WormMine: Gene WBGene00006804

• WormBase Gene ID: WBGene00006804
• Gene Name: unc-71
• Sequence Name: Y37D8A.13
• Brief Description: unc-71 encodes an ADAM, a disintegrin and metalloprotease-containing transmembrane protein that is a member of the metzincin superfamily of proteases; UNC-71 is required non-cell autonomously for motor axon guidance and sex myoblast migration; UNC-71 does not appear to have an active metalloprotease domain, but functions with UNC-6/netrin and integrins INA-1/PAT-3 to provide guidance cues during axonal migration; UNC-71 is expressed in a restricted pattern in the excretory and excretory gland cells, some head neurons, the sphincter muscles, and hypodermal cells surrounding the vulva.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable metalloendopeptidase activity. Predicted to be involved in membrane protein ectodomain proteolysis. Located in membrane. Expressed in several structures, including buccal cavity; excretory system; nerve ring; neuronal sheath cell; and neurons. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 61. Is an ortholog of human ADAM22 (ADAM metallopeptidase domain 22) and ADAM23 (ADAM metallopeptidase domain 23).
• Biotype: SO:0001217
• Genetic Position: III :19.2806 ±0.088498
• Length (nt): 10696

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006804

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y37D8A.13.1	Y37D8A.13.1	3410	III: 12881043-12891738

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y37D8A.13	Y37D8A.13	3129	III: 12881193-12881745

17 RNAi Result

• WBRNAi00107787
• WBRNAi00089746
• WBRNAi00066031
• WBRNAi00055870
• WBRNAi00026646
• WBRNAi00027515
• WBRNAi00007648
• WBRNAi00020213
• WBRNAi00077907
• WBRNAi00027827
• WBRNAi00092955
• WBRNAi00070196
• WBRNAi00089187
• WBRNAi00089942
• WBRNAi00090102
• WBRNAi00090260
• WBRNAi00110310

187 Allele

• gk963887
• gk963904
• gk963552
• gk189281
• gk189283
• gk189282
• gk189285
• gk189284
• gk189286
• gk189288
• gk189287
• gk189290
• gk189289
• gk189314
• gk189313
• gk189316
• gk189315
• gk189292
• gk189291
• gk189294
• gk189293
• gk189296
• gk189295
• gk189297
• gk189299
• gk189298
• gk189301
• gk189300
• gk189303
• gk189302

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006804
• Start: 12881043
• End: 12891738
• 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_chrIII_12880702..12881042
• Length (nt): 341
• Chromosome Location: III: 12880702-12881042
• Organism: Caenorhabditis elegans

186 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 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
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_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 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 L3 larva and Late reproduction stage (96 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_developing
	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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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 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
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_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 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
	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
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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
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
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_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
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:A-class-motor-neurons_L2-larva_expressed
	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

10 Expression Patterns

• Primary Identifier: Expr593
• Remark: See Expr594, and Expr595 for expression patterns for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: In L1: mRNA localized to cytosol of many cells indicating syncytial hypodermis. Other larval stages - adult: weaker staining of the hypodermis. Expression also observed in epithelial cells in the anus, deirids, buccal cavity and vulva. Also localized in the pharynx. Adm-1 mRNA is present throughout post embryonic development in the syncytial hypodermis, hypodermal-derived tissues, pharynx and in other cells.

• Primary Identifier: Expr594
• Remark: See Expr593, and Expr595 for expression patterns for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: ADM-1 localized to sperm in the gonads of adult males and inside spermathecae of hermaphrodite. Embryos from 2 cells - beginning of morphogenesis shows punctate staining between cells. Embryos from comma - 2-fold stages of elongation show staining localized between ventral hypodermal cells and in the head. Embryos from 2-fold to 3-fold show strong staining in luminal domains of the pharynx and buccal cavity. After hatching in different larval stages, there are punctate hypodermal staining, bp2 of ADM-1 staining in the head, two large cells stain close to sheath cells associated with chemosensory organs. Two smaller cells in tail correspond to the sheath cells of the phasmids. Staining in the area where sheath cells surround the sensory dendrites and in processes of the sheath cells. The monoclonal antibody stains in the sperm between embryonic cells in the pharyngeal apical domain in sheath cells surrounding sensory neurons, in vulva and in hypodermis. Expression is maintained from sperm throughout all of the embryonic and larval stages and in adults.
• Subcellular Localization: Staining was punctate in structures inside and surrounding the sperm but excluding their nuclei.

• Primary Identifier: Expr2572
• Reporter Gene: [unc-71::gfp] transcriptional fusion. To generate the unc-71 transcriptional GFP construct pCZ411, the 1.7 kb upstream regulatory region of unc-71 was amplified by PCR, and inserted into pPD95.79.
• Pattern: GFP expression was first observed in several posterior cells of comma stage embryos, then in the excretory cell and some head neurons in threefold stage embryos. In L1 to adult worms, continued expression of GFP was observed in several head neurons, the excretory cell and the excretory gland cells, as well as the sphincter muscles. One of the head neurons was identified as the AVG neuron based on the cell position and morphology. In addition, in L4 worms, GFP was seen in a set of hypodermal cells surrounding the vulva, which persisted in the hypodermal cells flanking the vulval opening in adult worms. No GFP expression was detected in the sensory neurons. Faint GFP expression was infrequently detected in one to four neurons in the ventral cord. No expression was observed in the sex myoblasts, nor was GFP detected in the body wall muscles at any stages.

• Primary Identifier: Expr595
• Remark: See Expr593, and Expr594 for expression patterns for the same locus. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Earliest staining against antipeptide antibodies was in embryo 430 mins after first cleavage that had elongated about 1.5-fold. Staining persists throughout development in the sheath cells of amphids and phasmids. At L2, the 16 sheath cells of anterior sensilla localized at the tip of the head area are detected by antibody against extracellular domains of ADM-1. Antibody against peptides bp2 and bp3 show syncytial hypodermis, vulva and mature sperm.
• Subcellular Localization: Staining in sperm, between embryonic cells, in the sheath cells and in the hypodermis appear to be associated with intracellular membranes and the plasma membrane.

• Primary Identifier: Expr2036038
• 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: Expr1032872
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1023584
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017902
• 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: Expr1159397
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2573
• Subcellular Localization: When this construct was expressed under the unc-115 promoter, it fully rescued the movement and motor axon guidance defects in unc-71 mutants. UNC-71::GFP was excluded from cell bodies, and was detected in the areas near the nerve ring and along the nerve cords. This UNC-71::GFP was also expressed in hypodermis using the Pe15*2 promoter, and found that GFP was associated to areas near the nerve cord. Thus, UNC-71 is likely associated with cell membranes.

12 GO Annotation

83 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006804
• Start: 12881043
• End: 12891738
• Strand: -1

12 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10696

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00006386
• WBStrain00005370
• WBStrain00005371
• WBStrain00004180

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_12891739..12905490
• Length (nt): 13752
• Chromosome Location: III: 12891739-12905490
• Organism: Caenorhabditis elegans