WormMine: Gene WBGene00004749

• WormBase Gene ID: WBGene00004749
• Gene Name: sdn-1
• Sequence Name: F57C7.3
• Brief Description: sdn-1 encodes a homolog of vertebrate syndecan-2, a type I transmembrane heparan sulfate proteoglycan; by homology, SDN-1 is predicted to play a role in cell-cell and cell-matrix adhesion; loss of sdn-1 activity via RNA-mediated interference (RNAi) indicates that SDN-1 is required for backward locomotion and for normal development of the egg-laying system, particularly gonadal and vulval structures; SDN-1 is expressed in a subset of neuronal cell bodies and their associated processes in the nerve ring, and also in select tail neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in embryo development; epidermis morphogenesis; and nematode larval development. Located in cell surface. Expressed in several structures, including neuroblasts; neurons; pharynx; somatic nervous system; and vulva. Human ortholog(s) of this gene implicated in several diseases, including Hodgkin's lymphoma; cleft lip; and glucose metabolism disease (multiple). Is an ortholog of human SDC1 (syndecan 1); SDC2 (syndecan 2); and SDC4 (syndecan 4).
• Biotype: SO:0001217
• Genetic Position: X :2.31221 ±0.009839
• Length (nt): 3565

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004749

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F57C7.3a.1	F57C7.3a.1	1508	X: 10589770-10593334
Transcript:F57C7.3b.1	F57C7.3b.1	1490	X: 10589785-10593334

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F57C7.3b	F57C7.3b	864	X: 10590355-10590530
CDS:F57C7.3a	F57C7.3a	867	X: 10590355-10590530

9 RNAi Result

• WBRNAi00048861
• WBRNAi00109625
• WBRNAi00033032
• WBRNAi00109237
• WBRNAi00065732
• WBRNAi00109334
• WBRNAi00102205
• WBRNAi00109528
• WBRNAi00109431

60 Allele

• gk964260
• gk962707
• WBVar01928180
• gk963252
• WBVar01759269
• gk292232
• gk723115
• WBVar02121065
• WBVar02074533
• gk463787
• gk411452
• WBVar02124143
• WBVar02120546
• WBVar01711115
• ev697
• zh20
• WBVar01551975
• WBVar00064044
• WBVar00064049
• WBVar00064054
• WBVar01620343
• gk292234
• gk292233
• gk544111
• gk292231
• gk643067
• gk292230
• gk407238
• gk292229
• gk411453

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004749
• Start: 10589770
• End: 10593334
• 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_10589735..10589769
• Length (nt): 35
• Chromosome Location: X: 10589735-10589769
• Organism: Caenorhabditis elegans

124 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
	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 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
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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: 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 mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	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
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_upregulated
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_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 animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult
	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
	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
	Developmentally modulated gene cluster.	self-organizing map	cgc4386_cluster_6_5
EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food.	Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:EtBr-exposed_vs_UVC-exposed_51h
24 hours of AgNPs exposure.	Genes downregulated more than 2 fold after 24 hours of AgNPs exposure.	Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL).	WBPaper00034661:AgNPs_downregulated

12 Expression Patterns

• Primary Identifier: Expr4386
• Pattern: SDN-1::GFP transgenes were expressed in many ventral neuroblasts during their migrations, prior to and during epidermal enclosure; in later embryogenesis SDN-1::GFP was mainly expressed in the nervous system (nerve ring localization, nr) and pharynx (ph).

• Primary Identifier: Expr3763
• Pattern: In embryos and L1 larvae, SDN-1::GFP was expressed in many tissues, including neurons, pharynx and hypodermis. In later larval stages and in adult worms, SDN-1::GFP was predominantly expressed in the nervous system, with strong expression in the nerve ring and the VNC motoneurons. Apart from the neuronal expression, SDN-1::GFP was also found at a lower level in the hypodermis and the vulval cells.

• Primary Identifier: Expr12387
• Pattern: Pmex-5-SDN-1:: GFP colocalized with the membrane marker pleckstrin homology domain PH::mCherry and appeared uniform on the surface of ABar and C at the six-cell stage.

• Primary Identifier: Expr13395
• Pattern: Expression of SDN-1::GFP is seen in the ALM and AVM mechanosensory neurons. Expression was also observed in the motor neurons, motor neuron commissures, dorsal nerve cord, and ventral nerve cord. SDN-1::GFP expression is seen in the HSN neurons. Expression was also detected in the motor neuron commissures and in the hypodermis around the seam cells.

• Primary Identifier: Expr12400
• Pattern: sdn-1/syndecan is expressed in the AVM neuron.

• Primary Identifier: Expr1032346
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3112
• Pattern: Immunoreactivity in heparitinase-treated adult nematodes showed a pattern restricted to neuronal cells, and more specifically, to a set of neuronal processes in the nerve ring and along the ventral and dorsal nerve cords. Immunoreactivity was also seen associated with the vulva of adult worms and the nervous system of L2-L3 larvae. A close localization of heparan sulfate proteoglycans to the nervous system is shown in the merged image. These results suggest that heparan sulfate proteoglycans localize to the nerve ring and close to the nerve cords that run ventrally and dorsally in C. elegans, and also to the vulva.
• Subcellular Localization: The inset shows a higher magnification indicating a close relationship between the neuronal bodies and the heparan sulfate proteoglycans along the ventral nerve cord, probably present in the extracellular matrix.

• Primary Identifier: Expr1152610
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2015666
• 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: Expr1025360
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr12386
• Pattern: A SDN-1::GFP translational fusion was expressed the eight-cell stage. At this stage, SDN-1 associates with a subset of midbody remnants.

• Primary Identifier: Expr2033899
• 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).

19 GO Annotation

15 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004749
• Start: 10589770
• End: 10593334
• Strand: -1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3565

1 Sequence Ontology Term