WormMine: Gene WBGene00004889

• WormBase Gene ID: WBGene00004889
• Gene Name: smp-1
• Sequence Name: Y54E5B.1
• Brief Description: smp-1 encodes a semaphorin; smp-1 activity is required for vulval morphogenesis, specifically for the movement of homologous pairs of vulval cells towards the vulval midline prior to cell fusion; smp-1 expression in vulval cells is regulated by the VAB-23 zinc-finger domain protein which binds smp-1 regulatory sequence in vivo.
• Organism: Caenorhabditis elegans
• Automated Description: Enables semaphorin receptor binding activity. Involved in nematode male tail mating organ morphogenesis. Predicted to be located in plasma membrane. Expressed in several structures, including hermaphrodite distal tip cell; non-striated muscle; ray; somatic nervous system; and vulval cell. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia; progressive myoclonus epilepsy; and rheumatoid arthritis. Is an ortholog of several human genes including SEMA3B (semaphorin 3B); SEMA3C (semaphorin 3C); and SEMA6C (semaphorin 6C).
• Biotype: SO:0001217
• Genetic Position: I :27.3982 ±0.247471
• Length (nt): 8292

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004889

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y54E5B.1c.1	Y54E5B.1c.1	2562	I: 14807462-14815729
Transcript:Y54E5B.1b.3	Y54E5B.1b.3	1631	I: 14807466-14813874
Transcript:Y54E5B.1b.2	Y54E5B.1b.2	2583	I: 14807466-14815753
Transcript:Y54E5B.1a.1	Y54E5B.1a.1	2546	I: 14807468-14815725
Transcript:Y54E5B.1b.1	Y54E5B.1b.1	2559	I: 14807468-14815725
Transcript:Y54E5B.1b.4	Y54E5B.1b.4	2581	I: 14807480-14815718

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y54E5B.1c	Y54E5B.1c	2145	I: 14807480-14807585
CDS:Y54E5B.1b	Y54E5B.1b	795	I: 14807480-14807585
CDS:Y54E5B.1a	Y54E5B.1a	2139	I: 14807480-14807585

7 RNAi Result

• WBRNAi00057388
• WBRNAi00091930
• WBRNAi00004745
• WBRNAi00022980
• WBRNAi00022981
• WBRNAi00116872
• WBRNAi00065917

144 Allele

• gk963849
• gk964175
• gk962681
• h13163
• h5231
• gk963947
• gk963269
• gk964059
• gk963714
• gk963713
• otn12856
• WBVar00247584
• gk130061
• gk130060
• gk130063
• gk130062
• gk130057
• gk130059
• gk130058
• gk130065
• gk130064
• gk130066
• gk130068
• gk130067
• gk130070
• gk130069
• gk130056
• gk130055
• WBVar01435083
• WBVar01435082

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004889
• Start: 14807462
• End: 14815753
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

133 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 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 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 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
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_aging
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
	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
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	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 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 that showed significantly increased expression in clk-1(qm30) 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:clk-1(qm30)_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) 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:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in isp-1(qm150) 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:isp-1(qm150)_upregulated
	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-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched

8 Expression Patterns

• Primary Identifier: Expr2034155
• 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: Expr1885
• Pattern: In animals transgenic for the smp-1::lacZ reporter constructs, beta-galactosidase is first detected in epidermal cells at the beginning of morphogenesis 200 minutes after fertilization. GFP fluorescence from smp-1::gfp expression is initially observed at approximately the 50 cell stage in the E lineage. Later, in larvae and adults, GFP can be seen in all body wall, vulval, uterine and enteric muscles, as well as male-specific muscles of the tail and copulatory system. In adults, smp-1::gfp is expressed in the tail tip (hyp 10), in ray 6 and in the spicules of the adult male. Approximately 10 sensory neuron support cells in the head with dendrites extending to the tip of the head, also express the smp-1 GFP and beta-galactosidase transcriptional reporters. GFP fluorescence is observed in several individual cells, including an interneuron (tentatively identified as AVL), the excretory channel, the distal tip cells (DTCs) throughout their migration, somatic cells of the gonad, and epidermal cells hyp 4 (and possibly hyp 3) and hyp 10. In the adult, expression was observed in the fused seam cell syncytium comprising the lateral epidermis. Although ray 6 expresses in the adult male tail, it is difficult to determine whether the ray 6 precursors or any other ray or SET precursors or progeny express smp-1::gfp during the L3 and L4 stages of development when the male tail is forming. This is because GFP fluorescence in the male sex-specific muscles is so bright at this stage as to obscure what may be faint expression of other cells in the male tail.

• Primary Identifier: Expr1032428
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3276
• Pattern: The smp-1::egfp expression was detected in all vulval precursor cells and their descendants. In addition to the vulva, smp-1::egfp was detected in larval seam cells, the epidermal cells of a larval male tail, and some neurons in the ventral cord and around the nerve rings. The ventral and dorsal cords also expressed GFP. hyp7 did not appear to express the transgene. The expression pattern resembled that of plx-1::egfp.

• Primary Identifier: Expr9188
• Pattern: smp- 1::gfp is strongly expressed in the male hook. Expression was observed at the cell membrane of the developing male hook precursors, the adult hook, in rays 7, 8 and 9, and in the bursa of the male tail. No expression was observed in ray 1-6 lineages.
• Subcellular Localization: [smp-1::gfp] is expressed at the cell membrane of the developing hook stage male and in adult hook cells in wild-type males.

• Primary Identifier: Expr1026364
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015922
• 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: Expr1160822
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

16 GO Annotation

70 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004889
• Start: 14807462
• End: 14815753
• Strand: 1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 8292

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00029151

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_14806474..14807461
• Length (nt): 988
• Chromosome Location: I: 14806474-14807461
• Organism: Caenorhabditis elegans