WormMine: Gene WBGene00006528

• WormBase Gene ID: WBGene00006528
• Gene Name: tba-1
• Sequence Name: F26E4.8
• Brief Description: tba-1 encodes one of nine C. elegans alpha-tubulins; in early embryos, tba-1 is required, partially redundantly with the closely related tba-2, for a number of microtubule-dependent processes and hence, for normal embryonic development; wild-type tba-1 activity is also required for cell migrations as well as motor neuron synapse and axon development; tba-1 is transcribed during oogenesis and widely expressed in the embryo; tba-1 is also expressed in neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Involved in embryo development; establishment of mitotic spindle orientation; and regulation of cytokinesis. Located in axon; somatodendritic compartment; and spindle. Expressed in several structures, including ganglia; germ line; intestine; neurons; and somatic nervous system. Is an ortholog of human TUBAL3 (tubulin alpha like 3).
• Biotype: SO:0001217
• Genetic Position: I :3.90611 ±0.002036
• Length (nt): 1844

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006528

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F26E4.8a.1	F26E4.8a.1	1515	I: 9785781-9787390
Transcript:F26E4.8b.1	F26E4.8b.1	1365	I: 9785933-9787624

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F26E4.8a	F26E4.8a	1350	I: 9785933-9786448
CDS:F26E4.8b	F26E4.8b	1365	I: 9785933-9786448

19 RNAi Result

• WBRNAi00095591
• WBRNAi00085576
• WBRNAi00081309
• WBRNAi00066710
• WBRNAi00045647
• WBRNAi00064969
• WBRNAi00090810
• WBRNAi00076345
• WBRNAi00063084
• WBRNAi00028215
• WBRNAi00000036
• WBRNAi00025254
• WBRNAi00025255
• WBRNAi00063082
• WBRNAi00063085
• WBRNAi00063086
• WBRNAi00065717
• WBRNAi00087201
• WBRNAi00063091

49 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• h3243
• h17884
• gk963405
• zd109
• or346
• ju975
• ju962
• ju973
• ju965
• ju980
• ju966
• ju964
• WBVar01342912
• ju987
• or594
• gk643580
• pg77
• gk775789
• gk770794
• gk1688
• gk415530
• gk878978
• gk562831
• gk897154
• gk451820
• WBVar01910205

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006528
• Start: 9785781
• End: 9787624
• 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_9785725..9785780
• Length (nt): 56
• Chromosome Location: I: 9785725-9785780
• Organism: Caenorhabditis elegans

215 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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
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 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
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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
	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 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
	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: 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
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
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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
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
	Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
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

14 Expression Patterns

• Primary Identifier: Expr2035444
• 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: Expr720
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Prominent staining of the entire nervous system, specially the axonal processes emanating from neuronal cell bodies is observed at all developmental stages. Neuronal processes including axonal and dendrites consistently stains brighter than the cell bodies. Staining is detected in the central neurophil (nerve ring) in the head, the ventral cord consisting of motor neurons along the body length, lateral nerve cords, lumbar commissures and neuronal cell bodies in the tail ganglia. Staining is observed in the six sets of touch receptor neurons ALML, ALMR, PLML, PLMR, AVM and PVM. In the head region, neurons and their axonal and dendritic processes in the anterior ganglia, lateral ganglia, ventral ganglion, retro-vesicular ganglion and the nerve ring consisting of axonal fibres from neurons located in the head and tail ganglia are brightly labeled. Neurons and their axonal processes are stained in the tail, which has a pair of bilaterally symmetric lumbar ganglia, a small dorso-rectal ganglion and the pre-anal ganglion at the posterior end of the ventral cord. Besides the major axonal bundle of the ventral nerve cord, the dorsal nerve cord and a set of lateral cords along the body length are also stained. Muscle cells, intestine and hypodermal cells stain weakly. Staining of the mitotic spindles in C. elegans are clearly visible in embryos and meiotic spindles in the germline cells in the gonad of adult hermaphrodites. Spindles are stained more strongly and non-spindle structures.
• Subcellular Localization: Stained in neuronal processes and cell bodies. Spindles are stained more strongly.

• Primary Identifier: Expr589
• Remark: Reporter gene fusion type not specified. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). tba-1 is referred as a-tubulin in the article.
• Pattern: Strong expression is observed during embryogenesis. Staining is observed in the ventral nerve cord motor neurons, both neuronal cell bodies and their axonal processes along the entire ventral cord in adult animals. Expression is also detected in 6 touch receptors sensory neurons (ALML/R, PLML/R, AVM and PVM), a set 38-39 motor neurons in the ventral nerve cord along the anterior posterior body length of the animal, and a few neurons in the head and tail ganglia.

• Primary Identifier: Expr13369
• Pattern: In lines tagging the amino terminus of TBA-1, we detected fluorescence in body wall muscle, pharynx, intestine, and neurons in the head, tail, and ventral nerve cord. To determine whether tba-1 was expressed in theTRNs, we combined the pg77 TagRFP-T insertionallele with uIs31, which drives expression of GFP exclusively in theTRNs. We found TBA-1 in all six TRNs.

• Primary Identifier: Expr719
• Remark: Reporter gene fusion type not specified. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: Fusion gene selectively expressed in a subset of the nervous system and is not expressed at detectable levels in non neural tissues such as muscle hypodermal tissues, gonad and intestine. Expression is observed in both embryonic and postembryonic development. At 44-cell stage, staining seen in a subset of cells, descendants of the AB founder cell which will form the cells of the nervous system. During the proliferation phase, intensity and number of cells increase considerably but it is difficult to identify individual cells. Most of these cells are clustered in the region that give rise to all ganglia in the head and tail region and the ventral nerve cord of the hatched animals. During late embryogenesis the intensity and number of cells expressing the fusion decreases. In L1 larvae, there is weak staining of the neurons in the head, tail and ventral cord but intensity increases greatly during L2-L4. At larval and adult stages, 6 touch receptor neurons (ALML, ALMR, PLML, PLMR, AVM AND PVM) are stained. The axonal processes of the postembryonic touch cells AVM and PVM are weakly stained, the axonal processes of the embryonic touch cells (ALML, ALMR, PLML, PLMR) are intensely stained. The touch neurons stain weakly in L1 larvae, but by L3 these cells are strongly stained. Among the motor neurons of the ventral nerve cord, embryonically generated DA, DB, motor neurons stain weakly in the embryos and larvae but during L3-L4 larval and adult development intense staining of the 38-39 motor neurons, which include the VA and VB classes.

• Primary Identifier: Expr8293
• Remark: Picture: Fig. 7, Fig. 5, and Fig. S2.
• Subcellular Localization: Meiotic spindle assembly initiates at nuclear envelope breakdown, when a diffuse cloud of microtubules fills the volume of the perforated nucleus. These microtubules then organize into a much smaller assembly of dense microtubule bundles by the time the oocyte ovulates into the spermatheca. By the time the embryo exits the spermatheca and enters the uterus, a bipolar, metaphase-length spindle is present within a vesicle-free zone visible by differential interference contrast. Before NEBD, GFP::TBG-1 became progressively more concentrated on the nuclear envelope as oocyte maturation progressed. At nuclear envelope breakdown, GFP::TBG-1 fluorescence entered the nuclear region, forming a diffuse cloud that might indicate association with either microtubules or vesicles derived from the nuclear envelope. This large, diffuse area of gamma-tubulin enrichment did not contract in diameter nor increase in local intensity, as did the alpha-tubulin. By the time the embryo exited the spermatheca into the uterus, no discrete localization of GFP::TBG-1 was observed in the vesicle-free zone that contains the metaphase I spindle. GFP::MEI-1 was also distributed throughout the volume of the perforated nucleus immediately after nuclear envelope breakdown. GFP::MEI-1 differed from GFP::TBG-1 in that it became highly concentrated on chromosomes and spindle poles during spindle assembly and remained concentrated on these structures throughout meiosis.

• Primary Identifier: Expr1032679
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13372
• Pattern: With conventional transcriptional fusions we detected fluorescence from expression of the tba-1 promoter throughout the body as well as in the TRNs.

• Primary Identifier: Expr2017309
• 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: Expr1013629
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr552
• Remark: Maternal mRNA. Protein description: Tubulin alpha.
• Pattern: Ubiquitous until the 550-cell stage, decreasing with age. After 100-cell stage, could not detect if a minority of cells were unstained

• Primary Identifier: Expr718
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: 0.5 kb fragment of 3' non coding region of the tba-1 tubulin cDNA clone labeled. Low level of transcription of the gene in the embryos, increases during L1-L3 reaching a maximum in L3 larvae. Around the L4 larval molt transcription returns to basal level as in embryos and is maintained at the same level in young adults and gravid adults.

• Primary Identifier: Expr748
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: A single band in the 54 kDa size range stained by 3A5.

• Primary Identifier: Expr1149559
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

23 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006528
• Start: 9785781
• End: 9787624
• Strand: -1

23 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1844

1 Sequence Ontology Term