WormMine: Gene WBGene00004732

• WormBase Gene ID: WBGene00004732
• Gene Name: sax-7
• Sequence Name: C18F3.2
• Brief Description: sax-7 encodes an ortholog of human L1CAM, and a paralog of lad-2; L1CAM is a member of the group of highly conserved transmembrane cell adhesion receptor molecules which belong to the immunuglobulin superfamily; SAX-7 is required for axon guidance, neurite outgrowth and maintenance of neuronal positioning through homophilic and heterophilic interactions; sax-7 also affects germline development, embryonic morphogenesis, gonadal morphogenesis and tissue attachment; SAX-7 function is regulated by its physical interaction with the ankyrin UNC-44, and the gamma-syntrophin STN-2; nonphosphorylated SAX-7 is ubiquitously expressed at sites of cell-cell contact and colocalizes with UNC-44.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ankyrin binding activity. Involved in several processes, including cell development; establishment of mitotic spindle orientation; and regulation of cell morphogenesis. Located in several cellular components, including axolemma; lateral plasma membrane; and somatodendritic compartment. Expressed in several structures, including gonad; neurons; pharynx; somatic nervous system; and vulval cell. Used to study MASA syndrome. Human ortholog(s) of this gene implicated in schizophrenia. Is an ortholog of human NFASC (neurofascin) and NRCAM (neuronal cell adhesion molecule).
• Biotype: SO:0001217
• Genetic Position: IV :3.5916 ±0.001877
• Length (nt): 21429

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004732

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C18F3.2c.1	C18F3.2c.1	5393	IV: 8062659-8084087
Transcript:C18F3.2b.1	C18F3.2b.1	4953	IV: 8062669-8083666
Transcript:C18F3.2a.1	C18F3.2a.1	4942	IV: 8066865-8084033
Transcript:C18F3.2d.1	C18F3.2d.1	3444	IV: 8067102-8082763
Transcript:C18F3.2f.1	C18F3.2f.1	2455	IV: 8080091-8084029
Transcript:C18F3.2e.1	C18F3.2e.1	759	IV: 8080530-8082763

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C18F3.2a	C18F3.2a	3435	IV: 8067102-8067188
CDS:C18F3.2d	C18F3.2d	3444	IV: 8067102-8067188
CDS:C18F3.2f	C18F3.2f	750	IV: 8080530-8080596
CDS:C18F3.2e	C18F3.2e	759	IV: 8080530-8080596
CDS:C18F3.2b	C18F3.2b	3987	IV: 8062732-8062780
CDS:C18F3.2c	C18F3.2c	3996	IV: 8062732-8062780

5 RNAi Result

• WBRNAi00001509
• WBRNAi00040967
• WBRNAi00011018
• WBRNAi00101409
• WBRNAi00110314

273 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• otn8751
• otn8752
• gk963416
• nj53
• WBVar01853637
• tm10458
• WBVar01453258
• WBVar01453257
• WBVar01966677
• gk206646
• gk667189
• WBVar01710265
• WBVar02020943
• WBVar02020942
• WBVar02020941
• gk946380
• gk946381
• gk946382
• WBVar00573607
• h8965
• h15192
• h13590
• gk790840
• gk654435
• gk864016
• gk751442

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004732
• Start: 8062659
• End: 8084087
• 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

198 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
	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 altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_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 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
starvation 12 hours	Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals.	EdgeR, FDR < 0.05, fold change >= 2.	WBPaper00067259:starvation_upregulated_intestine
	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 increased expression after 24-hour exposure to 10uM benzyl butyl phthalate (BBP) in col-121(nx3) animals.	DESeq2v1.38.3, FDR < 0.05	WBPaper00067417:benzyl-butyl-phthalate_regulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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 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 were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:dopaminergic-neurons_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:hypodermis_L3-L4-larva_expressed
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	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

20 Expression Patterns

• Primary Identifier: Expr4574
• Pattern: In wild-type animals, sax-7 is expressed in multiple tissues with robust SAX-7 accumulation in the nervous system. Expression was detected in pharynx, gonad, and the nerve ring and ventral nerve cord.

• Primary Identifier: Expr8960
• Remark: Picture: Fig 7.
• Pattern: SAX-7 is also expressed in muscle, as revealed by immunostaining of SAX-7 in wild-type animals.
• Subcellular Localization: SAX-7 is localized to sarcomeres and membrane boundaries; both signals are absent in sax-7(eq1) animals.

• Primary Identifier: Expr11329
• Reporter Gene: [Psax-7::sax-7::gfp::sl2::mCherry] translational fusion.
• Pattern: The mCherry signal revealed that SAX-7 was expressed in the hypodermal cells and in many neurons, but not in PVD. Expression and localization of SAX-7 was observed early in development during the L1 and early L2 stages, long before the formation of PVD branches.
• Subcellular Localization: Within the hypodermal cell, SAX-7::GFP showed specific localization to two sublateral stripes and the hypodermal-seam cell junctions.

• Primary Identifier: Expr1650
• Remark: No detailed description on postembryonic cellular localization.
• Pattern: LAD-1 visualized by immunofluorescence was expressed in all cells throughout development, starting at the onset of embryogenesis with its expression increasing dramatically during embryonic morphogenesis. LAD-1 was highly expressed in the nervous system. LAD-1 is localized to the plasma membrane of the cell bodies and axonal and dendritic processes and in nonneuronal tissues such as the pharynx, hypodermis, body wall muscles, and the germline. Localized LAD-1 was not detected in one-cell embryos, which lack sites of cellular contact.
• Subcellular Localization: LAD-1 is localized to the plasma membrane of the cell bodies and axonal and dendritic processes. LAD-1 was strikingly localized to the plasma membrane at sites of cellcell contact as early as just before the two-cell stage. Localized LAD-1 was not detected in one-cell embryos, which lack sites of cellular contact.

• Primary Identifier: Expr14626
• Pattern: Promoter reporter assays confirmed that sax-7 was expressed in the hypodermal cells and the neurons, including ALA and PVD.

• Primary Identifier: Expr13863
• Pattern: sax-7Spro is expressed throughout the nervous system and, within the amphid, is consistently expressed in AWC, ASE, and ASK.

• Primary Identifier: Expr1769
• Remark: Reference: personal communication from Oliver Hobert 2002-12-07.
• Pattern: Neuronal expression in: 4 labial sensory neurons; all touch neurons, RMG/ADA, CAN. Non-neuronal expression in: valve cells in tail, vulval cells

• Primary Identifier: Expr16122

• Primary Identifier: Expr1032334
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr11334
• Pattern: SAX-7 localized to both the ventral and dorsal nerve cords and thin lines in lateral positions to the nerve cords. This staining may be associated with the nervous system (e.g., the sublateral nerve cords) or the hypodermal ridges.

• Primary Identifier: Expr15287
• Pattern: Examination of a sax-7p::sax-7::gfp reporter revealed widespread expression in dauers and non-dauers, including neuronal and non-neuronal tissues.

• Primary Identifier: Expr14679
• Pattern: A fosmid transgene containing sax-7p::TY1::EGFP was expressed in the DTC and localized to the membrane (n = 7/7).

• Primary Identifier: Expr2015609
• 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: Expr1145009
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3224
• Subcellular Localization: When sax-7shortcDNA::GFP was expressed in sensory neurons or only in AFD neurons using the osm-6 or gcy-8 promoter, respectively, SAX-7short::GFP was localized to the plasma membranes of cell bodies, axons, and dendrites. The fluorescence of the SAX-7short::GFP was especially enriched on the surface.

• Primary Identifier: Expr2033844
• 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: Expr1200347
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1016254
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr15893
• Subcellular Localization: The CCC (HMP-2 and HMR-1) and SAX-7 localize to regions of cell-cell contact.

• Primary Identifier: Expr14628
• Subcellular Localization: SAX-7S::mCherry showed membrane localization

41 GO Annotation

15 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004732
• Start: 8062659
• End: 8084087
• Strand: 1

41 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 21429

1 Sequence Ontology Term

• Name: gene

17 Strains

• WBStrain00021995
• WBStrain00021998
• WBStrain00022007
• WBStrain00022004
• WBStrain00024192
• WBStrain00024194
• WBStrain00029515
• WBStrain00029514
• WBStrain00029513
• WBStrain00029512
• WBStrain00029519
• WBStrain00029518
• WBStrain00029517
• WBStrain00029516
• WBStrain00029741
• WBStrain00031900
• WBStrain00005232

0 Upstream Intergenic Region