WormMine: Gene WBGene00000223

• WormBase Gene ID: WBGene00000223
• Gene Name: atf-7
• Sequence Name: C07G2.2
• Brief Description: atf-7 encodes a basic-region leucine zipper (bZIP) transcription factor orthologous to members of the ATF2/ATF7/CREB5 family of cyclic AMP-response element binding (CREB)/activating transcription factors (ATFs); ATF-7 plays a key role in the innate immune response by regulating the expression of immune genes downstream of PMK-1/p38 MAPK; ATF-7 is likely converted from a transcriptional repressor to a transcriptional activator in response to phosphorylation by activated PMK-1 with which it physically interacts and serves as a substrate in heterologous expression assays; an ATF-7::GFP reporter fusion is expressed in the intestine and localizes to the nucleus.
• Organism: Caenorhabditis elegans
• Automated Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and mitogen-activated protein kinase binding activity. Involved in several processes, including defense response to bacterium; regulation of innate immune response; and regulation of transcription by RNA polymerase II. Acts upstream of or within serotonin biosynthetic process. Located in nucleus. Part of chromatin. Expressed in body wall musculature; hypodermis; intestine; neurons; and rectal epithelial cell. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; Huntington's disease; Pick's disease; and colorectal cancer. Is an ortholog of human ATF2 (activating transcription factor 2); ATF7 (activating transcription factor 7); and CREB5 (cAMP responsive element binding protein 5).
• Biotype: SO:0001217
• Genetic Position: III :-3.15041 ±0.001925
• Length (nt): 7419

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000223

Genomics

8 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C07G2.2a.1	C07G2.2a.1	2155	III: 4491627-4499043
Transcript:C07G2.2d.4	C07G2.2d.4	2057	III: 4491630-4494094
Transcript:C07G2.2d.3	C07G2.2d.3	2316	III: 4491630-4494447
Transcript:C07G2.2b.2	C07G2.2b.2	2083	III: 4491630-4498559
Transcript:C07G2.2b.1	C07G2.2b.1	2161	III: 4491630-4499043
Transcript:C07G2.2d.1	C07G2.2d.1	2204	III: 4491630-4499045
Transcript:C07G2.2c.1	C07G2.2c.1	2277	III: 4491631-4494450
Transcript:C07G2.2d.2	C07G2.2d.2	2362	III: 4491707-4499045

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C07G2.2b	C07G2.2b	1383	III: 4492306-4492416
CDS:C07G2.2d	C07G2.2d	1122	III: 4492786-4493101
CDS:C07G2.2a	C07G2.2a	1374	III: 4492306-4492416
CDS:C07G2.2c	C07G2.2c	1530	III: 4492306-4492416

9 RNAi Result

• WBRNAi00040020
• WBRNAi00040021
• WBRNAi00040022
• WBRNAi00028646
• WBRNAi00095299
• WBRNAi00093236
• WBRNAi00006802
• WBRNAi00094624
• WBRNAi00007139

100 Allele

• WBVar02067501
• WBVar01263076
• WBVar01263077
• qd137
• qd130
• qd141
• WBVar01656533
• gk929145
• gk172872
• gk928343
• gk172871
• gk393070
• gk172874
• gk668836
• gk172873
• WBVar01709981
• gk576115
• gk172868
• WBVar01709980
• gk172867
• mt12
• gk746862
• gk792347
• mt15
• gk172870
• gk882878
• WBVar01709982
• gk172869
• gk862008
• gk694761

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000223
• Start: 4491627
• End: 4499045
• 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_chrIII_4491393..4491626
• Length (nt): 234
• Chromosome Location: III: 4491393-4491626
• Organism: Caenorhabditis elegans

106 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
	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
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
	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 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
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
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
	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 spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food.	Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food).	Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first.	WBPaper00041939:EtBr-exposed_vs_UVC-exposed_51h
	Transcripts that showed significantly increased expression in sma-2(rax5) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-2(rax5)_upregulated
	Transcripts that showed significantly increased expression in sma-4(rax3) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-4(rax3)_upregulated

11 Expression Patterns

• Primary Identifier: Expr2009482
• 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: Expr1030140
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9790
• Pattern: Very strong nuclear-localized GFP was seen throughout development but most strongly in the L1. Expression was observed in possibly all neurons (in the head, the tail, and ventral nerve cord) as well as in the intestine, hypodermis, body wall muscle and rectal cells. GFP expression may be present in all cells.

• Primary Identifier: Expr9808
• Pattern: Very strong nuclear-localized GFP was seen throughout development but most strongly in the L1. Expression was observed in possibly all neurons (in the head, the tail, and ventral nerve cord) as well as in the intestine, hypodermis, body wall muscle and rectal cells. GFP expression may be present in all cells.

• Primary Identifier: Expr7421
• Remark: Clone: pUL#JRH/AA10
• Pattern: No expression seen in eight independent lines.

• Primary Identifier: Chronogram59
• Remark: Original chronogram file: chronogram.1050.xml
• Reporter Gene: [C07G2.2:gfp] transcriptional fusion.

• Primary Identifier: Chronogram15
• Remark: Original chronogram file: chronogram.1010.xml
• Reporter Gene: [C07G2.2:gfp] transcriptional fusion.

• Primary Identifier: Chronogram157
• Remark: Original chronogram file: chronogram.1161.xml
• Reporter Gene: [C07G2.2:gfp] transcriptional fusion.

• Primary Identifier: Expr2027719
• 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: Expr1144096
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1028575
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

27 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000223
• Start: 4491627
• End: 4499045
• Strand: -1

27 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C.	Transcripts that showed significantly increased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 4 hours at 25C, but atf-7(qd22qd130) animals showed reduced fold change after they went through the same infection.	DESeq2	WBPaper00056275:P.aeruginosa_upregulated_atf-7(qd22qd130)_dependent
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C.	Transcripts that showed significantly decreased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 4 hours at 25C, but atf-7(qd22qd130) animals showed reduced fold change after they went through the same infection.	DESeq2	WBPaper00056275:P.aeruginosa_downregulated_atf-7(qd22qd130)_dependent

1 Sequence

• Length: 7419

1 Sequence Ontology Term