WormMine: Gene WBGene00006914

• WormBase Gene ID: WBGene00006914
• Gene Name: vha-5
• Sequence Name: F35H10.4
• Brief Description: vha-5 encodes an ortholog of subunit a of the membrane-bound (V0) domainof vacuolar proton-translocating ATPase (V-ATPase); VHA-5 is orthologousto human ATP6N1A (OMIM:192130), ATP6V0A2, ATP6V0A4 (OMIM:605239, mutatedin distal renal tubular acidosis), and TCIRG1 (OMIM:604592, mutated inosteopetrosis); VHA-5 is expressed broadly in embryos (in dot- orcup-like perinuclear compartments in each cell), and in thepostembryonic pharynx, excretory cell, and epidermal syncytium; VHA-5 isrequired for survival past the L2 larval stage; VHA-5 is required forosmoregulation, since vha-5(mc38) die as fluid-filled L1 larvae; VHA-5is also required for apical secretion of the hedgehog-like proteinsWRT-2 and -8, and this requirement is genetically separable fromV-ATPase activity (i.e., WRT secretion may require only the V0 domain,acting separately from the V1 domain); VHA-5 is required for alaeformation, like the V0 subunits VHA-1 and VHA-4, but not like the V1subunits VHA-8 or VHA-13; in S. cerevisiae, different V0 a-subunits(Stv1p and Vph1p) direct the assembly of V-ATPases to differentmembranes and organelles, suggesting that the profusion of such subunitsin C. elegans (VHA-5, VHA-6, VHA-7, and six UNC-32 isoforms) may have asimilar function; VHA-5 is predicted to capture protons from V-ATPasetransmembrane rotor components and export the protons across themembrane.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable ATPase binding activity. Involved in several processes, including collagen and cuticulin-based cuticle development; exosomal secretion; and multicellular organismal-level water homeostasis. Located in apical plasma membrane; cell body membrane; and cytoplasmic vesicle. Part of vacuolar proton-transporting V-type ATPase complex. Expressed in several structures, including excretory cell; hypodermis; neuronal sheath cell; pharynx; and vulva. Human ortholog(s) of this gene implicated in several diseases, including autosomal recessive cutis laxa type IIA; autosomal recessive osteopetrosis 1; and developmental and epileptic encephalopathy 104. Is an ortholog of several human genes including ATP6V0A1 (ATPase H+ transporting V0 subunit a1); ATP6V0A2 (ATPase H+ transporting V0 subunit a2); and TCIRG1 (T cell immune regulator 1, ATPase H+ transporting V0 subunit a3).
• Biotype: SO:0001217
• Genetic Position: IV :3.70702 ±0.001493
• Length (nt): 3404

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006914

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F35H10.4.1	F35H10.4.1	2965	IV: 8303968-8307369
Transcript:F35H10.4.2	F35H10.4.2	2742	IV: 8303968-8307146
Transcript:F35H10.4.3	F35H10.4.3	2963	IV: 8303972-8307371

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F35H10.4	F35H10.4	2622	IV: 8303995-8304111

14 RNAi Result

• WBRNAi00069755
• WBRNAi00008751
• WBRNAi00046419
• WBRNAi00025394
• WBRNAi00066893
• WBRNAi00031814
• WBRNAi00065029
• WBRNAi00090911
• WBRNAi00103016
• WBRNAi00070602
• WBRNAi00103015
• WBRNAi00103013
• WBRNAi00103014
• WBRNAi00111083

40 Allele

• otn10019
• gk964278
• gk964500
• gk962765
• gk963722
• gk963417
• gk649789
• ok1588
• gk733743
• gk207050
• gk383691
• WBVar01853981
• WBVar02057951
• gk938072
• WBVar02057950
• gk911843
• gk583064
• gk666108
• gk809174
• gk768122
• gk429740
• gk207053
• gk530253
• gk207054
• gk357358
• gk207051
• gk753125
• gk207052
• gk486752
• mc37

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006914
• Start: 8303968
• End: 8307371
• 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

168 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
	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
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 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 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)
	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 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)
	Transcripts that showed significantly increased expression after 24 hours of induction of human beta Amyloid at young adult stage	A 2-fold change in expression level and a false discovery rate analog of p < 0.05.	WBPaper00064130:Beta-Amyloid_24h_upregulated_mRNA
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
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
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	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
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 decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C

11 Expression Patterns

• Primary Identifier: Expr4810
• Remark: Picture: Fig. 1, D and E. Reporter gene fusion type not specified.
• Pattern: VHA-5 is expressed in the H-shaped excretory cell. It is also expressed in the main epidermal syncytium, which had previously been overlooked. VHA-5 colocalized apically with the V1 subunit VHA-8 in both tissues.

• Primary Identifier: Expr4811
• Remark: Picture: Fig. 1 G.
• Subcellular Localization: VHA-5 was localized at the level of apical membrane stacks by immunogold staining.

• Primary Identifier: Expr4813
• Remark: Picture: Figure 7, C and D.
• Pattern: Expression was observed throughout development, starting at midembryogenesis. VHA-5 was also detected at the lumen of the vulva and rectum. In addition, authors found VHA-5 expressed in the sheath cells associated with head and tail sensory organs. Three-dimensional reconstructions showed that VHA-5 and RDY-2 formed a sixfold symmetrical pattern, which includes a larger spot that presumably corresponds to the amphid.
• Subcellular Localization: In the amphid sheath cell, VHA-5 was found in the most distal part of the cell lining the sheath pocket, which can be equated to its apical side.

• Primary Identifier: Expr2403
• Remark: Antibody staining result showed that VHA-5 expression was not observed in the pharynx, where the vha-5::GFP reporter was active, indicating that the expression may be due to an increased copy number of the reporter plasmid. See Expr2406. Reporter gene fusion type not specified.
• Pattern: In transgenic worms carrying the vha-5::GFP construct, a fluorescent signal was strongly detected in an H-shaped excretory cell and the pharynx at the L2 and adult stages. In addition to these cells, the vha-5::GFP fusion was found in hypodermal cells around the vulvae of adult worms.

• Primary Identifier: Expr2036127
• 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: Expr1032931
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1150287
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr850
• Pattern: Precocious and widespread embryonic expression, followed by a more restricted pattern in larvae and adults. mRNAs are present in many tissues where unc-32 is also expressed, but the detailed patterns were different, because the gene is also expressed in the excretory cell and canals and probably some somatic gonad cells.

• Primary Identifier: Expr2406
• Subcellular Localization: VHA-5 was detectable in a dot-like compartment in every embryonic cell. The compartment was found exclusively around the nucleus and observed during embryogenesis. A cup-shaped structure was often observed around nuclei instead of the dot-like compartment. On the other hand, VHA-5 expression changed dramatically at the larval stage and became dominant in an H-shaped excretory cell, consistent with the results for transgenic worms carrying the vha-5::GFP fusion gene. See Expr2403 for vha-5 GFP analysis.

• Primary Identifier: Expr1028179
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017991
• 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).

26 GO Annotation

20 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006914
• Start: 8303968
• End: 8307371
• Strand: 1

26 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3404

1 Sequence Ontology Term