WormMine: Gene WBGene00004767

• WormBase Gene ID: WBGene00004767
• Gene Name: sel-10
• Sequence Name: F55B12.3
• Brief Description: sel-10 encodes two isoforms of an F-box and WD-repeat-containing protein that is a component of an E3 ubiquitin ligase; SEL-10 functions as a negative regulator of the LIN-12/Notch-like signaling pathway in C. elegans and thus may contribute to cell fate decisions mediated by LIN-12; SEL-10 physically interacts with LIN-12 and with SEL-12, a C. elegans presenilin, and as such, is proposed to regulate the levels and/or activity of these proteins; SEL-10 also plays a role in sexual fate determination by regulating sexually dimorphic apoptosis of hermaphrodite- and male-specific neurons; the targets of SEL-10 in these sex-specific fate decisions are not yet known.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein homodimerization activity and protein kinase binding activity. Involved in several processes, including negative regulation of Notch signaling pathway; negative regulation of centrosome duplication; and regulation of vulval development. Located in axon and cytoplasm. Expressed in body wall musculature; gonad; intestine; neurons; and pharynx. Human ortholog(s) of this gene implicated in developmental delay, hypotonia, and impaired language. Is an ortholog of human FBXW7 (F-box and WD repeat domain containing 7).
• Biotype: SO:0001217
• Genetic Position: V :5.60769 ±0.009351
• Length (nt): 3620

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004767

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:F55B12.3b.1	F55B12.3b.1	2361	V: 13819361-13822977
MRNA	Transcript:F55B12.3a.1	F55B12.3a.1	2370	V: 13819361-13822980
NcPrimaryTranscript	Transcript:F55B12.3c	F55B12.3c	1881	V: 13819365-13822378

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F55B12.3a	F55B12.3a	1764	V: 13819365-13819454
CDS:F55B12.3b	F55B12.3b	1758	V: 13819365-13819454

16 RNAi Result

• WBRNAi00089813
• WBRNAi00068020
• WBRNAi00000317
• WBRNAi00048450
• WBRNAi00048451
• WBRNAi00015695
• WBRNAi00092205
• WBRNAi00076481
• WBRNAi00027833
• WBRNAi00062270
• WBRNAi00092204
• WBRNAi00092220
• WBRNAi00081625
• WBRNAi00089919
• WBRNAi00090079
• WBRNAi00090237

72 Allele

• gk963271
• gk963706
• gk963301
• gk964458
• gk964459
• WBVar02062103
• WBVar02062102
• h16008
• gk511954
• gk723809
• gk849019
• gk696432
• gk589527
• gk516164
• gk518418
• gk674758
• gk705568
• e2055
• n3717
• gk739754
• gk827605
• gk632950
• gk715513
• WBVar01744153
• gk313336
• gk603119
• gk485281
• n3854
• gk339428
• gk571600

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004767
• Start: 13819361
• End: 13822980
• 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_chrV_13822981..13823051
• Length (nt): 71
• Chromosome Location: V: 13822981-13823051
• Organism: Caenorhabditis elegans

117 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 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
	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 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 expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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 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 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 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)
	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
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 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 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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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
	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
Fungi infection: Haptoglossa zoospora.	Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours.	Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01.	WBPaper00062354:H.zoospora_6h_regulated
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)
	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)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA

9 Expression Patterns

• Primary Identifier: Expr4827
• Remark: Picture: fig. S3 B, C, D.
• Subcellular Localization: SEL-10::GFP was diffusely localized along the entire axon throughout development.

• Primary Identifier: Expr4826
• Remark: Picture: fig. S3 A.
• Pattern: A transgene containing the sel-10 promoter driving green fluorescent protein (GFP) labeled a subset of neurons including the HSNL, which suggests that sel-10 is expressed in the HSNL. sel-10 promoter driven GFP is widely expressed in body wall muscles (not consistent though), intestine(not consistent), pharynx, distal tip cell, spermatheca, and within nervous system, it is expressed in HSNs, some ventral cord neurons, a bunch of unidentified head neurons and a few tail neurons. --Pers. Comm. from Mei Ding 11-20-07.

• Primary Identifier: Expr8730
• Remark: Picture: Fig 7. The lack of early embryonic expression could be due to transgene silencing in the maternal germline, a frequent outcome for maternally expressed genes in transgenic C. elegans strains.
• Pattern: No expression of GFP::SEL-10 was detected in early embryos, but cytoplasmic expression in some cells beginning at about the 50-cell stage were seen. Higher levels of cytoplasmic expression were detected beginning at about the bean stage, after the completion of most embryonic cell divisions, in many cells throughout the embryo. In larvae and adults, expression was observed in head and tail neurons and in unidentified cells along the entire length of the body.
• Subcellular Localization: Cytoplasmic expression.

• Primary Identifier: Expr1032361
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13756
• Subcellular Localization: SEL-10 is generally expressed in proliferative and meiotic cells but accumulates in midpachytene.

• Primary Identifier: Expr1152240
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1024366
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015728
• 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: Expr2033961
• 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).

34 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004767
• Start: 13819361
• End: 13822980
• Strand: 1

34 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3620

1 Sequence Ontology Term