WormMine: Gene WBGene00001439

• WormBase Gene ID: WBGene00001439
• Gene Name: fkh-7
• Sequence Name: F26D12.1
• Brief Description: fkh-7 encodes one of 15 forkhead transcriptional regulators encoded by the C. elegans genome; by homology, FKH-7 is predicted to function as a transcription factor that regulates gene expression during development; however, as loss of fkh-7 activity via RNA-mediated interference (RNAi) does not result in any obvious abnormalities, the precise role of FKH-7 in C. elegans development and/or behavior is not yet known; however, reporter gene studies indicate that fkh-7 expression is detected only in neurons of the head and tail ganglia, the nerve cord, and the male tail, suggesting that FKH-7 likely functions in nervous system differentiation.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Expressed in several structures, including intestine; neurons; pharynx; reproductive system; and ventral nerve cord. Human ortholog(s) of this gene implicated in several diseases, including carcinoma (multiple); communication disorder (multiple); and tuberculosis (multiple). Is an ortholog of human FOXP2 (forkhead box P2).
• Biotype: SO:0001217
• Genetic Position: IV :1.89836 ±0.001556
• Length (nt): 25695

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001439

Genomics

16 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:F26D12.1g.1	F26D12.1g.1	3024	IV: 5584684-5610373
MRNA	Transcript:F26D12.1a.1	F26D12.1a.1	3079	IV: 5584684-5610371
MRNA	Transcript:F26D12.1k.1	F26D12.1k.1	3086	IV: 5584684-5610371
MRNA	Transcript:F26D12.1j.1	F26D12.1j.1	3150	IV: 5584684-5610378
MRNA	Transcript:F26D12.1l.1	F26D12.1l.1	1737	IV: 5601707-5609523
MRNA	Transcript:F26D12.1m.1	F26D12.1m.1	1680	IV: 5601707-5609523
MRNA	Transcript:F26D12.1b.1	F26D12.1b.1	1779	IV: 5601707-5609629
MRNA	Transcript:F26D12.1h.1	F26D12.1h.1	1722	IV: 5601707-5609629
MRNA	Transcript:F26D12.1n.1	F26D12.1n.1	846	IV: 5606230-5609523
MRNA	Transcript:F26D12.1o.1	F26D12.1o.1	789	IV: 5606230-5609523
MRNA	Transcript:F26D12.1e.1	F26D12.1e.1	888	IV: 5606230-5609629
MRNA	Transcript:F26D12.1i.1	F26D12.1i.1	831	IV: 5606230-5609629
NcPrimaryTranscript	Transcript:F26D12.1c	F26D12.1c	3192	IV: 5607131-5610322
MRNA	Transcript:F26D12.1p.1	F26D12.1p.1	258	IV: 5608363-5609523
MRNA	Transcript:F26D12.1f.1	F26D12.1f.1	300	IV: 5608363-5609629
NcPrimaryTranscript	Transcript:F26D12.1d	F26D12.1d	1826	IV: 5608497-5610322

Other

14 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F26D12.1g	F26D12.1g	2280	IV: 5584684-5585184
CDS:F26D12.1a	F26D12.1a	2337	IV: 5584684-5585184
CDS:F26D12.1m	F26D12.1m	1680	IV: 5601707-5601859
CDS:F26D12.1h	F26D12.1h	1722	IV: 5601707-5601859
CDS:F26D12.1p	F26D12.1p	258	IV: 5608363-5608444
CDS:F26D12.1f	F26D12.1f	300	IV: 5608363-5608444
CDS:F26D12.1b	F26D12.1b	1779	IV: 5601707-5601859
CDS:F26D12.1e	F26D12.1e	888	IV: 5606230-5606441
CDS:F26D12.1i	F26D12.1i	831	IV: 5606230-5606441
CDS:F26D12.1j	F26D12.1j	2295	IV: 5584684-5585184
CDS:F26D12.1k	F26D12.1k	2238	IV: 5584684-5585184
CDS:F26D12.1l	F26D12.1l	1737	IV: 5601707-5601859
CDS:F26D12.1n	F26D12.1n	846	IV: 5606230-5606441
CDS:F26D12.1o	F26D12.1o	789	IV: 5606230-5606441

13 RNAi Result

• WBRNAi00001459
• WBRNAi00045621
• WBRNAi00045622
• WBRNAi00013934
• WBRNAi00013935
• WBRNAi00065592
• WBRNAi00113575
• WBRNAi00113597
• WBRNAi00022898
• WBRNAi00113705
• WBRNAi00113701
• WBRNAi00065591
• WBRNAi00065590

277 Allele

• gk964500
• gk963722
• gk963417
• otn8730
• gk963150
• gk963375
• gk963416
• tm11341
• WBVar01896551
• WBVar01609432
• WBVar02124896
• gk793
• WBVar02020626
• WBVar00189048
• WBVar00189049
• WBVar00189050
• gk465696
• gk728594
• gk876809
• gk632766
• gk496587
• gk447026
• gk649760
• gk933155
• gk753909
• gk876810
• gk427622
• gk551111
• gk611011
• gk896138

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001439
• Start: 5584684
• End: 5610378
• 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_5610379..5610477
• Length (nt): 99
• Chromosome Location: IV: 5610379-5610477
• Organism: Caenorhabditis elegans

185 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 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 in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	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 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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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 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
	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 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
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
	Transcripts that showed significantly increased expression at the intestine cells of daf-2(e1370) comparing to the intestine cells of N2 animals at L2 larva stage.	DESeq2 (version 1.24.0), fold change >= 2, FDR < 0.05	WBPaper00064632:daf-2(e1370)_upregulated_intestine
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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 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 increased expression in daf-2(e1370;mes-1(bn84ts) comparing to in mes-1(bn84ts).	DESeq2 was used for differential expression analysis. A BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a significance cutoff.	WBPaper00049368:daf-2(e1370)_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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome

13 Expression Patterns

• Primary Identifier: Expr1030864
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9772
• Pattern: Faint neuronal GFP expression was mostly visible in head and tail throughout development. There was also expression in the pharynx and possibly some weak hypodermal/muscle expression.

• Primary Identifier: Expr9773
• Pattern: Broad GFP expression with a relatively strong, nuclear-localized signal throughout development. Expression may occur in all neurons, with particularly high levels in the head and tail. However GFP was also present in the hypodermis or muscle throughout the length of the body, in the developing reproductive system and in the pharynx. Intestinal expression was comparatively low and inconsistent.

• Primary Identifier: Expr9732
• Pattern: Very broad nuclear-localised GFP from the comma stage embryo to the mature adult. Many cells in the head expressed GFP: neurons, hypodermis, pharynx, and possibly body wall muscle. Many cells through the length of the body to the tail expressed GFP: probably hypodermis and muscle. In the L3 and L4, there was possibly some weak GFP expression in the ventral nerve cord. In UL3075, the transgenic strain with the strongest reporter expression, GFP was visible in the spermatheca and vulva, as well as in the intestine although this latter component was only observed inconsistently.

• Primary Identifier: Expr9822
• Pattern: Broad GFP expression was observed from the L1 to the adult. This included extensive neuronal expression in the head and tail. Intestinal expression of GFP was seen in adults inconsistently but was stronger and more consistent in young larvae. There was also GFP expression in the pharynx, which was particularly strong in the L1.

• Primary Identifier: Expr2338
• Remark: Reporter gene fusion type not specified.
• Pattern: Reporter gene expression was observed in many nerve cells in the head ganglia, the nerve cord and in the tail ganglia. Expression was also observed in the pharynx although such expression has been attributed to use of an incomplete promoter fragment as is likely to be the case in this instance. Expression in the male tail was restricted to two nerve cells. The identities of the nerve cells have not been determined.

• Primary Identifier: Expr2339
• Remark: Reporter gene fusion type not specified.
• Pattern: Reporter gene expression was observed in many nerve cells in the head ganglia, the nerve cord and in the tail ganglia. Expression was also observed in the pharynx although such expression has been attributed to use of an incomplete promoter fragment as is likely to be the case in this instance. Expression in the male tail was restricted to two nerve cells. The identities of the nerve cells have not been determined.

• Primary Identifier: Expr9733
• Pattern: Low level GFP expression was observed throughout development, although strongest in the L1. GFP could be seen in a few neurons in the head and tail. Also there was some very faint nuclear localized GFP in the intestine and throughout the body wall, particularly in the adult, which may be hypodermis or muscle.

• Primary Identifier: Expr9831
• Pattern: GFP was observed from the bean stage embryo through to the adult. Fluorescence was diffuse, throughout the body wall, in what appeared to be the hypodermis. The GFP looked to be excluded from the nucleus in some tissues such as the ventral nerve cord. The brightest fluorescence was in neurons in the nerve ring and in other cells in the head, in some cells round the rectum, in the spermathecae, in the ventral nerve cord and in the intestine. Fluorescence was brightest from L2 to L4. UL4077 gave the clearest expression pattern, with the GFP fluorescence much weaker and more diffuse in UL4078 and UL4079, making it difficult to identify components.

• Primary Identifier: Expr2011809
• 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: Expr1016234
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149535
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2030047
• 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).

13 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001439
• Start: 5584684
• End: 5610378
• Strand: 1

13 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 25695

1 Sequence Ontology Term