WormMine: Gene WBGene00001833

• WormBase Gene ID: WBGene00001833
• Gene Name: hcp-6
• Sequence Name: Y110A7A.1
• Brief Description: hcp-6 encodes a HEAT motif-containing protein that displays similarity to the XCAP-D2/CNAP1/Cnd1/YCS4 family of proteins that are homologous to the condensin complex subunit 1; HCP-6 activity is required during mitosis for some aspects of mitotic chromosome condensation, attachment of microtubules to kinetochores, mitotic chromosome alignment, and mitotic sister chromatid segregation; during interphase, HCP-6 is detectable in a punctate pattern in the nucleoplasm; at prophase, HCP-6 becomes associated with condensed chromosomes, colocalizing with the centromeric component HCP-3; HCP-6 localization to chromosomes depends upon the activity of HCP-3 and HCP-4, a C. elegans CENP-C-like protein.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable histone binding activity. Involved in attachment of mitotic spindle microtubules to kinetochore; embryo development; and mitotic chromosome condensation. Located in condensed chromosome, centromeric region and nucleoplasm. Part of condensin complex. Human ortholog(s) of this gene implicated in primary autosomal recessive microcephaly. Is an ortholog of human NCAPD3 (non-SMC condensin II complex subunit D3).
• Biotype: SO:0001217
• Genetic Position: I :-0.329448 ±0.00309
• Length (nt): 6166

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001833

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y110A7A.1b.1	Y110A7A.1b.1	5298	I: 5165148-5171313
Transcript:Y110A7A.1a.1	Y110A7A.1a.1	5285	I: 5165152-5171309

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y110A7A.1a	Y110A7A.1a	5175	I: 5165157-5165340
CDS:Y110A7A.1b	Y110A7A.1b	5277	I: 5165157-5165340

29 RNAi Result

• WBRNAi00073327
• WBRNAi00073329
• WBRNAi00073328
• WBRNAi00099957
• WBRNAi00055321
• WBRNAi00036548
• WBRNAi00100862
• WBRNAi00101233
• WBRNAi00101290
• WBRNAi00116721
• WBRNAi00099351
• WBRNAi00099755
• WBRNAi00101252
• WBRNAi00101271
• WBRNAi00099553
• WBRNAi00101145
• WBRNAi00000214
• WBRNAi00022776
• WBRNAi00100114
• WBRNAi00080300
• WBRNAi00100301
• WBRNAi00100488
• WBRNAi00100675
• WBRNAi00101049
• WBRNAi00101212
• WBRNAi00080297
• WBRNAi00116025
• WBRNAi00116022
• WBRNAi00112095

68 Allele

• gk962706
• gk963902
• otn9311
• WBVar01431564
• WBVar01431563
• gk558014
• gk344914
• gk787669
• gk613531
• gk396671
• gk738871
• gk904054
• gk502532
• gk589214
• gk409199
• gk824615
• gk472484
• gk728841
• gk745696
• gk537164
• gk443092
• gk916140
• gk366652
• gk927362
• gk796842
• gk598142
• gk344913
• gk411947
• gk918918
• gk321012

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001833
• Start: 5165148
• End: 5171313
• 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

156 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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
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
	Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	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
	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 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: 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
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
	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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
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
	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
	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
	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:PVD-OLL-neurons_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 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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
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)

7 Expression Patterns

• Primary Identifier: Expr1031078
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019090
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• 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: Expr2030617
• 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: Expr1158850
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1925
• Remark: No detailed description on cellular expression patterns.
• Subcellular Localization: This antigen localizes to the poleward faces of the metaphase plate, a pattern previously shown to correspond with the holocentric centromere of C. elegans. A double staining experiment with HCP-3, a centromeric histone H3-like protein was performed to confirmed this pattern. Although both of these proteins display a punctate staining pattern in terphase, there was no detectable overlap between the two. In contrast, examination of prophase, metaphase, and anaphase chromosomes revealed that there was nearly complete colocalization between these two proteins. These results confirm that HCP-6 localizes to the C. elegans centromere during mitosis.

• Primary Identifier: Expr2012381
• 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).

24 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001833
• Start: 5165148
• End: 5171313
• Strand: 1

24 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6166

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00000213
• WBStrain00000214

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_5164885..5165147
• Length (nt): 263
• Chromosome Location: I: 5164885-5165147
• Organism: Caenorhabditis elegans