WormMine: Gene WBGene00000099

• WormBase Gene ID: WBGene00000099
• Gene Name: air-2
• Sequence Name: B0207.4
• Brief Description: air-2 encodes an aurora/Ipl1-related serine/threonine protein kinase that affects embryonic viability and chromosome segregation during meiosis and mitosis and is required for cytokinesis; AIR-2 has two functions during mitosis, one in chromosome segregation, and a second, independent function in cytokinesis through ZEN-4; AIR-2 and ZEN-4 may act in parallel to a second pathway that includes CYK-1; AIR-2 phosphorylates two adjacent, evolutionarily conserved C-terminal serines of the inner centromere protein ICP-1; AIR-2 i modified in vitro by the GEI-17 E3 SUMO ligase; AIR-2 forms a robust complex with CSC-1, BIR-1, and ICP-1; air-2 is expressed highly in embryos, in the mature oocytes, spermatocytes, and extruded polar bodies.
• Organism: Caenorhabditis elegans
• Automated Description: Enables ATPase binding activity; kinesin binding activity; and protein kinase activity. Involved in several processes, including chromosome condensation; regulation of actomyosin contractile ring contraction; and spindle midzone assembly. Located in condensed nuclear chromosome and spindle midzone. Expressed in oocyte and sperm. Human ortholog(s) of this gene implicated in several diseases, including carcinoma (multiple); invasive ductal carcinoma; and prostate carcinoma in situ. Is an ortholog of human AURKB (aurora kinase B).
• Biotype: SO:0001217
• Genetic Position: I :0.482005 ±0.002155
• Length (nt): 1687

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000099

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0207.4.2	B0207.4.2	1191	I: 5937195-5938881
Transcript:B0207.4.1	B0207.4.1	1112	I: 5937477-5938876

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:B0207.4	B0207.4	918	I: 5937484-5937551

63 RNAi Result

• WBRNAi00070221
• WBRNAi00085260
• WBRNAi00083323
• WBRNAi00080506
• WBRNAi00086671
• WBRNAi00086666
• WBRNAi00086675
• WBRNAi00027839
• WBRNAi00099900
• WBRNAi00100340
• WBRNAi00108297
• WBRNAi00084092
• WBRNAi00086692
• WBRNAi00086690
• WBRNAi00038718
• WBRNAi00116256
• WBRNAi00091265
• WBRNAi00117207
• WBRNAi00069120
• WBRNAi00117212
• WBRNAi00092746
• WBRNAi00116253
• WBRNAi00100714
• WBRNAi00101229
• WBRNAi00101286
• WBRNAi00099294
• WBRNAi00099496
• WBRNAi00099698
• WBRNAi00101248
• WBRNAi00101267

19 Allele

• gk962858
• gk962706
• gk963902
• gk964505
• WBVar01694800
• WBVar01782760
• or207
• h12728
• gk408895
• gk602594
• ok298
• gk407288
• WBVar00153878
• h289
• gk112064
• e2631
• ttTi265
• gk814531
• gk323145

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000099
• Start: 5937195
• End: 5938881
• 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_5938882..5942389
• Length (nt): 3508
• Chromosome Location: I: 5938882-5942389
• Organism: Caenorhabditis elegans

168 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	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)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
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
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
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 with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	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 (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
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly decreased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_downregulated
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
	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 the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated

11 Expression Patterns

• Primary Identifier: Expr2009278
• 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: Expr1030049
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8787
• Remark: Picture: Figure 5C.
• Subcellular Localization: During spermatogenesis, AIR-2 localized along the axes of pachytene chromosomes and departed during early diplotene as in oogenesis. However, AIR-2 exhibited a phased reassociation to chromosomes during karysome formation reaching high levels on late karyosome nuclei and concentrating in discrete regions visible on the external surface. As spermatocytes detached from the rachis and transitioned to prometaphase, AIR-2 localized on the short arm of the bivalents. This shift in AIR-2 localization may reflect active cycles of AIR-2 unbinding and rebinding the chromatin or, alternatively, the passive movement of chromatin-bound AIR-2 on structurally dynamic chromosomes.

• Primary Identifier: Expr2027515
• 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: Expr11619
• Remark: Temporal description.
• Subcellular Localization: In wild-type embryos, GFP::AIR-2 was localized to prophase and metaphase chromosomes. Following chromosome separation, GFP::AIR-2 was present on both chromosomes and midzone microtubules. In telophase, GFP::AIR-2 was predominantly localized to midzone microtubules.

• Primary Identifier: Expr1200199
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1258
• Pattern: AIR-2 protein was specifically localized to meiotic chromosomes. Diffuse AIR-2 staining was found in the syncytial distal gonad and the cellularized oocytes of the proximal gonad. In the oocyte most proximal to the spermatheca, a striking localization of AIR-2 to meiotic chromosomes was found. Occasionally, faint AIR-2 staining of chromosomes was noticed in the neighboring oocyte as well. AIR-2 immunostaining of fixed gonads dissected from C. elegans males revealed that AIR-2 was also present on meiotic chromosomes in spermatocytes. AIR-2 staining was also found in mature sperm present in both males and hermaphrodites. However, in this case staining did not appear to be chromatin associated. Instead, AIR-2 appeared to be present in the cytoplasm and/or on the sperm membrane.
• Subcellular Localization: AntiAIR-2 staining of meiotic chromosomes persisted throughout both meiotic divisions and remained on the extruded polar body chromatin throughout embryogenesis. The staining of meiotic chromatin appeared to be localized to the interior face of the chromosomes. During both meiotic anaphases, AIR-2 staining was localized between the separating chromosomes.

• Primary Identifier: Expr1902
• Remark: No detailed description on cellular expression patterns.
• Subcellular Localization: At anaphase I, when homologues separate, AIR-2 is detected only in the microtubule midzone between homologues.

• Primary Identifier: Expr1889
• Remark: No detailed description on cellular expression patterns.
• Subcellular Localization: During late diakinesis and metaphase I, AIR-2 is restricted to a defined short segment of the bivalents (the highly condensed pairs of homologs). At anaphase I, AIR-2 relocalize to the midzone of the meiotic spindle.

• Primary Identifier: Expr1142927
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1025517
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

50 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000099
• Start: 5937195
• End: 5938881
• Strand: 1

50 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1687

1 Sequence Ontology Term