WormMine: Gene WBGene00000870

• WormBase Gene ID: WBGene00000870
• Gene Name: cyd-1
• Sequence Name: Y38F1A.5
• Brief Description: cyd-1 encodes a cyclin D homolog that is required for escape from G1 cycle arrest in postembryonic blast cells, affects movement and larval viability, and may physically interact with CDK-46 and CKI-1; expressed embryonically primarily in the head, ventral cord, tail, and is later expressed primarily in the seam cells and in the somatic gonad.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Involved in several processes, including developmental process involved in reproduction; regulation of cell cycle process; and regulation of cell division. Acts upstream of or within nematode male tail tip morphogenesis. Predicted to be located in centrosome; cytoplasm; and nucleus. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Expressed in gonad; hypodermis; intestine; neurons; and vulva. Human ortholog(s) of this gene implicated in several diseases, including breast carcinoma (multiple); carcinoma (multiple); and hematologic cancer (multiple). Is an ortholog of human CCND3 (cyclin D3).
• Biotype: SO:0001217
• Genetic Position: II :13.2907 ±0.135916
• Length (nt): 12527

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000870

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y38F1A.5.2	Y38F1A.5.2	2012	II: 12980591-12993117
Transcript:Y38F1A.5.1	Y38F1A.5.1	1776	II: 12988223-12993112

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y38F1A.5	Y38F1A.5	1218	II: 12988223-12988336

23 RNAi Result

• WBRNAi00056036
• WBRNAi00007201
• WBRNAi00007202
• WBRNAi00099827
• WBRNAi00100490
• WBRNAi00022478
• WBRNAi00036855
• WBRNAi00100864
• WBRNAi00071231
• WBRNAi00099221
• WBRNAi00099625
• WBRNAi00099423
• WBRNAi00106162
• WBRNAi00111699
• WBRNAi00022988
• WBRNAi00022989
• WBRNAi00065767
• WBRNAi00100116
• WBRNAi00100303
• WBRNAi00084454
• WBRNAi00100677
• WBRNAi00101051
• WBRNAi00075862

333 Allele

• gk963801
• gk963053
• gk962684
• gk962526
• gk962527
• q626
• WBVar00240486
• WBVar02067230
• gk668205
• gk674464
• ok423
• WBVar01560849
• WBVar01605893
• WBVar00246977
• WBVar00246980
• WBVar01261239
• WBVar01823192
• h4469
• otn2827
• gk942565
• WBVar02048027
• WBVar01936405
• WBVar01936404
• WBVar01936403
• gk942563
• gk942564
• WBVar02010124
• WBVar01249137
• WBVar01539366
• WBVar01249142

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000870
• Start: 12980591
• End: 12993117
• 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_chrII_12993118..12994353
• Length (nt): 1236
• Chromosome Location: II: 12993118-12994353
• Organism: Caenorhabditis elegans

193 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
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	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 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
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_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 expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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 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: 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 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 increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
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 aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	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 increased expression in adr-1(tm668) and adr-1(gv6) comparing to in N2 at L4 larva stage.	DESeq FDR <= 0.05	WBPaper00056617:adr-1_upregulated_L4_transcript
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
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 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals.	CuffDiff, fold change > 2.	WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C

7 Expression Patterns

• Primary Identifier: Expr1030537
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1155
• Remark: mid-embryogenesis (author) = elongating embryo --wjc.
• Pattern: Initially expressed during mid-embryogenesis, primarily in postproliferative hypodermal cells and neurons in the head, ventral cord and tail. This expression fades during morphogenesis so that when the larvae hatch expression is seen primarily in lateral hypodermal cells known as seam cells. Common sites of expression included the P cells and their descendents, lateral seam cells, and somatic gonad and vulva. Expression in the P lineage, whose descendents give rise to numerous ventral cord neurons, often disappeared once proliferation of the lineage was complete whereas expression in the seam cells and somatic gonad often persisted. The somatic gonad expression of cyd-1::GFP was restricted to the spermathecal cells and their precursors. The cyd-1::GFP reporter only showed sporadic expression in intestinal cells reminiscent of ectopic expression sites commonly seen among many different reporter genes.

• Primary Identifier: Expr12577

• Primary Identifier: Expr2010653
• 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: Expr1159559
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1022984
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2028893
• 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).

32 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000870
• Start: 12980591
• End: 12993117
• Strand: 1

32 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes upregulated by CYD-1/CDK-4 for more than two fold.	Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed.	WBPaper00040426:CYD-1_CDK-4_upregulated
	Genes downregulated by CYD-1/CDK-4 for more than two fold.	Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed.	WBPaper00040426:CYD-1_CDK-4_downregulated

1 Sequence

• Length: 12527

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00030564
• WBStrain00034604
• WBStrain00034602
• WBStrain00035845
• WBStrain00047322
• WBStrain00054804

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_12978172..12980590
• Length (nt): 2419
• Chromosome Location: II: 12978172-12980590
• Organism: Caenorhabditis elegans