WormMine: Gene WBGene00003738

• WormBase Gene ID: WBGene00003738
• Gene Name: nid-1
• Sequence Name: F54F3.1
• Brief Description: nid-1 encodes the single C.elegans homolog of the nidogen (entactin) protein; members of the nidogen protein family are structural components of basement membranes and are believed to connect laminin and collagen IV networks together; in C. elegans, nid-1 is not required for basement membrane assembly, however, nid-1 is required for the proper positioning of the longitudinal neurons and to direct axons during migration; nid-1 is also required for synaptogenesis and for normal cholinergic synaptic transmission; nid-1 is expressed in body wall muscle, the PLM neurons, intestinal cells and the distal tip cell and is localized to basement membranes and presynaptic zones.
• Organism: Caenorhabditis elegans
• Automated Description: An extracellular matrix structural constituent. Involved in several processes, including cholinergic synaptic transmission; nervous system development; and positive regulation of anterior/posterior axon guidance. Located in basal part of cell and basement membrane. Expressed in several structures, including enteric muscle; gonad; labial sensillum; neurons; and vulval cell. Is an ortholog of human NID1 (nidogen 1).
• Biotype: SO:0001217
• Genetic Position: V :4.72708 ±0.001213
• Length (nt): 7115

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003738

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F54F3.1b.1	F54F3.1b.1	4830	V: 12910107-12917196
Transcript:F54F3.1c.1	F54F3.1c.1	4018	V: 12910107-12917221
Transcript:F54F3.1a.1	F54F3.1a.1	4997	V: 12910113-12917198

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F54F3.1a	F54F3.1a	4755	V: 12910118-12910222
CDS:F54F3.1b	F54F3.1b	4584	V: 12910118-12910222
CDS:F54F3.1c	F54F3.1c	3747	V: 12910118-12910222

7 RNAi Result

• WBRNAi00093570
• WBRNAi00067111
• WBRNAi00068034
• WBRNAi00068104
• WBRNAi00048375
• WBRNAi00015655
• WBRNAi00092929

106 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• WBVar02061603
• WBVar02061604
• WBVar02061605
• WBVar01868637
• WBVar01868638
• WBVar01868639
• WBVar01868625
• WBVar01868626
• WBVar01868627
• WBVar01868628
• WBVar01868629
• WBVar01868633
• WBVar01868634
• WBVar01868635
• WBVar01868636
• WBVar01868630
• WBVar01868631
• WBVar01868632
• gk893492
• gk501743
• gk355388
• gk932234
• gk847991
• gk572239
• gk520136
• ttTi42482

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003738
• Start: 12910107
• End: 12917221
• 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_12917222..12917449
• Length (nt): 228
• Chromosome Location: V: 12917222-12917449
• Organism: Caenorhabditis elegans

218 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 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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_upregulated
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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	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 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_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
mitochondrial sulfide delivery molecule (mtH2S) AP39	Transcripts that showed significantly increased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:mtH2S-AP39-D0-treatment_upregulated_Day11
	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 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)
	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 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)
Bacteria infection: Photorhabdus luminescens	Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection.	MAANOVA and BRB-Array-Tools.	WBPaper00030985:Photorhabdus_luminescens_downregulated
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_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 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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

10 Expression Patterns

• Primary Identifier: Expr1031748
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019999
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr14282
• Pattern: mkate2::NID-1strongly localized to intestinal BM and localized to gonadal BM and nerve ring, consistent with previous reports. Interestingly, we found that EMB-9::mcherry strongly localized to BM in pharynx, although mkate2::NID-1 was faintly localized at pharyngeal BM. We also confirmed strong expression of EMB-9::mcherry in coelomocytes, but not in the strain expressing mkate2::NID-1. The mkate2::NID-1 and EMB-9::mcherry are similarly localized to BM at gonad and uterus.

• Primary Identifier: Expr1074
• Remark: lima stage (author) = bean embryo (wjc).
• Pattern: NID-1 was first detected in embryos at the beginning of morphogenesis (lima stage) localized to body wall muscle cells. As embryos elongate strong NID-1 staining is seen around body wall muscle cells and diffuse stain begins to accumulate on the surfaces of the pharyngeal and intestinal primordia. Once the embryo has elongated to the 2-fold stage, NID-1 has localized to the basal face of the body wall muscles and shows strong accumulation on the surfaces of the pharyngeal, intestinal, and gonad primordia. In three- and fourfold stage embryos, NID-1 accumulates to higher levels and remains localized under the four body wall muscle quadrants and on the surfaces of the pharynx, intestine, and gonad. In L1 larvae the intensity of staining of body wall muscle, pharynx, and intestine appears reduced, and strong staining associated with the nerve ring becomes apparent. This pattern continues through the L2 and L3 larval stages, with the addition of stronger staining of the distal tip cells as they lead the growth of the gonad. In late L3 to L4 stage larvae particularly strong NID-1 accumulation is seen associated with the distal tip cells and the developing somatic structures of the gonad, the spermatheca, uterus, and vulva. Under the body wall muscles of larval and adult stage animals NID-1 is organized as punctate lines. These lines follow the rows of dense bodies within the muscle cells. NID-1 also accumulates strongly at the outer edges of the muscle quadrants and more weakly at the boundaries between muscle cells within each quadrant. Less organized NID-1 staining is seen in the regions between the body wall muscle quadrants, presumably associated with the epidermal basement membranes in these regions. NID-1 accumulates along the four sublateral nerves that run beneath the center of each muscle quadrant. The sublateral nerves extend along dorso- and ventrolateral tracts from the nerve ring in the anterior of the animal to near the middle of the animal where they turn further lateral to positions coincident with the lateral edges of the body wall muscle quadrants. NID-1 accumulation on these nerves is seen in larval and adult animals and is similar in intensity to the staining at the edges of the body wall muscle quadrants. Staining along the edges of the body wall muscle quadrants appears to be associated with the muscle edges rather than the nerves in these regions because the staining closely follows the edge of the muscles and it does not display the left/right asymmetry expected for the ventral and dorsal nerve cords. Less organized NID-1 staining is also present in the regions between body wall muscle quadrants.
• Subcellular Localization: membranes

• Primary Identifier: Expr1029
• Pattern: Expression is first detected in late gastrulation by the cephalic, inner labial, and outer labial cells. As the embryo elongates and morphogenesis begins, expression in body wall muscle cells is detected by in situ hybridization and is observed by using the GFP reporter. In addition, GFP is observed in the left and right lateral ALM neurons and the anal depressor and intestinal muscle cells. As embryogenesis continues, expression in the body wall muscle declines and is not observed in the larval stages. During the larval and adult stages, GFP expression by the PLM neurons, the intestinal cells, and the distal tip cells of the gonad is observed. In addition, transient expression is observed in HSN neurons during the L3 and L4 stages and in ventral nerve cord neurons during the early L2 stage.

• Primary Identifier: Expr1028
• Pattern: Larvae stained with anti-nidogen antiserum show that nidogen is localized to body wall basement membranes. Intense staining is associated with the basement membrane of the body wall muscle.
• Subcellular Localization: basement membrane

• Primary Identifier: Expr1152164
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2567
• Subcellular Localization: At the light microscope level, it is not possible to determine whether NID-1 or CLE-1 is present within or excluded from synaptic clefts. However, these molecules are present at higher concentrations along the lateral region of the nerve cord, where synaptic junctions are abundant, relative to the medial region, which has many fewer synapses. The CLE-1 and NID-1 proteins appear to be present on different faces of the nerve cords relative to synaptic domains. NID-1 is present lateral to the region where synapses form, between the nerve cord and the muscle. CLE-1 is concentrated between the nerve cords and the pseudocoelomic space or overlying muscle arms, i.e., along the dorsal face of the ventral nerve cord and the ventral face of the dorsal nerve cord. Although CLE-1 and NID-1 are found overlapping or closely apposed to UNC-17 along the nerve cords, no consistent association of NID-1 or CLE-1 with UNC-17 puncta was observed, and vice versa. UNC-17 is not present at all of the presynaptic zones in the nerve cords. Similar distributions of CLE-1 and NID-1 relative to a marker for GABAergic presynaptic zones, juIs1, was observed. NID-1 and CLE-1 are also detected in nonsynaptic regions of the nerve cords, but generally at significantly lower levels.

• Primary Identifier: Expr2032501
• 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: Expr2014261
• 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

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003738
• Start: 12910107
• End: 12917221
• Strand: 1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7115

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00022049
• WBStrain00022050
• WBStrain00050778
• WBStrain00005030
• WBStrain00005029

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_12906833..12910106
• Length (nt): 3274
• Chromosome Location: V: 12906833-12910106
• Organism: Caenorhabditis elegans