WormMine: Gene WBGene00000231

• WormBase Gene ID: WBGene00000231
• Gene Name: atx-2
• Sequence Name: D2045.1
• Brief Description: atx-2 is required for early embryonic patterning; it encodes an ortholog of human ataxin-2.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable mRNA binding activity. Involved in several processes, including gamete generation; positive regulation of reproductive process; and regulation of cell cycle. Located in cytoplasm. Expressed in body wall musculature; dorsal nerve cord; germ line; gonad; and ventral nerve cord. Used to study autosomal dominant cerebellar ataxia. Human ortholog(s) of this gene implicated in late onset Parkinson's disease and spinocerebellar ataxia type 2. Is an ortholog of human ATXN2 (ataxin 2) and ATXN2L (ataxin 2 like).
• Biotype: SO:0001217
• Genetic Position: III :2.51032 ±0.003566
• Length (nt): 6663

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000231

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:D2045.1d.1	D2045.1d.1	3213	III: 10461389-10467412
Transcript:D2045.1a.1	D2045.1a.1	3613	III: 10461628-10468051
Transcript:D2045.1c.1	D2045.1c.1	3529	III: 10461713-10468044
Transcript:D2045.1b.1	D2045.1b.1	1913	III: 10464456-10467412

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:D2045.1d	D2045.1d	3213	III: 10461389-10461724
CDS:D2045.1a	D2045.1a	2889	III: 10461713-10461724
CDS:D2045.1b	D2045.1b	1905	III: 10464464-10464815
CDS:D2045.1c	D2045.1c	2802	III: 10461713-10461724

46 RNAi Result

• WBRNAi00043482
• WBRNAi00065646
• WBRNAi00064285
• WBRNAi00062720
• WBRNAi00062721
• WBRNAi00064289
• WBRNAi00062717
• WBRNAi00062718
• WBRNAi00062719
• WBRNAi00064288
• WBRNAi00064290
• WBRNAi00085627
• WBRNAi00007270
• WBRNAi00091001
• WBRNAi00006170
• WBRNAi00062715
• WBRNAi00062714
• WBRNAi00062716
• WBRNAi00062707
• WBRNAi00062708
• WBRNAi00062709
• WBRNAi00062710
• WBRNAi00062711
• WBRNAi00062712
• WBRNAi00062713
• WBRNAi00064291
• WBRNAi00064286
• WBRNAi00080505
• WBRNAi00068317
• WBRNAi00068313

108 Allele

• gk964518
• gk963887
• gk963675
• gk963676
• gk963083
• WBVar01542258
• WBVar01542259
• WBVar01267822
• WBVar01267826
• WBVar01267834
• WBVar01267833
• WBVar01548857
• h6991
• gk184136
• gk184135
• gk184138
• gk184137
• gk184134
• gk184133
• gk184144
• gk184143
• gk184140
• gk184139
• gk184142
• gk184141
• WBVar00565096
• WBVar01416302
• WBVar01332860
• tm3562
• WBVar01939751

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000231
• Start: 10461389
• End: 10468051
• 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_10468052..10468057
• Length (nt): 6
• Chromosome Location: III: 10468052-10468057
• Organism: Caenorhabditis elegans

121 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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 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 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
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_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
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
	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 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
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
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	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
	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 decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
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 found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups).	To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%.	WBPaper00031532:Larva_Pan_Neuronal_Depleted
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

12 Expression Patterns

• Primary Identifier: Expr2009520
• 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: Expr1030148
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12343
• Pattern: atx-2 mRNA was detected throughout the larval and adult germline. (Kohara et al., the Nematode Expression Pattern Database, http://nematode.lab.nig.ac.jp.)

• Primary Identifier: Expr847
• Remark: Reporter gene fusion type not specified.
• Pattern: Expression in the embryos starts at around 4 cell stage. Not expressed in the germline. Expression was seen in neurons and body-wall muscle. Strong beta-gal staining and green fluorescence were observed in the central nervous system. Dorsal and ventral nerve cord also gave a strong signal. Staining was also found in the intestinal lining and the body wall muscle. Transgenic chromosomal arrays are not usually expressed in the germline. However, they are observed to express in early embryos. micro-array data shows that atx-2 present in the germline of L3 and L4 larvae.

• Primary Identifier: Expr4011
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Broadly expressed in gonad.

• Primary Identifier: Expr3070
• Subcellular Localization: In whole-mount preparations of wild-type hermaphrodites and males, the anti-ATX-2 Abs stained throughout the cytoplasm in many, if not all, cell types, with slightly stronger staining in the gonad. This staining is specific to ATX-2, as the gonads of atx-2(RNAi) worms did not stain, nor did somatic cells, with the exception of neurons.

• Primary Identifier: Expr2027757
• 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: Expr13024
• Subcellular Localization: ATX-2: exhibits diffuse cytoplasmic expression in early embryo with occasional punctate foci.

• Primary Identifier: Expr14426
• Subcellular Localization: In mitosis, ATX-2- GFP decorated dynamic puncta of various sizes throughout the cytoplasm of early embryos. These puncta were similar in size to P-granules, except that they did not polarize to the posterior pole after pronuclear meeting, suggesting that they may be RNA stress granules, a previously attributed function for Ataxin-2 in mammalian cells (Nonhoff et al., 2007; Kaehler et al., 2012).

• Primary Identifier: Expr14427
• Subcellular Localization: In metaphase-stage embryos, we detected an enrichment of ATX-2 puncta adjacent to the metaphase plate (white arrowheads), around the centrosomes in anaphase (white arrowheads), on the spindle midzone, and at the midbody during telophase. During anaphase, we observed enrichment of ATX-2- GFP on a round structure in the anterior of the embryo, likely an organelle or vesicle-like structure 2 μm in size. In late-stage (~100 cell) embryos, ATX-2 localized to cytoplasmic puncta, as well as around the periphery of the germline precursor nuclei, Z2 and Z3 cells. Overall we determined that ATX-2 localizes to nonpolarizing cytoplasmic granules, around germline precursor nuclei, and to spindle-associated structures.

• Primary Identifier: Expr1147473
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1016075
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

67 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000231
• Start: 10461389
• End: 10468051
• Strand: 1

67 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6663

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00007402

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_10460552..10461388
• Length (nt): 837
• Chromosome Location: III: 10460552-10461388
• Organism: Caenorhabditis elegans