WormMine: Gene WBGene00001438

• WormBase Gene ID: WBGene00001438
• Gene Name: fkh-6
• Sequence Name: B0286.5
• Brief Description: fkh-6 encodes one of 15 C. elegans forkhead transcription factors; fkh-6 is required for several aspects of male gonadogenesis including asymmetric cell division, cell migration and sex determination and appears to act downstream of tra-1; FKH-6 is specifically expressed in the gonad of both sexes during L1; expression is hermaphrodite specific during L4 and adult stages in spermatheca and sheath cells.
• Organism: Caenorhabditis elegans
• Automated Description: Enables sequence-specific DNA binding activity. Involved in male germ-line sex determination and male gonad development. Predicted to be located in nucleus. Expressed in gonadal sheath cell; male gonad; somatic gonad precursor; spermatheca; and in male. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 4 and otosclerosis 11. Is an ortholog of human FOXI2 (forkhead box I2) and FOXI3 (forkhead box I3).
• Biotype: SO:0001217
• Genetic Position: II :-4.7304 ±0.005862
• Length (nt): 3822

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001438

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0286.5.1	B0286.5.1	1388	II: 4379585-4383406

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:B0286.5	B0286.5	972	II: 4379883-4380035

25 RNAi Result

• WBRNAi00000360
• WBRNAi00038884
• WBRNAi00038886
• WBRNAi00022897
• WBRNAi00008291
• WBRNAi00099901
• WBRNAi00061163
• WBRNAi00100342
• WBRNAi00028067
• WBRNAi00113572
• WBRNAi00100716
• WBRNAi00071129
• WBRNAi00101089
• WBRNAi00099295
• WBRNAi00099497
• WBRNAi00099699
• WBRNAi00099968
• WBRNAi00100155
• WBRNAi00070161
• WBRNAi00024377
• WBRNAi00085503
• WBRNAi00100529
• WBRNAi00100903
• WBRNAi00101156
• WBRNAi00092016

84 Allele

• gk963801
• gk963053
• h4640
• h7373
• q641
• gk963890
• gk963891
• WBVar01695497
• tm439
• WBVar01719530
• WBVar01719531
• gk5164
• WBVar01626469
• gk962856
• WBVar01626470
• WBVar02006936
• WBVar01239129
• WBVar01247940
• ez16
• WBVar00103575
• WBVar01504952
• WBVar01504950
• WBVar01504951
• WBVar01413351
• WBVar00171330
• WBVar00171333
• WBVar00171334
• WBVar01934557
• WBVar00171331
• WBVar00171332

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001438
• Start: 4379585
• End: 4383406
• 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

104 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
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 glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_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 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 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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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 increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	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 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 significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_upregulated
	Transcripts that showed significantly decreased 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_downregulated
	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)
Bacteria: B.thuringiensis	Transcripts in N2 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_N2
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts that showed siginificantly increased expression in nmad-1(ok3133) comparing to in N2 at 25 entigrade.	edgeR, FDR < 0.05, fold change > 2.	WBPaper00056997:nmad-1(ok3133)_upregulated_germline_25C

10 Expression Patterns

• Primary Identifier: Expr1030863
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13927
• Pattern: In addition to recapitulating previously reported expression patterns [in the gonad from mid-L1 larval stage until around the L1/L2 molt in both sexes and from the L3 larval stage through adult in the hermaphrodite gonad in the spermatheca and sheath cells], this new construct revealed expression of FKH-6::GFP in 2-4 male gonadal cells in the L3 larval stage. This is the first report of FKH-6 expression in males after the L1/L2 molt. The expression of FKH-6::GFP in the gonad of the L3 male is reproducible, appearing in 54 of the 58 male animals observed during this time period, but the expression is short-lived, and coincides with the period when the proximal region of the migrating male gonad is extending past the distal tip of the gonad.

• Primary Identifier: Expr2341
• Remark: Reporter gene fusion type not specified.
• Pattern: Expression was observed in all cells of the spermatheca from the L3 stage onwards and at a lower level in oviduct sheath cells.

• Primary Identifier: Expr2342
• Remark: Reporter gene fusion type not specified.
• Pattern: Expression was observed in all cells of the spermatheca from the L3 stage onwards and at a lower level in oviduct sheath cells.

• Primary Identifier: Expr2011808
• 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: Expr2972
• Pattern: The two reporters have the same expression pattern. Both are expressed in Z1 and Z4 of XO and XX L1 larvae. However, later during L1, the timing of expression is sexually dimorphic: in XO larvae reporter expression persists until late L1 in Z1/Z4 descendants, whereas in XX larvae it decreases in mid L1 and is undetectable by late L1. Later expression also is sexually dimorphic. In L3 hermaphrodites, the fkh-6 reporters resume expression in sheath-spermathecal precursor cells, continuing through adulthood in spermatheca and weakly in proximal sheath. By contrast, no expression was observed in XO animals past the L1 stage. No expression was detectable outside the gonad in larvae or adults of either sex.

• Primary Identifier: Expr2030046
• 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: Expr12422
• Pattern: In wild-type animals of both sexes, fkh-6::GFP expression began in the somatic gonadal precursors at about 6 hr after hatching.

• Primary Identifier: Expr1143072
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1025052
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

16 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001438
• Start: 4379585
• End: 4383406
• Strand: -1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3822

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00037919
• WBStrain00006451
• WBStrain00006445

0 Upstream Intergenic Region