WormMine: Gene WBGene00013034

• WormBase Gene ID: WBGene00013034
• Gene Name: tat-1
• Sequence Name: Y49E10.11
• Brief Description: tat-1 encodes one of six C. elegans subfamily IV P-type ATPase that, by sequence similarity, is proposed to function as an aminophospholipid translocase (flippase); TAT-1 activity is required for regulating phosphatidylserine asymmetry on the plasma membrane and thus, for regulation of phagocytic engulfment of cells; in addition, TAT-1 activity is required for phosphatidylserine transport across membranes and elements of membrane trafficking, including the biogenesis of lysosome-derived storage organelles and an early step in endocytosis; a tat-1::gfp promoter fusion is first expressed during embryogenesis and continues through larval and adult stages with expression seen in the intestine, the germ line, the epidermis, body wall and pharyngeal muscles, and the nervous system; in intestinal cells, a TAT-1::GFP isoform localizes to the apical and basolateral cell membranes as well as to organelles such as the Golgi and those of the endosomal pathway; in the germ line, a TAT-1::FLAG fusion protein localizes to the plasma membrane; the TAT-1C isoform, which is expressed in the intestine, physically interacts with the NUM-1A PTB domain.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ATPase-coupled intramembrane lipid transporter activity. Involved in several processes, including lysosome organization; phospholipid translocation; and regulation of phagocytosis, engulfment. Located in several cellular components, including apical plasma membrane; basolateral plasma membrane; and endosome. Expressed in several structures, including intestine. Human ortholog(s) of this gene implicated in cerebellar ataxia, mental retardation and dysequlibrium syndrome. Is an ortholog of human ATP8A2 (ATPase phospholipid transporting 8A2).
• Biotype: SO:0001217
• Genetic Position: III :17.5913 ±0.072775
• Length (nt): 22818

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00013034

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y49E10.11c.1	Y49E10.11c.1	4705	III: 12398901-12421570
Transcript:Y49E10.11a.1	Y49E10.11a.1	4185	III: 12398901-12421718
Transcript:Y49E10.11a.2	Y49E10.11a.2	3936	III: 12398914-12420731
Transcript:Y49E10.11b.1	Y49E10.11b.1	3270	III: 12404132-12420664

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y49E10.11a	Y49E10.11a	3420	III: 12399363-12399460
CDS:Y49E10.11c	Y49E10.11c	3579	III: 12401682-12402063
CDS:Y49E10.11b	Y49E10.11b	3270	III: 12404132-12404204

21 RNAi Result

• WBRNAi00097558
• WBRNAi00057005
• WBRNAi00078010
• WBRNAi00006804
• WBRNAi00097530
• WBRNAi00097531
• WBRNAi00037286
• WBRNAi00097554
• WBRNAi00097557
• WBRNAi00077999
• WBRNAi00078000
• WBRNAi00097549
• WBRNAi00097548
• WBRNAi00097551
• WBRNAi00097550
• WBRNAi00097553
• WBRNAi00097552
• WBRNAi00077712
• WBRNAi00077718
• WBRNAi00077721
• WBRNAi00099120

833 Allele

• gk963887
• gk964363
• gk964364
• otn11178
• gk188302
• gk188301
• gk188304
• gk188303
• gk188306
• gk188305
• gk188307
• gk188309
• gk188308
• gk188311
• gk188310
• gk188313
• gk188312
• gk188315
• gk188314
• gk188316
• gk188318
• gk188317
• gk188320
• gk188319
• gk188322
• gk188321
• gk188298
• gk188300
• gk188299
• gk188346

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00013034
• Start: 12398901
• End: 12421718
• 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

85 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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in daf-2(e1370) 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:daf-2(e1370)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_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 significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria.	Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.	WBPaper00065732:Cry5Ba_upregulated_N2
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly increased 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_upregulated_glp-1(e2141)
24 hours of AgNPs exposure.	Genes downregulated more than 2 fold after 24 hours of AgNPs exposure.	Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL).	WBPaper00034661:AgNPs_downregulated
	Transcripts that showed significantly increased expression in lin-22(ot269) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot269)_upregulated

9 Expression Patterns

• Primary Identifier: Expr2035434
• 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: Expr8396
• Remark: Picture: Figure S1, Figure 2F,I.
• Subcellular Localization: Co-staining with FM4-64, which in C. elegans has been shown to label the later part of the endosomal system and lysosomes: TAT-1C-GFP partially colocalized with the dye, although GFP fluorescence was also clearly seen in parts of the cell not labeled by FM4-64. Co-staining with LysoTracker, which predominantly labels acidified lysosomes, revealed that most TAT-1C-GFP fluorescence was not coincident with that of LysoTracker. TAT-1C-GFP colocalized with monomeric red fluorescent protein (mRFP)-RAB-5, a marker for early endosomes and with mRFP-RAB-7, a marker for early and late endosomes. However, TAT-1C appears not to be restricted to early endosomes because colocalization was also seen with RME-1, a marker for recycling endosomes, and with GRASP55, which labels Golgi. In contrast, little overlap was seen between TAT-1C and the endoplasmic reticulum marker HDEL. The fusion protein, which efficiently rescued the mutant phenotype, localized to the basolateral and apical cell membrane as well as to many internal structures within the cytoplasm. The relative amount of GFP fluorescence associated with the membrane or with cytoplasm varied somewhat during development: in L1 and L2 animals, most GFP fluorescence was cytoplasmic but in older animals, in which the fluorescence was generally weaker, the plasma membrane was also labeled.

• Primary Identifier: Expr8087
• Remark: Picture: Fig. 4.
• Subcellular Localization: Immunostaining of gonads from the smIs142 animals using a monoclonal antibody (M2) to the FLAG epitope revealed that TAT-1 localizes predominantly on the plasma membrane.

• Primary Identifier: Expr9235
• Subcellular Localization: The subcellular localization of TAT-1 in the intestine was determined by expressing TAT-1::CFP under control of the intestine-specific promoter vha-6 (Pvha-6tat-1::yfp). TAT-1 was localized to both plasma membranes and intracellular tubular and vesicular structures and colocalized with CHAT-1. The intestinal tubular and vesicular localization pattern was also observed when the expression of TAT-1 was controlled by the endogenous promoter. To determine the identities of the cytosolic compartments labeled by TAT-1, mCHERRY fusions of different endocytic markers were coexpressed together with CHAT-1::GFP and TAT-1 (Pvha-6chat-1::gfp +Pvha-6tat-1). TAT-1 was included to ensure efficient ER export of CHAT-1::GFP; this combination is subsequently referred to as CHAT-1::GFP for simplicity. CHAT- 1::GFP displayed a tubular and vesicular staining pattern, which did not overlap with either the Golgi marker MANS or the lysosomal marker Lysotracker Red, indicating that CHAT-1 is not on the Golgi or mature lysosomes. No CHAT-1::GFP was found on the RAB-7-positive ring-like structures, suggesting that it is not enriched on late endosomes or early lysosomes. CHAT-1 partially overlapped with RAB-5 on punctate structures, but not on tubule-like structures that were negative for mCHERRY::RAB-5. Thus, a proportion of CHAT-1/ TAT-1 may localize to RAB-5-positive early endosomes. CHAT-1/TAT-1 associates with the tubular membrane of early endosomes and ERCs. CHAT-1::GFP overlapped with mRFP::RME-1 on basolateral tubulo-vesicular structures, indicating that CHAT-1 also localizes to RME-1- positive recycling endosomes.

• Primary Identifier: Expr2017299
• 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: Expr1035794
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9234
• Pattern: TAT-1 was expressed from early embryogenesis through all larval and adult stages in various cell types where CHAT-1 is also expressed. When specifically expressed in intestine cells, CHAT-1 and TAT-1 were found to colocalize to both apical and basolateral membranes as well as various intracellular structures.

• Primary Identifier: Expr1160451
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1025931
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

39 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00013034
• Start: 12398901
• End: 12421718
• Strand: -1

39 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 22818

1 Sequence Ontology Term

• Name: gene

0 Strains

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_12421719..12426892
• Length (nt): 5174
• Chromosome Location: III: 12421719-12426892
• Organism: Caenorhabditis elegans