WormMine: Gene WBGene00004254

• WormBase Gene ID: WBGene00004254
• Gene Name: pxf-1
• Sequence Name: T14G10.2
• Organism: Caenorhabditis elegans
• Automated Description: Enables guanyl-nucleotide exchange factor activity. Involved in collagen and cuticulin-based cuticle development; epidermis development; and molting cycle. Located in collagen and cuticulin-based cuticle extracellular matrix. Expressed in several structures, including cholinergic neurons; hermaphrodite somatic gonadal cell; hyp4; intestine; and somatic nervous system. Human ortholog(s) of this gene implicated in familial adult myoclonic epilepsy 7. Is an ortholog of human RAPGEF2 (Rap guanine nucleotide exchange factor 2) and RAPGEF6 (Rap guanine nucleotide exchange factor 6).
• Biotype: SO:0001217
• Genetic Position: IV :4.5551 ±0.000934
• Length (nt): 10054

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004254

Genomics

11 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T14G10.2a.1	T14G10.2a.1	4745	IV: 10164288-10174341
Transcript:T14G10.2b.1	T14G10.2b.1	4928	IV: 10164288-10174341
Transcript:T14G10.2b.2	T14G10.2b.2	4784	IV: 10164331-10174339
Transcript:T14G10.2b.3	T14G10.2b.3	4882	IV: 10164372-10174330
Transcript:T14G10.2b.4	T14G10.2b.4	4715	IV: 10164375-10174330
Transcript:T14G10.2c.1	T14G10.2c.1	258	IV: 10164609-10164915
Transcript:T14G10.2e.1	T14G10.2e.1	3918	IV: 10164609-10170299
Transcript:T14G10.2d.1	T14G10.2d.1	4044	IV: 10164609-10171677
Transcript:T14G10.2b.5	T14G10.2b.5	4550	IV: 10164609-10174330
Transcript:T14G10.2g.1	T14G10.2g.1	3441	IV: 10165839-10170299
Transcript:T14G10.2f.1	T14G10.2f.1	3567	IV: 10165839-10171677

Other

7 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T14G10.2a	T14G10.2a	4413	IV: 10164609-10164646
CDS:T14G10.2d	T14G10.2d	4044	IV: 10164609-10164646
CDS:T14G10.2b	T14G10.2b	3936	IV: 10165839-10165852
CDS:T14G10.2g	T14G10.2g	3441	IV: 10165839-10165852
CDS:T14G10.2c	T14G10.2c	258	IV: 10164609-10164646
CDS:T14G10.2e	T14G10.2e	3918	IV: 10164609-10164646
CDS:T14G10.2f	T14G10.2f	3567	IV: 10165839-10165852

19 RNAi Result

• WBRNAi00053331
• WBRNAi00099893
• WBRNAi00100470
• WBRNAi00018716
• WBRNAi00101880
• WBRNAi00035570
• WBRNAi00100844
• WBRNAi00099691
• WBRNAi00099287
• WBRNAi00099489
• WBRNAi00062373
• WBRNAi00060546
• WBRNAi00060545
• WBRNAi00060547
• WBRNAi00060548
• WBRNAi00100096
• WBRNAi00100283
• WBRNAi00100657
• WBRNAi00101031

117 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963603
• WBVar02021096
• WBVar02021097
• otn670
• WBVar00574047
• WBVar01730597
• WBVar01966882
• WBVar01730598
• WBVar01730595
• WBVar01730596
• WBVar01730599
• WBVar01730593
• WBVar01730594
• gk746981
• gk778138
• gk340118
• gk638749
• gk893343
• gk364970
• gk610390
• gk398328
• gk407413
• gk549247
• gk909393
• gk413027
• gk431028

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004254
• Start: 10164288
• End: 10174341
• 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

122 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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 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 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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
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
	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 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
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 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 decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	Transcripts that were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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 decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched

9 Expression Patterns

• Primary Identifier: Expr3310
• Pattern: Expression was detected first in neuronal precursor cells at the comma stage. Slightly later strong expression was found in the hypodermal cells. In newly hatched L1 larvae this construct continued to be expressed in neuronal cells in the head and tail, in cells of the ventral nerve cord and of the pharynx. During the early L1 stage hypodermal expression disappeared. The GFP-positive neurons in animals carrying pT14G10.2::GFP-II were identified as the RMDD, RMD, RMDV, SMDD, and SMDV, which are ring motoneurons. Also the more posteriorly located BDU cells and the ALN, PVR, and PVT cells in the tail expressed GFP. Analysis of synchronized worms showed that GFP is present around the time of molting, but is barely detectable during part of the intermolts or in adults. During the outgrowth of the gonadal primordium expression was seen in the distal tip cell and oviduct sheath cells.

• Primary Identifier: Expr1032098
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr3309
• Pattern: Expression was first seen at the comma stage in endodermal precursor and slightly later in the hypodermal cells of the embryo. During elongation and larval stages many cells of the embryo express GFP, but particularly strong staining was seen in the hypodermis and gut. In addition, several neurons in the head were brightly labeled. In general, expression in the lateral seam cells and hyp10 was most prominent. However, expression could also clearly be seen in the other hypodermal cells, like the syncytial hyp7 and the Pn.p cells during and after the time of vulval induction. In the adult new sites of strong expression included the hermaphrodite-specific neurons (HSNs) and the oviduct sheath cells. The lateral seam cells, which are fused in the adult and other hypodermal cells were also GFP positive.

• Primary Identifier: Expr16433
• Pattern: PXF-1:3xFLAG was visible in the nerve ring labeled by UNC-10. In the ventral nerve cord, FLAG staining also was observed in axon/dendrites and the cell bodies of motorneurons.

• Primary Identifier: Expr1023061
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015198
• 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: Expr1156917
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2033432
• 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: Expr3634
• Remark: No expression.

15 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004254
• Start: 10164288
• End: 10174341
• Strand: -1

15 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10054

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00029005
• WBStrain00031925
• WBStrain00035167

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10174342..10174394
• Length (nt): 53
• Chromosome Location: IV: 10174342-10174394
• Organism: Caenorhabditis elegans