WormMine: Gene WBGene00006868

• WormBase Gene ID: WBGene00006868
• Gene Name: vab-1
• Sequence Name: M03A1.1
• Brief Description: vab-1 encodes an ephrin receptor; during development, vab-1 activity is required for neural and epithelial morphogenesis as well as for proper axon targeting and neuronal cell migration; in addition, VAB-1 functions as a major sperm protein receptor in a sperm-sensing control mechanism that regulates oocyte meiotic maturation; VAB-1::GFP reporters are expressed in neuronal cells and in oocytes and sheath cells of the proximal gonad.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ephrin receptor activity and protein domain specific binding activity. Involved in several processes, including cell development; embryonic morphogenesis; and regulation of axon guidance. Located in axon and plasma membrane. Expressed in several structures, including P9/10L; hypodermal cell; neuroblasts; neurons; and somatic nervous system. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; aortic dissection; cataract 6 multiple types; and gastrointestinal system cancer (multiple). Is an ortholog of several human genes including EPHB1 (EPH receptor B1); EPHB2 (EPH receptor B2); and EPHB3 (EPH receptor B3).
• Biotype: SO:0001217
• Genetic Position: II :-3.85469 ±0.013028
• Length (nt): 18971

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006868

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:M03A1.1.1	M03A1.1.1	3901	II: 4572000-4590970

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:M03A1.1	M03A1.1	3354	II: 4572089-4572182

27 RNAi Result

• WBRNAi00114278
• WBRNAi00114043
• WBRNAi00114122
• WBRNAi00114201
• WBRNAi00087928
• WBRNAi00087927
• WBRNAi00068257
• WBRNAi00027421
• WBRNAi00025980
• WBRNAi00050843
• WBRNAi00017144
• WBRNAi00022853
• WBRNAi00068573
• WBRNAi00068571
• WBRNAi00068572
• WBRNAi00008221
• WBRNAi00068991
• WBRNAi00068993
• WBRNAi00068992
• WBRNAi00111829
• WBRNAi00086134
• WBRNAi00114005
• WBRNAi00078908
• WBRNAi00078910
• WBRNAi00091858
• WBRNAi00091860
• WBRNAi00091859

418 Allele

• gk963801
• gk963053
• h7172
• h7374
• h12391
• h17103
• WBVar02068148
• WBVar01603719
• WBVar01603723
• WBVar01603722
• WBVar01603721
• WBVar01603720
• WBVar01603727
• WBVar01603726
• WBVar01603725
• WBVar01603724
• WBVar01437534
• WBVar01437532
• WBVar01437533
• WBVar01437531
• WBVar01437538
• WBVar01437539
• WBVar01437543
• WBVar01437544
• WBVar01437541
• WBVar01437542
• WBVar01437540
• WBVar01371978
• WBVar01371989
• WBVar01371956

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006868
• Start: 4572000
• End: 4590970
• 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

164 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 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
	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 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 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
	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 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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_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
	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
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
	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:GABAergic-motor-neurons_L2-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
	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:PVD-OLL-neurons_L3-L4-larva_expressed
	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
	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 pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed

16 Expression Patterns

• Primary Identifier: Expr1439
• Pattern: During ventral enclosure of the epidermis, VAB-1::GFP was expressed in clusters of cells of the head and tail regions. In the head region, VAB-1::GFP was expressed in clusters of presumptive neuronal cells. Early in enclosure these cells appear to lie beneath the epidermal leading cells; later in enclosure, the VAB-1 expressing cells lie anterior to the leading cells. VAB-1::GFP was not detectably expressed in the epidermal leading cells at any stage during ventral enclosure. In the posterior of the embryo, VAB-1::GFP was expressed in several cells, including QV5 and the ventral hyp7 cells posterior to the rectum; VAB-1::GFP was also expressed in several pharyngeal cells. In late embryogenesis and throughout larval and adult development, VAB-1::GFP was localized to the axons of many neurons throughout the nervous system. Thus, in most stages following gastrulation, VAB-1::GFP is widely expressed in the developing nervous system. During ventral enclosure of the epidermis, VAB-1::GFP was expressed in clusters of cells of the head and tail regions. In the head region, VAB-1::GFP was expressed in clusters of presumptive neuronal cells. Early in enclosure these cells appear to lie beneath the epidermal leading cells; later in enclosure, the VAB-1expressing cells lie anterior to the leading cells. VAB-1::GFP was not detectably expressed in the epidermal leading cells at any stage during ventral enclosure. In the posterior of the embryo, VAB-1::GFP was expressed in several cells, including QV5 and the ventral hyp7 cells posterior to the rectum; VAB-1::GFP was also expressed in several pharyngeal cells. In late embryogenesis and throughout larval and adult development, VAB-1::GFP was localized to the axons of many neurons throughout the nervous system. Thus, in most stages following gastrulation, VAB-1::GFP is widely expressed in the developing nervous system.
• Subcellular Localization: Located at axons of many neurons.

• Primary Identifier: Expr11226
• Pattern: vab-1-GFP is expressed in amphid neurons, including ASI, and in nerve ring in larvae.

• Primary Identifier: Expr8834
• Remark: In the overexpressing line (quIs18) DAF-18/PTEN's neuronal expression is restricted to a subset of the head amphid neurons and is expressed weakly in the nerve cord. DAF-18::GFP was also detected in the amphids and ventral nerve cord. Picture: Fig 2.
• Pattern: Immuno-histochemistry experiments reveal that DAF-18/PTEN and VAB-1/EphR are both expressed in the Z2/Z3 germline precursor cells, oocytes, as well as neuronal tissues. In the neuronal tissues, VAB-1/EphR is localized to the ventral nerve cord, nerve ring, and some head neurons.
• Subcellular Localization: VAB-1/EphR is expressed on the membrane of the proximal oocytes, whereas DAF-18/PTEN appears to show membrane and nuclear expression of multiple oocytes in both hermaphrodites and females.

• Primary Identifier: Expr2036084
• 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: Expr1032910
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8095
• Remark: Picture: Figure 2B, 2E,S1.
• Subcellular Localization: In the distal germline, VAB-1::GFP localizes to the plasma membrane of the syncytial germ cells as visualized with an mCherry::PH domain fusion. In proximal oocytes, VAB-1::GFP is predominantly associated with intracellular vesicles both in the interior and at the cortex. The VAB-1::GFP-containing intracellular vesicles vary in size from small puncta to large (0.5 to 1.0 um diameter) ring-like structures. Cortically localized VAB-1::GFP-containing vesicles abut, or are adjacent to, the plasma membrane, and only a small fraction of the VAB-1::GFP signal exhibits colocalization with the mCherry::PH domain plasma-membrane marker.

• Primary Identifier: Expr3782
• Pattern: To investigate the nmr-1 expression pattern, a GFP::NMR-1 translational reporter strain was examined. In dissected gonads, GFP expression is detectable in oocytes and sheath cells of transgenic animals, but not in controls. An identical pattern is observed in VAB-1::GFP-expressing gonads.
• Subcellular Localization: GFP fluorescence co-localizes with F-actin at the oocyte cortex, and it appears enriched at contact sites between the oocytes. VAB-1 and NMR-1 are expressed at the oocyte surface, where they co-localize with F-actin.

• Primary Identifier: Expr2306
• Pattern: Although VAB-1 GFP fluorescence is difficult to detect in all expressing cell types in intact hermaphrodites, it is detectable in dissected gonads using sensitive optical techniques. VAB-1 GFP is observed in oocytes and sheath cells of the proximal gonad arm in transgenics, but not in controls. GFP fluorescence appeared enriched between oocytes, and in the thin sheath cells surrounding them, in a pattern similar to that observed in wild-type gonads incubated with MSP-FITC.

• Primary Identifier: Expr9971
• Subcellular Localization: NCK-1 and VAB-1 co-localized in the cell body and axon of the PLM neurons.

• Primary Identifier: Expr1021751
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr10006
• Pattern: At the onset of pocket closure vab-1 reporters expresses in right and left side analogs of V3 (sporadically), V4, QV5, and P9/10. The reporter also expresses in bridge and scaffold cells, which together comprise a band of PLX-2 and VAB-1 expressing cells that cross the open pocket, referred to below as the plexin band. Expression in all of these cells continues throughout pocket closure and beyond. Among the P cells, expression is most prominent in P9/10 right (R) and left (L) for all reporters.

• Primary Identifier: Expr1107
• Remark: Postembryonic expressed pattern was not described. Reporter gene fusion type not specified.
• Reporter Gene: GFP-tagged VAB-1 was expressed from rescuing transgenes, and detected by staining with anti-GFP antibody.
• Pattern: During ventral enclosure, VAB-1 was expressed in head neurons anterior to the leading cells of the epidermis, and in the ventral body of the embryo.

• Primary Identifier: Expr1154537
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12575
• Pattern: Not detected in ALML nor PLML.

• Primary Identifier: Expr2017948
• 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: Expr1170053
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

31 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006868
• Start: 4572000
• End: 4590970
• Strand: 1

31 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 18971

1 Sequence Ontology Term

• Name: gene

24 Strains

• WBStrain00029414
• WBStrain00029413
• WBStrain00029412
• WBStrain00029425
• WBStrain00029424
• WBStrain00029421
• WBStrain00029420
• WBStrain00036452
• WBStrain00040665
• WBStrain00049277
• WBStrain00005659
• WBStrain00005660
• WBStrain00005368
• WBStrain00008611
• WBStrain00005410
• WBStrain00008609
• WBStrain00005414
• WBStrain00004075
• WBStrain00005346
• WBStrain00005351
• WBStrain00005355
• WBStrain00005347
• WBStrain00005349
• WBStrain00005357

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_4565806..4571999
• Length (nt): 6194
• Chromosome Location: II: 4565806-4571999
• Organism: Caenorhabditis elegans