WormMine: Gene WBGene00000440

• WormBase Gene ID: WBGene00000440
• Gene Name: ceh-17
• Sequence Name: D1007.1
• Brief Description: ceh-17 encodes a phox-2-like homeodomain protein that is a member of the Q50 paired-like class of homeobox proteins and the vertebrate orthologue of Phox2a and Phox2b; that affects ALA and SIA axonal development; ceh-17 affects ALA and SIA antero-posterior axonal growth and navigation, and is expressed in five neurons of the ring ganglia (ALA and the 4 SIAs) with strongest expression in embryos and in L1 stage larvae.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in axon guidance; positive regulation of transcription by RNA polymerase II; and regulation of axon extension. Located in nucleus. Expressed in DA8; head muscle; head neurons; and somatic nervous system. Human ortholog(s) of this gene implicated in several diseases, including congenital central hypoventilation syndrome; congenital fibrosis of the extraocular muscles 2; and neuroblastoma. Is an ortholog of human PHOX2A (paired like homeobox 2A).
• Biotype: SO:0001217
• Genetic Position: I :-1.0462 ±0.001888
• Length (nt): 1263

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000440

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:D1007.1.1	D1007.1.1	914	I: 4568765-4570027

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:D1007.1	D1007.1	714	I: 4568962-4569284

4 RNAi Result

• WBRNAi00043320
• WBRNAi00003251
• WBRNAi00030301
• WBRNAi00084772

25 Allele

• gk962706
• gk963902
• gk964159
• gk964070
• tm10850
• tm250
• gk552484
• gk539863
• gk709239
• gk702315
• gk932437
• gk434574
• gk831942
• gk718755
• gk855205
• gk604711
• gk451756
• gk342022
• gk109511
• gk109510
• WBVar00153165
• WBVar00153164
• WBVar01313139
• h12552
• np1

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000440
• Start: 4568765
• End: 4570027
• 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_chrI_4568399..4568764
• Length (nt): 366
• Chromosome Location: I: 4568399-4568764
• Organism: Caenorhabditis elegans

71 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	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
	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 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
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	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 increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
	Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:cfp-1(tm6369)_upregulated
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:sin-3(tm1276)_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C.	Transcripts that showed significantly increased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C.	DESeq2, fold change > 2.	WBPaper00061081:E.faecalis_upregulated_skpo-1(ok1640)
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_RNAseq
	Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
	Transcripts that showed significantly decreased expression in crh-1(n3315) comparing to in N2 animals.	DESeq2 v1.26.0, FDR < 0.01. Fold change > 2.	WBPaper00062440:crh-1(n3315)_downregulated
	Genes with significant increase of expression in NBAS smgl-1(RNAi) comparing to control.	Bioconductor package LIMMA was used to determine differentially expressed genes. The P-values were adjusted for multiple testing with a false-discovery rate (50). Probe sets with fold-change > 1.5 and q-value < 0.05 were used as a cut-off for C. elegans microarrays	WBPaper00042561:smgl-1(RNAi)_upregulated
Bacteria infection: Photorhabdus luminescens	Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_RNAseq
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly increased 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_upregulated_hpx-2(dg047)
	Genes up regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_up_regulated
	Transcripts that showed significantly decreased expression in plp-1(ok2155) adult animals comparing to in wild type.	DESeq2. Genes with at least 2-fold upregulation with a raw P value <= 0.05 only are listed.	WBPaper00060526:plp-1(ok2155)_downregulated
	Larval Pan-neural Enriched Genes.	A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets.	WBPaper00030839:Larval_Pan_Neuronal

10 Expression Patterns

• Primary Identifier: Expr2009863
• 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: Expr7489
• Remark: Clone: pUL#JRH/AF10
• Pattern: In late stage embryos can see expression in lines of cells down the sides of the body. Post hatching expression is seen in ventral and dorsal nerve cords as well as several other nerve nuclei and processes within the head. Also weak expression seen in anterior muscles of the head in all stages post hatching.

• Primary Identifier: Chronogram86
• Remark: Original chronogram file: chronogram.1096.xml
• Reporter Gene: [D1007.1:gfp] transcriptional fusion.

• Primary Identifier: Chronogram88
• Remark: Original chronogram file: chronogram.1098.xml
• Reporter Gene: [D1007.1:gfp] transcriptional fusion.

• Primary Identifier: Expr1039
• Pattern: Antibody staining: CEH-17 expression was strong at the 3-fold to L1 stage and decreased thereafter to reach barely detectable levels in adults. At the L1 stage, CEH-17 was detected exclusively in the nuclei of five neurons of the ring ganglia. One of the five CEH-17+ neurons was dorsal and just posterior to the nerve ring, while the four others were ventral and close to the posterior bulb of the pharynx. pceh-17::GFP show that the dorsal neuron could be seen projecting two processes towards the ring, which then turned back and coursed along the lateral cords, all the way to the tail of the animal, identifying this neuron as ALA. The four ventral CEH-17 positive neurons were located just posterior to the SMBs, as was described for the SIAs. The four ventral ceh-17 expressing neurons are believed to be the SIA neurons (SIADR, SIADL, SIAVR and SIAVL). In addition to ALA and the four SIAs, a few other neurons also expressed the pceh-17::GFP construct. flceh-17::GFP staining resulted in the same expression pattern. ceh-17 HD::GFP showed effectively restricted GFP expression to the five neurons seen with the antibody (i.e. ALA and the four SIAs). The fluorescence had a granular appearance and was restricted to the cell body, possibly due to trapping of the chimeric protein in the endoplasmic reticulum. pceh-17::GFP::3 resulted in the same expression pattern (i.e. ALA and the four SIAs), but with axonal staining. The latter construct (pceh-17::GFP::3 ) was used to examine embryonic expression of ceh-17. At the comma stage, expression was detected in two dorsal neurons in the head, presumably corresponding to ALA and its sister RMED, and in six cells on the ventral side of the head, just anterior to the excretory pore. These cells probably correspond to the four SIAs, in which the GFP signal was strongest and revealed sprouting axons, and the two SIBVs, sisters of the SIADs. Two other weakly positive cells on the ventral side were detected, one in the mid-body region and one in the tail, at positions fitting those of motor neurons DB5 and DA8, sisters of the SIAVs. The earliest time at which could detect ceh-17::GFP expression was at the end of gastrulation in four pairs of cells, which could correspond to the four SIAs and their sisters or to the four SIA mothers and their own sisters. Since this is the time when the mothers of SIAs are undergoing their last division, it is not clear whether ceh-17 expression precedes or follows the last cell division.
• Subcellular Localization: nuclei, cell body, axonal staining.

• Primary Identifier: Expr15566

• Primary Identifier: Chronogram57
• Remark: Original chronogram file: chronogram.1049.xml
• Reporter Gene: [D1007.1:gfp] transcriptional fusion.

• Primary Identifier: Expr2028103
• 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: Expr1017681
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1147298
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

17 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000440
• Start: 4568765
• End: 4570027
• Strand: -1

17 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1263

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00035301
• WBStrain00035300
• WBStrain00035312
• WBStrain00052001
• WBStrain00008608

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_4570028..4571191
• Length (nt): 1164
• Chromosome Location: I: 4570028-4571191
• Organism: Caenorhabditis elegans