; egl-13 is required for maintenance of the uterine pi cell fate; mutations in egl-13 affect the cell fusion process that makes the vulval-uterine connection and consequently egg laying; egl-13 is expressed in the pi cells, transiently expressed in the rho lineage, in the anchor cell following fusion, and in neurons, body wall muscles, and intestinal cells; egl-13 expression during pi cell fate specification is dually controlled by LAG-1 and FOS-1/JUN-1.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including cell fate commitment; regulation of DNA-templated transcription; and vulval development. Located in nucleus. Expressed in several structures, including developing hermaphrodite gonad; egg-laying apparatus; intestinal cell; neurons; and uterine pi cell. Human ortholog(s) of this gene implicated in high grade glioma. Is an ortholog of human SOX13 (SRY-box transcription factor 13); SOX5 (SRY-box transcription factor 5); and SOX6 (SRY-box transcription factor 6).
• Biotype: SO:0001217
• Genetic Position: X :-4.40892 ±0.006608
• Length (nt): 10231

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001182

Genomics

13 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:T22B7.1a.1	T22B7.1a.1	2169	X: 5663837-5674067
MRNA	Transcript:T22B7.1a.3	T22B7.1a.3	2220	X: 5666111-5674067
MRNA	Transcript:T22B7.1a.2	T22B7.1a.2	2073	X: 5668320-5674045
NcPrimaryTranscript	Transcript:T22B7.1g	T22B7.1g	1542	X: 5668321-5673386
NcPrimaryTranscript	Transcript:T22B7.1h	T22B7.1h	1706	X: 5668321-5673386
MRNA	Transcript:T22B7.1c.1	T22B7.1c.1	1269	X: 5669687-5673386
MRNA	Transcript:T22B7.1b.1	T22B7.1b.1	1937	X: 5669687-5674054
MRNA	Transcript:T22B7.1e.1	T22B7.1e.1	1317	X: 5669932-5673386
MRNA	Transcript:T22B7.1b.2	T22B7.1b.2	1978	X: 5669937-5674052
MRNA	Transcript:T22B7.1d.1	T22B7.1d.1	2411	X: 5669995-5674056
MRNA	Transcript:T22B7.1d.2	T22B7.1d.2	2351	X: 5671365-5674056
MRNA	Transcript:T22B7.1b.3	T22B7.1b.3	1861	X: 5671366-5674054
MRNA	Transcript:T22B7.1f.1	T22B7.1f.1	942	X: 5672228-5673386

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T22B7.1c	T22B7.1c	1269	X: 5669687-5669769
CDS:T22B7.1d	T22B7.1d	960	X: 5672210-5672357
CDS:T22B7.1a	T22B7.1a	1413	X: 5668321-5668464
CDS:T22B7.1b	T22B7.1b	951	X: 5671732-5671740
CDS:T22B7.1e	T22B7.1e	1317	X: 5669932-5670062
CDS:T22B7.1f	T22B7.1f	942	X: 5672228-5672357

17 RNAi Result

• WBRNAi00089858
• WBRNAi00053792
• WBRNAi00053793
• WBRNAi00026443
• WBRNAi00027490
• WBRNAi00019006
• WBRNAi00019457
• WBRNAi00069478
• WBRNAi00027865
• WBRNAi00065338
• WBRNAi00090488
• WBRNAi00090394
• WBRNAi00090233
• WBRNAi00090075
• WBRNAi00089915
• WBRNAi00090535
• WBRNAi00090441

215 Allele

• gk964260
• gk575365
• gk281056
• gk281055
• gk962903
• WBVar02063933
• WBVar02063932
• WBVar02063935
• WBVar02063934
• WBVar02063937
• WBVar02063936
• gk523464
• gk910319
• h18114
• WBVar01758490
• WBVar01758491
• gk816539
• gk878887
• WBVar01601779
• WBVar00079289
• WBVar00079290
• WBVar00079288
• WBVar00079287
• WBVar01544478
• tm11515
• oxTi98
• n5937
• n6675
• rp23
• rp26

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001182
• Start: 5663837
• End: 5674067
• 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_5674068..5675176
• Length (nt): 1109
• Chromosome Location: X: 5674068-5675176
• Organism: Caenorhabditis elegans

192 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 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
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. 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.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	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
mitochondrial sulfide delivery molecule (mtH2S) AP39	Transcripts that showed significantly increased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:mtH2S-AP39-D0-treatment_upregulated_Day11
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	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 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	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
	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
	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
	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 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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly increased 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)_upregulated_PA14

17 Expression Patterns

• Primary Identifier: Expr4977
• Remark: Picture: Fig. 1C.
• Pattern: Following the specification event at the late L3 stage and just prior to division at L3 lethargus, fluorescence from an egl-13::GFP transcriptional reporter (pWH17) was initiated in pi nuclei. Expression of this reporter, persisted through division, differentiation, and morphogenesis.

• Primary Identifier: Expr11223
• Pattern: egl-13 started to be expressed after Q.a divisions and GFP fluorescence reached the maximum level in Q.ap upon differentiation. By contrast, the GFP signal was barely detected in the Q.p lineage, and the mCherry fluorescence in Q cells did not change during Q cell development. egl-13 was continuously expressed in A/PQR during larval development, indicating that EGL-13 can be involved in neuronal fate initiation and maintenance.

• Primary Identifier: Expr1030756
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr11016
• Pattern: Expression is first detected in 4 neuronal cells at around 350 min post-fertilization, which is the time at which the BAG and URX neurons are born. Expression is restricted to these 4 neurons during embryogenesis. At the first larval stage, egl-13 expression is observed in the BAG and URX neurons plus occasionally in a small number of unidentified cells in the head and tail (including the AQR and PQR neurons). Later during larval development, egl-13 expression is observed in body wall muscle and vulval cells (data not shown). Neuronal expression is restricted to the O2 and CO2-sensing neurons in the adult.

• Primary Identifier: Expr12604
• Pattern: the egl-13 and sox-4 fosmid reporters are expressed only in a few neurons during late embryogenesis, when all embryonic neurons are already born.

• Primary Identifier: Expr7672
• Remark: Clone: pUL#IAH7A6
• Pattern: Expression was observed in body wall and vulval muscle of L4s and adults. Expression was also seen in the mature embryo and all postembryonic stages in 6 to 8 nerve cells in the head, which included but did not appear restricted to amphids, and 1 nerve cell in the tail, which was probably a phasmid. The axon projections were clearly visible. The expression pattern was seen in 7 of 8 independent lines, with no expression observed in the eighth line. Expression was strongest in UL2526. UL2525 appears an integrated line and expresses almost as strongly.

• Primary Identifier: Expr16300
• Pattern: We further tested egl-13 expression using a GFP transcriptional reporter and found that egl-13 was expressed in a number of cells, including the AIAs, of wild-type worms, although expression in the AIAs appeared to dissipate over the course of larval development

• Primary Identifier: Expr1295
• Pattern: The cog-2::gfp transcriptional fusion is expressed in a similar pattern to the translational fusion in the pi and pi lineages. The expression pattern of the transcriptional fusion differs from the translational fusion in that the body wall muscles express the fusion protein at a higher level than any other cell and fewer neurons expressing cog-2::gfp can be detected with the transcriptional fusion, although the same brightly expressing cells that stand out with the translational fusion are visible. Translational construct: cog-2::gfp is expressed in a dynamic pattern in cells of the pi-lineage. No expression is visible in the gonad until the pi cell precursors are born. At this point, expression is evident in all pi cell precursors as well as in the single pi precursor on each side that has a pi cell precursor as a sister. After the pi cell precursors undergo their single and final division, cog-2::gfp expression is still bright in the pi cells, but expression is usually no longer evident in the lineage. Most animals show no expression of COG-2::GFP expression past the precursor stage in the pi lineage, although in a few animals, faint GFP expression was observed in the daughters, but never the granddaughters, of the expressing pi precursor. cog-2::gfp expression remains strong in the lineage throughout the L4 stage, becoming slightly brighter in the pi cells that adopt the uv1 fate. In addition, the AC nucleus begins to express cog-2::gfp after fusion with the utse cell. Expression in the AC is not detectable before the time of fusion. cog-2::gfp expression is not detectable in the vulva at any stage, in any other part of the gonad including the distal tip cells, or in the hypodermis. cog-2::gfp is expressed in most, if not all, neurons in the head and the tail of the animal. However, four unidentified cells in the head express cog-2::gfp at a higher level than others. Expression is also faintly visible in the body wall muscles and the intestinal cells.
• Subcellular Localization: Translational construct: COG-2::GFP is a nuclear protein.

• Primary Identifier: Expr9800
• Pattern: GFP expression was observed through all stages. GFP was seen in a few nuclei in the head, thought to be of neurons. Occasionally, 1 tail cell expressed GFP. The signal was very faint, weaker than with the other recombineered egl-13 reporter gene fusions constructed in this series (see UL3401, UL3393 and UL3196), although a bit stronger in embryos.

• Primary Identifier: Expr9735
• Pattern: GFP observed in several neurons in the head, laterally as well as in the nerve ring, and about 3 neurons in the tail. Sometimes GFP was seen, but extremely faintly, in body wall muscle. The expression pattern stays the same through all postembryonic stages. Cells showing GFP expression in the embryo were not identified.

• Primary Identifier: Expr2011206
• 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: Expr9745
• Pattern: The GFP expression pattern looks the same as for fUL#JW16, with gfp inserted directly upstream of the egl-13 stop codon. Signal intensity varied considerably between different transgenic strains.

• Primary Identifier: Expr9746
• Pattern: GFP expression was seen in a few cells of the developing gonad from L1-L4. No head or tail neuronal expression, as with the egl-13 reporter gene fusion arrangements present in UL3393 or UL3196, was seen.

• Primary Identifier: Expr2029442
• 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: Expr1013667
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr11013
• Pattern: In wild-type animals, the six uterine pi cell express cog-2::gfp at the early- to mid-L4 stage.

• Primary Identifier: Expr1157343
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

19 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001182
• Start: 5663837
• End: 5674067
• Strand: 1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10231

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00026510
• WBStrain00026783
• WBStrain00051962
• WBStrain00051616
• WBStrain00051617
• WBStrain00051615
• WBStrain00052574
• WBStrain00052013

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_5663224..5663836
• Length (nt): 613
• Chromosome Location: X: 5663224-5663836
• Organism: Caenorhabditis elegans