WormMine: Gene WBGene00004953

• WormBase Gene ID: WBGene00004953
• Gene Name: spd-2
• Sequence Name: F32H2.3
• Brief Description: spd-2 encodes a protein with three predicted coiled-coil domains; SPD-2 activity is essential for centrosome maturation and duplication, and hence for proper mitotic spindle assembly; in regulating the early steps of centrosome maturation, SPD-2 acts together with the coiled-coil protein SPD-5, the Aurora-A kinase AIR-1, and the cytoplasmic dynein DHC-1; in regulating centrosome duplication, SPD-2 likely acts together with the ZYG-1 kinase; in both processes, SPD-2 may function to recruit centrosomal components such as ZYG-9 and microtubule-nucleating gamma-tubulin complexes to the developing centrosome; within centrosomes, SPD-2 localizes to both centrioles and the pericentriolar material; efficient centrosomal localization depends upon AIR-1 and DHC-1, while localization specifically to the pericentriolar material depends upon SPD-5.
• Organism: Caenorhabditis elegans
• Automated Description: Enables molecular adaptor activity and protein kinase binding activity. Involved in several processes, including centriole replication; embryo development; and vulval development. Located in centriole; cytoplasm; and pericentriolar material. Expressed in intestinal cell.
• Biotype: SO:0001217
• Genetic Position: I :3.3366 ±0.001372
• Length (nt): 3097

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004953

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F32H2.3.1	F32H2.3.1	2595	I: 8966985-8970081

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F32H2.3	F32H2.3	2475	I: 8967095-8967425

54 RNAi Result

• WBRNAi00065067
• WBRNAi00066991
• WBRNAi00067055
• WBRNAi00067222
• WBRNAi00067730
• WBRNAi00067810
• WBRNAi00067918
• WBRNAi00063850
• WBRNAi00046161
• WBRNAi00081308
• WBRNAi00099926
• WBRNAi00099932
• WBRNAi00100408
• WBRNAi00100430
• WBRNAi00077880
• WBRNAi00031698
• WBRNAi00071758
• WBRNAi00063851
• WBRNAi00087246
• WBRNAi00087694
• WBRNAi00100782
• WBRNAi00100804
• WBRNAi00071035
• WBRNAi00101235
• WBRNAi00101273
• WBRNAi00101292
• WBRNAi00099320
• WBRNAi00099326
• WBRNAi00099522
• WBRNAi00099528

49 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• gk964252
• WBVar01822911
• gk117840
• gk117841
• gk117842
• gk117843
• gk117844
• gk117845
• or1089
• gk435633
• gk465508
• gk383857
• gk809613
• gk671589
• gk752911
• or293
• or493
• or454
• or655
• gk506887
• gk454237
• gk669400
• mhs580
• wow61
• gk312525

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004953
• Start: 8966985
• End: 8970081
• 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

159 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
	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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
	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
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_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
	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
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	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:Cisplatin_downregulated_WT
	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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	Transcripts that showed significantly decreased expression in pfd-6(gk493446); daf-2(e1370) comparing to in daf-2(e1370).	Limma version 3.24.15. Fold change < 0.67 (p < 0.05).	WBPaper00055827:pfd-6(gk493446)_downregulated
	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

12 Expression Patterns

• Primary Identifier: Expr4224
• Subcellular Localization: These antibodies label preferentially centrioles and, to a lesser extent, the PCM, in a manner indistinguishable from other SPD-2 antibodies. In addition, the signal recognized by these antibodies in the wild-type is abolished in spd-2(RNAi) embryos.

• Primary Identifier: Expr2034260
• 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: Expr1032467
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1150051
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12487
• Subcellular Localization: In wild type larvae, throughout the L1 stage and until 3 hours after the nuclear division, SPD-2 was present at the centrioles in the majority of the intestinal cells. However, SPD- 2 became undetectable during progression through the L2 stage: only half of the intestinal nuclei possessed SPD-2 foci 6-8 hours after the nuclear division. This progressive loss of SPD- 2 precedes its complete elimination by the L3 stage.

• Primary Identifier: Expr2922
• Subcellular Localization: SPD-2 not only associates with centrosomes, but it does so at nearly all of the developmental stages examined. In the hermaphrodite gonad, SPD-2 localizes as discrete perinuclear foci in the mitotic portion of the germline. These foci were also evident during the early stages of oogenesis but were absent in mature oocytes. In contrast, mature sperm retained these SPD-2 foci with each male gamete containing a single dot adjacent to the nucleus. Similarly, in meiotic stage embryos, a single SPD-2-positive dot was observed next to the male pronucleus. In slightly older embryos, one or two perinuclear foci of SPD-2 staining were observed. The intensity of the foci increased with the age of the embryos and at mitosis both spindle poles were brightly stained. As embryos progressed through anaphase and telophase, the intensity of staining gradually diminished. Careful examination of the staining pattern at this stage revealed a diffuse area of SPD-2 material centered on one or two very bright dots. To determine if these central dots corresponded to the position of centrioles, SPD-2 distribution was examined in a strain expressing a GFP-tagged version of the centriole marker SAS-4 and it was found that the SPD-2 and SAS-4-positive dots coincided. SPD-2 probably localizes to both centrioles as well the pericentriolar region. Centrosome staining was also evident in older embryos and SPD-2-positive puncta were seen in young larvae, suggesting that SPD-2 is present at the centrosome throughout the entire life cycle. SPD-2 staining, however, was not restricted to the centrosome. Varying amounts of SPD-2 were also noticed present in the cytoplasm and nuclei of oocytes and embryos.

• Primary Identifier: Marker115
• Pattern: Marker for centrosome.

• Primary Identifier: Expr1024300
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2016025
• 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: Expr2995
• Subcellular Localization: Time-lapse imaging of wild type embryos showed that the level of SPD-2 present on the centrosome increased over time, reaching a maximum at the metaphase to anaphase transition.

• Primary Identifier: Expr1200211
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr2923
• Subcellular Localization: Like the endogenous protein, GFPN-SPD-2 localized to centrosomes throughout the cell cycle. GFP fluorescence was first detected as one or two small foci associated with the male pronucleus. The size and intensity of these foci increased as the cell cycle progressed and peaked during mitosis. As in the case of fixed specimens, fluorescence intensity diminished by telophase, leaving behind two small brightly stained dots. These two dots persisted into the next cell cycle when once again fluorescence intensity gradually increased as the cells progressed toward mitosis. As with immunofluorescence, weak localization of SPD-2 were detected to nuclei.

26 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004953
• Start: 8966985
• End: 8970081
• Strand: -1

26 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3097

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00034761
• WBStrain00040367
• WBStrain00007306
• WBStrain00007385
• WBStrain00007287
• WBStrain00007355
• WBStrain00007382

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_8970082..8970290
• Length (nt): 209
• Chromosome Location: I: 8970082-8970290
• Organism: Caenorhabditis elegans