WormMine: Gene WBGene00012735

• WormBase Gene ID: WBGene00012735
• Gene Name: sptf-3
• Sequence Name: Y40B1A.4
• Brief Description: sptf-3 encodes a C2H2 zinc finger domain-containing protein that is a member of the Sp1 family of transcription factors; SPTF-3 activity is required for caspase-dependent and -independent apoptotic cell death of the sisters of two cells: the M4 pharyngeal motor neuron and the AQR sensory neuron; in addition, SPTF-3 plays a role in cell fate specification, embryonic and larval development, and morphogenesis; SPTF-3 regulates apoptosis through transcriptional control of the pro-apoptotic gene egl-1 and of pig-1, which encodes a protein related to AMP-activated protein kinases; an SPTF-3::GFP promoter fusion is expressed ubiquitously in embryos and early larvae, and localizes to the nucleus.
• Organism: Caenorhabditis elegans
• Automated Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific and chromatin binding activity. Involved in several processes, including generation of neurons; nematode larval development; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Expressed in several structures, including MSpaa; hypodermal cell; intestine; pharyngeal cell; and somatic nervous system. Human ortholog(s) of this gene implicated in congenital heart disease and dilated cardiomyopathy. Is an ortholog of human SP1 (Sp1 transcription factor); SP3 (Sp3 transcription factor); and SP4 (Sp4 transcription factor).
• Biotype: SO:0001217
• Genetic Position: I :19.3658 ±0.125194
• Length (nt): 6836

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00012735

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y40B1A.4.1	Y40B1A.4.1	1927	I: 13360053-13366888

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y40B1A.4	Y40B1A.4	1239	I: 13360675-13360843

49 RNAi Result

• WBRNAi00097786
• WBRNAi00106770
• WBRNAi00026682
• WBRNAi00004607
• WBRNAi00056317
• WBRNAi00026683
• WBRNAi00097787
• WBRNAi00106740
• WBRNAi00071074
• WBRNAi00107543
• WBRNAi00036974
• WBRNAi00085653
• WBRNAi00097784
• WBRNAi00112456
• WBRNAi00107155
• WBRNAi00107420
• WBRNAi00107310
• WBRNAi00106775
• WBRNAi00106753
• WBRNAi00106728
• WBRNAi00111757
• WBRNAi00075439
• WBRNAi00104756
• WBRNAi00104757
• WBRNAi00104760
• WBRNAi00104755
• WBRNAi00104758
• WBRNAi00104759
• WBRNAi00104762
• WBRNAi00104761

223 Allele

• gk963849
• gk964175
• h5228
• h6570
• gk963138
• WBVar02066573
• WBVar02066574
• WBVar02066572
• WBVar02066575
• WBVar02124454
• WBVar01434403
• WBVar01434404
• gk126958
• gk126959
• gk126960
• gk126961
• gk126962
• gk126963
• gk126964
• tm608
• tm607
• WBVar01822938
• gk539916
• gk522707
• gk926237
• gk584355
• gk574352
• gk908420
• gk934931
• gk545017

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00012735
• Start: 13360053
• End: 13366888
• 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_chrI_13359644..13360052
• Length (nt): 409
• Chromosome Location: I: 13359644-13360052
• Organism: Caenorhabditis elegans

61 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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 that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_upregulated
	Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:oocyte_vs_mitosis_upregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
	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
	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)
	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 significantly altered expression after 24 hour exposure to nitroguanidine (NQ).	Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%.	WBPaper00055899:nitroguanidine_regulated
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
	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
	Transcripts that showed significantly increased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(zr2012)_upregulated
	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
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated
	Transcripts that showed significantly increased expression in sur-5p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:sur-5p-jmjd-1.2(+)_upregulated
	Transcripts with significantly increased expression in isp-1(qm150) vs. N2, and in isp-1(qm150) ced-4(n1162) vs. ced-4(n1162).	Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets.	WBPaper00045263:isp-1(qm150)_upregulated
	Transcripts with significantly increased expression in nuo-6(qm200) vs. N2, and in nuo-6(qm200);ced-4(n1162) vs. ced-4(n1162).	Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets.	WBPaper00045263:nuo-6(qm200)_upregulated
	Transcripts that showed significantly decreased expression in pals-22(jy3) comparing to in N2 at L4 larva stage.	Differential expression analysis was performed in RStudio (v1.1.453) using R (v3.50) and Bioconductor (v3.7) packages. As outlined in the RNAseq123 vignette, data was imported, filtered and normalized using edgeR, and linear modeling and differential expression analysis was performed using limma. An FDR cutoff of <0.01 was used to define differentially expressed genes; no fold-change criteria was used.	WBPaper00056034:pals-22(jy3)_downregulated
	Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector.	Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples.	WBPaper00051039:germline_enriched
	Genes with differential expression under 0.5mg/l Chlorpyrifos (CPF) treatment at 16 centigrade.	To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade.	WBPaper00040210:Chlorpyrifos_16C_regulated
	Genes with expression level regulated by genotype (N2 vs CB4856) at Old adults stage (214 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0136.	WBPaper00040858:eQTL_regulated_old

9 Expression Patterns

• Primary Identifier: Expr2034338
• 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: Expr7713
• Remark: Clone: pUL#JRH7B9
• Pattern: Weak ubiquitous expression in early and comma stage embryos. Late embryo to adult, expression is seen in the intestine, ventral and dorsal nerve cords and two nerves lateral to the terminal pharyngeal bulb.

• Primary Identifier: Expr3939
• Remark: Reporter gene fusion type not specified.
• Pattern: GFP is expressed ubiquitously in early embryos and at the comma stage. From late embryos to adults GFP is restricted to intestine, ventral and dorsal nerve cords as well two neurons in the head close to the posterior pharyngeal bulb.

• Primary Identifier: Expr11138
• Pattern: GFP::SPTF-3 was expressed ubiquitously in embryos and early larval animals; its expression in the M4 neuron and g1A cells decreased during larval development. GFP::SPTF-3 was strongly expressed in the seam cells and the hyp7 cells. GFP::SPTF-3 expression was observed in MSpaa in embryos and in the M4 neuron at the first larval stage.
• Subcellular Localization: GFP::SPTF-3 localized exclusively to nuclei, consistent with the presumed function of SPTF-3 as a transcription factor.

• Primary Identifier: Expr1035638
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1159805
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2016103
• 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: Expr1026328
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr12484
• Subcellular Localization: A fluorescent SPTF-3 fusion protein localized to all nuclei in gastrulation-stage embryos.

15 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00012735
• Start: 13360053
• End: 13366888
• Strand: -1

15 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6836

1 Sequence Ontology Term