WormMine: Gene WBGene00001122

• WormBase Gene ID: WBGene00001122
• Gene Name: dyf-6
• Sequence Name: F46F6.4
• Brief Description: dyf-6 encodes several proteins that, while novel, contain orthologs in Drosophila and mammals; during development, dyf-6 activity is essential for establishing the normal dendritic length of the amphid and phasmid chemosensory neurons; a DYF-6::GFP reporter is expressed in amphid and phasmid neurons where it: 1) localizes to dendritic bodies and endings as well as to cell bodies, and 2) appears to undergo intraflagellar transport (IFT); DYF-6::GFP is also seen in hypodermal cells and in additional neurons, including inner labial neurons and a lateral neuron in the vicinity of PDE; genetic mosaic analyses indicate that dyf-6 functions autonomously at the level of the amphid dendritic bundle to regulate proper dendritic morphology.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in intraciliary transport and non-motile cilium assembly. Located in dendrite and neuronal cell body. Expressed in ciliated neurons and hypodermis. Is an ortholog of human IFT46 (intraflagellar transport 46).
• Biotype: SO:0001217
• Genetic Position: X :2.16901 ±0.003805
• Length (nt): 6816

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001122

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F46F6.4a.1	F46F6.4a.1	1707	X: 10379693-10386508
Transcript:F46F6.4c.1	F46F6.4c.1	1212	X: 10379700-10383585
Transcript:F46F6.4d.1	F46F6.4d.1	1146	X: 10379700-10383585
Transcript:F46F6.4c.2	F46F6.4c.2	1555	X: 10379709-10385951
Transcript:F46F6.4b.1	F46F6.4b.1	1033	X: 10385009-10386508

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F46F6.4a	F46F6.4a	1416	X: 10379934-10380149
CDS:F46F6.4b	F46F6.4b	477	X: 10385515-10385648
CDS:F46F6.4c	F46F6.4c	963	X: 10379934-10380149
CDS:F46F6.4d	F46F6.4d	897	X: 10379934-10380149

3 RNAi Result

• WBRNAi00047565
• WBRNAi00047566
• WBRNAi00015120

113 Allele

• gk964260
• gk962707
• WBVar01928133
• WBVar01928134
• WBVar01928135
• WBVar01759143
• WBVar01759145
• WBVar01759144
• WBVar00244859
• WBVar00244860
• WBVar00244862
• WBVar00244861
• WBVar01602130
• WBVar01825262
• otn1020
• otn1021
• WBVar00099845
• WBVar00099844
• WBVar00099846
• m175
• WBVar00082464
• WBVar00082466
• WBVar01981234
• mn346
• WBVar01551801
• WBVar01551800
• WBVar01551799
• WBVar01551798
• WBVar01551797
• gk951834

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001122
• Start: 10379693
• End: 10386508
• 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

134 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	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 glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	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
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in isp-1(qm150) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:isp-1(qm150)_upregulated
	Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:nuo-6(qm200)_upregulated
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in wdr-23(mac32) embryos from parents fed with E. coliHB101, comparing to N2 embryos parents fed with E. coli HB101.	DESeq2, Fold Change > 2 or < 0.5.	WBPaper00059566:wdr-23(mac32)_upregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus
	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
	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

6 Expression Patterns

• Primary Identifier: Expr4523
• Pattern: Expression of DYF-6::GFP is restricted to a few cells from hatching to adulthood. Of particular note, DYF-6::GFP is consistently expressed in the cell bodies, dendritic bodies, and dendritic endings of the phasmid neurons. Expression was also very evident in the dendritic bodies and endings of the amphid sensilla. DYF-6::GFP was faintly and irregularly expressed in the cell bodies of the dye-filling amphid neurons. Expression of DYF-6::GFP was also seen in the hypodermis and in several neuronal cell bodies in the region of the inner labial cell bodies. Finally, expression can be seen in a lateral neuronal cell body in the region of the PDE cell body in older larvae and adults.
• Subcellular Localization: DYF-6::GFP was also expressed in the cell and dendritic bodies of the phasmid neurons in the six dauer larvae (the dendritic bodies were often kinked, as though their linearity had been affected by shrinkage of the body during formation of the dauer state). In four of the animals, DYF-6::GFP indicated that the phasmid neurons had proper dendritic endings, and IFT of the GFP could be easily seen in the endings. In the other two animals, however, DYF-6::GFP did not provide evidence for the existence of dendritic endings for the phasmid neurons, indicating that the endings might occasionally be severely retracted or modified in dauer larvae. For both the amphid and phasmid neurons, the greatest intensity of DYF-6::GFP was in the transition zone between the dendritic bodies and their ciliary endings. Of particular note, anterograde and, to a lesser extent, retrograde movement of GFP particles could be seen along the length of the dendritic endings of both the amphid and phasmid neurons. In the amphid neurons, the particles moved in the anterograde direction over the combined middle and distal segments of the ciliary axoneme at 0.9 +/- 0.1 m/sec. IFT could be seen prior to hatching and throughout postembryonic development and adulthood. IFT of DYF-6::GFP in dauer larvae: Six dauer larvae from SP2730 were picked from plates exhausted of bacteria to NGM plates without bacteria, followed by a further incubation of 3 days. DYF-6::GFP was expressed in the cell bodies and in the dendritic bodies and endings of the dye-filling amphid neurons. Moreover, IFT could be easily seen in the dendritic endings, but there appeared to be fewer GFP particles undergoing IFT in the amphid bundles relative to that seen in non-dauer animals.

• Primary Identifier: Expr1030717
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1151403
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2011136
• 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: Expr2029372
• 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: Expr1017659
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

20 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001122
• Start: 10379693
• End: 10386508
• Strand: -1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6816

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00034417
• WBStrain00034381
• WBStrain00036858
• WBStrain00036887

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_10386509..10392823
• Length (nt): 6315
• Chromosome Location: X: 10386509-10392823
• Organism: Caenorhabditis elegans