WormMine: Gene WBGene00003111

• WormBase Gene ID: WBGene00003111
• Gene Name: mab-20
• Sequence Name: Y71G12B.20
• Brief Description: mab-20 encodes the C. elegans Semaphorin-2A ortholog; during development, mab-20 activity is required for proper epidermal morphogenesis and axon guidance; specifically, MAB-20, which functions to prevent ectopic, adhesive cell contacts, is required for ventral enclosure during embryogenesis, normal body morphology, and proper formation of sensory rays in the male tail; co-immunoprecipitation experiments demonstrate that MAB-20 interacts with the PLX-2 receptor and that this interaction is strengthened by LAD-2 which can interact with both proteins independently; a MAB-20::GFP reporter, which localizes to the cell surface, is expressed ubiquitously in embryos beginning at morphogenesis; in larvae and adults, MAB-20::GFP is seen in dividing seam cells, neurons, vulval cells, the distal tip cell in hermaphrodites and in males, is additionally seen in the linker cell, cells in the posterior ganglia, and the 9 R(n) ray precursor cells.
• Organism: Caenorhabditis elegans
• Automated Description: Enables semaphorin receptor binding activity. Involved in several processes, including anatomical structure morphogenesis; axonal fasciculation; and regulation of locomotion. Located in cell surface. Expressed in several structures, including linker cell; ray neurons; ray precursor cell; somatic nervous system; and vulval cell. Human ortholog(s) of this gene implicated in rheumatoid arthritis. Is an ortholog of human SEMA3B (semaphorin 3B) and SEMA3C (semaphorin 3C).
• Biotype: SO:0001217
• Genetic Position: I :-13.6256 ±0.025952
• Length (nt): 6870

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003111

Genomics

4 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:Y71G12B.20a.1	Y71G12B.20a.1	2462	I: 1644588-1651457
MRNA	Transcript:Y71G12B.20d.1	Y71G12B.20d.1	1446	I: 1644871-1648439
MRNA	Transcript:Y71G12B.20c.1	Y71G12B.20c.1	1617	I: 1644871-1649497
NcPrimaryTranscript	Transcript:Y71G12B.20b	Y71G12B.20b	2864	I: 1644871-1651255

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y71G12B.20a	Y71G12B.20a	1977	I: 1644871-1645025
CDS:Y71G12B.20c	Y71G12B.20c	1617	I: 1644871-1645025
CDS:Y71G12B.20d	Y71G12B.20d	1446	I: 1644871-1645025

3 RNAi Result

• WBRNAi00000882
• WBRNAi00058207
• WBRNAi00065918

183 Allele

• gk963902
• gk963630
• gk963701
• WBVar01430286
• WBVar00247981
• WBVar01711903
• WBVar01711905
• WBVar01711904
• WBVar01711906
• WBVar02120756
• gk963316
• WBVar02120561
• WBVar01820953
• WBVar01820954
• WBVar01820955
• WBVar01545795
• WBVar01930987
• WBVar01930986
• WBVar01930985
• WBVar00149249
• ttTi366
• WBVar00149250
• WBVar00533843
• WBVar00149253
• WBVar00149254
• WBVar00149251
• WBVar00149252
• WBVar01661717
• WBVar01408601
• WBVar01661716

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003111
• Start: 1644588
• End: 1651457
• 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_chrI_1644116..1644587
• Length (nt): 472
• Chromosome Location: I: 1644116-1644587
• Organism: Caenorhabditis elegans

174 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
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
	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 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
	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 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 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)
	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 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
	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 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 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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	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
	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:all-neurons_L2-larva_expressed
	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

6 Expression Patterns

• Primary Identifier: Expr1031470
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1034
• Remark: 240 minutes of development (author) = late cleavage stage embryo (curator) Lineage expression: Rn descandents.
• Pattern: Except for an earlier onset of GFP expression from both evpPRII.67 and evpPRII.75, all reporters displayed very similar expression patterns. Embryonic GFP expression reported by evpPRII.14 is first visible at approximately 240 minutes of development and is ubiquitous, a pattern that persists until hatching. At the beginning of each larval stage, dividing seam cells express mab-20::GFP, as do both daughter cells in males and hermaphrodites. After the anterior daughter fuses with surrounding hyp7, mab-20::GFP expression is downregulated or shut off in the both daughters. Other hypodermal expression is not evident in males or hermaphrodites. Other cells that express mab-20::GFP in hermaphrodites include the hermaphrodite-specific neurons at the L4 stage, vulva cells A to F throughout development, the migrating distal tip cells during the L4 stage, and several unidentified neurons within the nerve ring and ventral nerve cord. Expression in males include cells in the posterior ganglia, the migrating male linker cell beginning at the L3 to L4 transition, and the same nerve ring and ventral nerve cord expression observed in hermaphrodites. About 35 hours after hatching, mid-L3 males express mab-20::GFP in the 9 R(n) cells that give rise to the ray precursor clusters. Interior neuronal ganglia also express lower levels of mab-20::GFP at this stage. At 38-40 hours, when ray papillae are just visible, the 9 R(n)s and their descendents express mab-20::GFP. However, the underlying neural ganglia express the same level of GFP as the ray precursors at this stage. This pattern of expression continues until adulthood.

• Primary Identifier: Expr2013323
• 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: Expr2031555
• 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: Expr1161623
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1027836
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

30 GO Annotation

70 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003111
• Start: 1644588
• End: 1651457
• Strand: -1

30 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6870

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00029150
• WBStrain00037940
• WBStrain00007155
• WBStrain00007175

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_1651458..1652875
• Length (nt): 1418
• Chromosome Location: I: 1651458-1652875
• Organism: Caenorhabditis elegans