WormMine: Gene WBGene00000458

• WormBase Gene ID: WBGene00000458
• Gene Name: ceh-37
• Sequence Name: C37E2.5
• Brief Description: ceh-37 encodes one of three C. elegans proteins with an OTX-like homeodomain; however, CEH-37 lacks other domains found in OTX proteins, and the CEH-37 homeodomain is predicted to resemble the Myb domain of telomere-binding proteins; CEH-37 binds the telomeric sequence 'TTAGGC' if it is repeated at least 1.5 times, and is mainly localized to the telomere in vivo; ceh-37 mutants have a weak increase in chromosomal nondisjunction; CEH-37 is involved in specifying some aspects of the AWB olfactory neuron fate, such as expression of an AWB-specific odorant receptor and a LIM-class homeodomain protein, LIM-4; CEH-37 is expressed broadly in the early embryo, while in larvae and adults it is expressed solely in the excretory cell.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA binding activity, bending and double-stranded telomeric DNA binding activity. Involved in neuron fate specification; olfactory behavior; and regulation of transcription by RNA polymerase II. Located in chromosome, telomeric region. Expressed in several structures, including ABarpaap; dorsal nerve cord; excretory cell; head muscle; and head neurons. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 7 and cone-rod dystrophy 2. Is an ortholog of human CRX (cone-rod homeobox).
• Biotype: SO:0001217
• Genetic Position: X :16.6652 ±0.001448
• Length (nt): 10629

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000458

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C37E2.5a.1	C37E2.5a.1	1208	X: 14197372-14199731
Transcript:C37E2.5b.1	C37E2.5b.1	1194	X: 14197373-14199097
Transcript:C37E2.5d.1	C37E2.5d.1	1396	X: 14197373-14208000
Transcript:C37E2.5c.1	C37E2.5c.1	1096	X: 14197377-14198823

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C37E2.5b	C37E2.5b	756	X: 14197741-14197986
CDS:C37E2.5d	C37E2.5d	879	X: 14197741-14197986
CDS:C37E2.5a	C37E2.5a	837	X: 14197741-14197986
CDS:C37E2.5c	C37E2.5c	732	X: 14197741-14197986

6 RNAi Result

• WBRNAi00042117
• WBRNAi00011722
• WBRNAi00029643
• WBRNAi00106222
• WBRNAi00107118
• WBRNAi00090702

260 Allele

• gk964260
• gk964029
• gk962707
• gk964028
• gk963810
• gk963581
• otn11722
• gk300462
• gk300461
• gk300464
• gk300463
• gk300458
• gk300457
• gk300460
• gk300459
• gk300466
• gk300465
• gk300467
• gk300473
• gk300472
• gk300475
• gk300474
• gk300469
• gk300468
• gk300471
• gk300470
• gk300476
• gk300478
• gk300477
• gk300479

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000458
• Start: 14197372
• End: 14208000
• 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_14186567..14197371
• Length (nt): 10805
• Chromosome Location: X: 14186567-14197371
• Organism: Caenorhabditis elegans

178 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
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
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
	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 that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_upregulated
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_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 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 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_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)
	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: 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
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa 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:ASE_parent
	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
	Top 300 transcripts enriched in excretory duct, excretory pore 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:Excretory_duct_and_pore
	Transcripts enriched in AMso according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:AMso_enriched
	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 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 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
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated

14 Expression Patterns

• Primary Identifier: Expr2009881
• 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: Expr1030262
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15300
• Pattern: ceh-37::GFP expression is seen early starting at around 40 cells in the daughters of AB.alaa and AB.arpa, and in their daughters in the next division. Then the expression fades. Later expression is seen in the precursors of the neurons, in which ceh-37 has been shown to be expressed and function. The early expression is in different blast cells than those where the later expression is seen, which are daughters of AB.p, AB.alp, and AB.ara. Thus, the early expression is not a precursor for that in later neuroblasts.

• Primary Identifier: Expr7469
• Remark: Clone: pUL#JRH8H11
• Pattern: Early and comma stage embryos show expression in two cells in the anterior region. From late embryo to adult, expression is seen in the dorsal nerve cord and two nerves lateral to the terminal pharyngeal bulb. There is also very strong expression in the most anterior two rings of intestinal cells and weak expression in head muscles.

• Primary Identifier: Expr15585

• Primary Identifier: Expr2742
• Pattern: The expression pattern of ceh-37::gfp was similar to that of ceh-37::myc. A pair of neuronal cells that showed strong expression of gfp was identified as the AWB neurons based on their characteristic ciliary morphology. Expression in the AWB and additional neurons was transient such that expression was no longer observed by the early L1 larval stages. However, expression in nonneuronal cells, including the excretory cell and intestine, was maintained through adult stages.

• Primary Identifier: Expr11103

• Primary Identifier: Expr2741
• Remark: Reporter gene fusion type not specified.
• Pattern: Animals transgenic for a rescuing ceh-37 genomic fragment tagged with the Myc epitope expressed Myc in multiple cells prior to the comma stage of embryogenesis. Expression of ceh-37::myc was also observed in two cells in the posterior. By the 3-fold stage, expression was largely restricted to the head region, with expression observed in neuronal and additional nonneuronal cells.

• Primary Identifier: Expr2028121
• 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: Chronogram868
• Remark: Original chronogram file: chronogram.1910.xml
• Reporter Gene: [C37E2.5:gfp] transcriptional fusion.

• Primary Identifier: Expr1146118
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2614
• Subcellular Localization: CEH-37 GFP fluorescence was primarily co-localized to the ends of the chromosomes at least in the metaphase.

• Primary Identifier: Expr1015270
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1170022
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

26 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000458
• Start: 14197372
• End: 14208000
• Strand: -1

26 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10629

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00024200
• WBStrain00024201
• WBStrain00031536
• WBStrain00048942
• WBStrain00055073
• WBStrain00003219

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_14208001..14208111
• Length (nt): 111
• Chromosome Location: X: 14208001-14208111
• Organism: Caenorhabditis elegans