WormMine: Gene WBGene00009254

• WormBase Gene ID: WBGene00009254
• Gene Name: capg-1
• Sequence Name: F29D11.2
• Brief Description: capg-1 encodes the C. elegans homolog of human CAP-G, a subunit of the condensin I complex that functions to organize chromosomal structure and regulate chromosome segregation; immunoprecipitation experiments using C. elegans embryonic extracts demonstrate that CAPG-1 is a member of two distinct condensin I complexes, condensin I and condensin I-DC, that regulate meiotic and mitotic chromosome segregation and dosage compensation, respectively; immunofluorescence demonstrates that CAPG-1 localizes to meiotic and mitotic chromosomes in a pattern distinct from condensin II subunits and also to X chromosomes during hermaphrodite dosage compensation; CAPG-1 localization to the X chromosome is dependent upon the presence of other condensin I-DC members, such as DPY-26, DPY-27, and DPY-28.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in embryo development; meiotic sister chromatid segregation; and mitotic sister chromatid segregation. Part of dosage compensation complex.
• Biotype: SO:0001217
• Genetic Position: I :2.21072 ±0.00012
• Length (nt): 5294

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00009254

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F29D11.2.1	F29D11.2.1	3830	I: 7634492-7639785

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F29D11.2	F29D11.2	3462	I: 7634838-7634935

27 RNAi Result

• WBRNAi00080266
• WBRNAi00080265
• WBRNAi00080288
• WBRNAi00045928
• WBRNAi00025313
• WBRNAi00025314
• WBRNAi00074253
• WBRNAi00074252
• WBRNAi00074254
• WBRNAi00074257
• WBRNAi00074256
• WBRNAi00003529
• WBRNAi00066107
• WBRNAi00074255
• WBRNAi00080294
• WBRNAi00072459
• WBRNAi00072460
• WBRNAi00031579
• WBRNAi00074251
• WBRNAi00080270
• WBRNAi00080274
• WBRNAi00062069
• WBRNAi00080301
• WBRNAi00080290
• WBRNAi00080289
• WBRNAi00080283
• WBRNAi00080287

63 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• WBVar01432123
• WBVar01432127
• WBVar01432126
• WBVar01432125
• gk319405
• gk856178
• gk856696
• gk751158
• gk801833
• tm1514
• gk703086
• gk684271
• gk824142
• gk558665
• gk738346
• gk870116
• gk716760
• gk437220
• gk694524
• gk596370
• gk650878
• gk805591
• gk325529
• gk922036
• gk894446
• gk370409

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00009254
• Start: 7634492
• End: 7639785
• 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_7634144..7634491
• Length (nt): 348
• Chromosome Location: I: 7634144-7634491
• Organism: Caenorhabditis elegans

128 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
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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
	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
	Transcripts that showed significantly increased 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_upregulated
	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 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 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 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
	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 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
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
	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 altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated
	Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_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 altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated

7 Expression Patterns

• Primary Identifier: Expr2009718
• 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: Expr1034035
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8708
• Remark: Picture: Fig 3, Fig S3.
• Subcellular Localization: In early hermaphrodite embryos, before dosage compensation initiates, DPY-27 appears diffusely nuclear in interphase and absent from mitotic chromosomes. In contrast, CAPG-1 associates with mitotic chromosomes in a discontinuous coating pattern, similar to DPY-26 and DPY-28. The three class I CAPs share this pattern and they colocalize on mitotic chromosomes. This class I CAP pattern differs from the outlining of condensed chromosomes by KLE-2, a pattern observed for other condensin II subunits and coincident with centromere proteins along the outer face of C. elegans holocentric chromosomes. The three class II CAPs share this pattern and they colocalize, although there is little overlap between class I and class II CAP patterns.

• Primary Identifier: Expr9851
• Subcellular Localization: After nuclear envelope breakdown (NEBD), the two condensin complexes occupied distinct domains. Condensin I was found at the interface between homologs marked by reduced DAPI staining ("DAPI-free zone"), whereas condensin II localizes to sister chromatids throughout meiosis. During anaphase, condensin I localized on the acentrosomal meiotic spindle between separating chromosomes. As in mitosis, condensin I colocalized with AIR-2 on chromosomes during prometaphase and metaphase of meiosis, and on the spindle during anaphase. Condensin I localizes to the short arms of bivalents, where cohesion between the exchanged parts of sister chromatids holds homologs together. Condensin localization in the male germline followed the same general pattern. Both condensins I and II began to accumulate in nuclei by late pachytene. Condensin II associated with chromosomes before NEBD, but condensin I chromosomal enrichment was not seen until after NEBD in late diakinesis. Following NEBD, condensin I was between aligned homologs (meiosis I) and between sisters (meiosis II), whereas condensin II remained associated with sister chromatids throughout. Interestingly, condensin I behavior in sperm and oocytes differed at anaphase. In oocytes, condensin I colocalized with microtubules and AIR-2 between separating chromosomes during anaphase. In sperm, AIR-2 and microtubules were not prominent between separating chromosomes, and condensin I was absent from this region. Instead, condensin I and AIR-2 colocalized on the inner edges of separating chromosomes. In early prophase, only condensin II associated with chromosomes. Condensin I loaded onto chromosomes after nuclear pore complexes disassembly in prometaphase. From prometaphase to anaphase, the spatial patterns of condensins I and II were different, with condensin II in a centromere-like pattern and condensin I diffusely coating all chromosomes. During anaphase, condensin I was also seen colocalizing with microtubules at the spindle midzone in addition to the chromosomal signal. The other condensin I CAP subunits, DPY-26 and DPY-28, associated with chromosomes at the same time and with similar patterns to that of CAPG-1. Furthermore, the chromosomal association of CAPG-1 was dependent on the presence of DPY-26 and DPY-28, indicating that the condensin I CAP subunits associate with mitotic chromosomes as a complex.

• Primary Identifier: Expr2027957
• 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: Expr1022216
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149828
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

15 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00009254
• Start: 7634492
• End: 7639785
• Strand: -1

15 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5294

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00007139

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_7639786..7640347
• Length (nt): 562
• Chromosome Location: I: 7639786-7640347
• Organism: Caenorhabditis elegans