WormMine: Gene WBGene00016405

• WormBase Gene ID: WBGene00016405
• Gene Name: hecd-1
• Sequence Name: C34D4.14
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable ubiquitin protein ligase activity. Involved in several processes, including hemidesmosome assembly; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and regulation of Notch signaling pathway. Predicted to be located in nuclear speck. Is an ortholog of human HECTD1 (HECT domain E3 ubiquitin protein ligase 1).
• Biotype: SO:0001217
• Genetic Position: IV :3.29078 ±8.2e-05
• Length (nt): 10376

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00016405

Genomics

10 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C34D4.14a.2	C34D4.14a.2	8466	IV: 7134345-7144571
Transcript:C34D4.14e.2	C34D4.14e.2	8458	IV: 7134346-7144570
Transcript:C34D4.14e.1	C34D4.14e.1	8564	IV: 7134346-7144719
Transcript:C34D4.14f.1	C34D4.14f.1	8576	IV: 7134346-7144719
Transcript:C34D4.14g.1	C34D4.14g.1	8466	IV: 7134346-7144720
Transcript:C34D4.14c.1	C34D4.14c.1	8442	IV: 7134347-7144715
Transcript:C34D4.14h.1	C34D4.14h.1	8452	IV: 7134347-7144719
Transcript:C34D4.14a.1	C34D4.14a.1	8561	IV: 7134349-7144713
Transcript:C34D4.14b.1	C34D4.14b.1	8450	IV: 7134349-7144713
Transcript:C34D4.14d.1	C34D4.14d.1	8549	IV: 7134349-7144713

Other

8 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C34D4.14a	C34D4.14a	7947	IV: 7134857-7134964
CDS:C34D4.14b	C34D4.14b	7836	IV: 7134857-7134964
CDS:C34D4.14f	C34D4.14f	7953	IV: 7134857-7134964
CDS:C34D4.14h	C34D4.14h	7830	IV: 7134857-7134964
CDS:C34D4.14c	C34D4.14c	7824	IV: 7134857-7134964
CDS:C34D4.14d	C34D4.14d	7935	IV: 7134857-7134964
CDS:C34D4.14e	C34D4.14e	7941	IV: 7134857-7134964
CDS:C34D4.14g	C34D4.14g	7842	IV: 7134857-7134964

17 RNAi Result

• WBRNAi00094722
• WBRNAi00041872
• WBRNAi00011596
• WBRNAi00076193
• WBRNAi00098190
• WBRNAi00081784
• WBRNAi00081819
• WBRNAi00081848
• WBRNAi00029520
• WBRNAi00083097
• WBRNAi00083123
• WBRNAi00083122
• WBRNAi00001654
• WBRNAi00084240
• WBRNAi00081904
• WBRNAi00110802
• WBRNAi00103055

138 Allele

• gk964500
• gk963722
• gk963417
• gk963416
• WBVar00243462
• WBVar01828109
• WBVar01828110
• h5773
• gk314401
• gk763949
• gk519570
• gk452995
• gk348142
• gk763948
• gk763947
• gk678543
• gk763946
• gk735890
• gk632783
• gk852961
• gk361890
• gk876154
• gk467680
• gk404387
• gk361889
• gk771046
• gk642148
• gk448134
• gk474248
• gk573364

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00016405
• Start: 7134345
• End: 7144720
• 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_chrIV_7134084..7134344
• Length (nt): 261
• Chromosome Location: IV: 7134084-7134344
• Organism: Caenorhabditis elegans

132 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 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
	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 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 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
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_N2
	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
	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
	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
	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 expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:coelomocytes_L2-larva_expressed

7 Expression Patterns

• Primary Identifier: Expr9355
• Pattern: hecd-1 is broadly expressed.

• Primary Identifier: Expr1037027
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2012392
• 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: Expr1022675
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1145889
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr16050
• Subcellular Localization: Using a fluorescent anti-FLAG antibody in fixed embryos, expression of HECD-1 was ubiquitous in the cytoplasm of the developing embryo, but was absent from the nucleus. Embryonic FLAG::HECD-1 had ubiquitous cytosolic expression, including during both meiosis and mitosis, with no detectible enrichment on microtubules.

• Primary Identifier: Expr2030628
• 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).

22 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00016405
• Start: 7134345
• End: 7144720
• Strand: -1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10376

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00032018
• WBStrain00032033

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_7144721..7145351
• Length (nt): 631
• Chromosome Location: IV: 7144721-7145351
• Organism: Caenorhabditis elegans