WormMine: Gene WBGene00001967

• WormBase Gene ID: WBGene00001967
• Gene Name: hlh-28
• Sequence Name: F31A3.2
• Brief Description: hlh-28 encodes a protein with two bHLH domains, required (with HLH-29) for late embryonic viability, and for normal fat metabolism, yolk protein transport, gonadal and vulval development, bordering behavior, and chemosensory responses, and repression of tax-4 and osm-9 transcription; HLH-28 is identical to residues 1-239 of HLH-29, shares near-identical promoter regions in a inverted duplex, and is likely to be highly redundant with HLH-29; HLH-28's paralogs include HLH-25 through HLH-29 and (more distantly) REF-1; hlh-28 is transcribed in the early MS and E lineages, probably due to MED-1/2 binding of clustered sites in the hlh-28/hlh-29 shared promoter region; hlh-28/29 mRNA is present throughout development, but varies roughly 30-fold in quantity, with 3.5-fold more mRNA in L1 larvae than in adults; hlh-28/29 transcription is inhibited by LIN-12 and MED-1.
• 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 E; Ea; Ep; MSa; and MSp.
• Biotype: SO:0001217
• Genetic Position: X :24.3464 ±0.040077
• Length (nt): 1148

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001967

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F31A3.2.1	F31A3.2.1	1047	X: 17551055-17552202

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F31A3.2	F31A3.2	720	X: 17551057-17551226

19 RNAi Result

• WBRNAi00045978
• WBRNAi00045979
• WBRNAi00070039
• WBRNAi00070036
• WBRNAi00070035
• WBRNAi00014127
• WBRNAi00014129
• WBRNAi00070038
• WBRNAi00115873
• WBRNAi00070034
• WBRNAi00070033
• WBRNAi00070042
• WBRNAi00070043
• WBRNAi00070044
• WBRNAi00070037
• WBRNAi00084010
• WBRNAi00070041
• WBRNAi00092719
• WBRNAi00070040

8 Allele

• gk964260
• gk963810
• gk963581
• gk964446
• tm458
• gk471014
• gk750261
• gk859760

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001967
• Start: 17551055
• End: 17552202
• 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_chrX_17552203..17553418
• Length (nt): 1216
• Chromosome Location: X: 17552203-17553418
• Organism: Caenorhabditis elegans

18 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
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
	Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
	Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:sre-33-ZK1025.1_8337
	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 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 decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin_downregulated
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 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:Rapamycin-Rifampicin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Psora_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin-Psora_downregulated
	Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12	Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01.	WBPaper00040221:DAF-12_target_ALF4
	Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 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:Rapamycin-Psora-Allantoin_downregulated
	Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 20C.	N.A.	WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_20C
	Transcripts that showed differential expression in adult mir-34(OverExpression) vs adult N2 animals at 20C.	N.A.	WBPaper00050488:mir-34(OverExpression)_vs_N2_regulated_adult_20C
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_downregulated
	Transcripts that showed significantly increased 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)_upregulated
	Proteins that showed significantly decreased expression in prx-5(RNAi) animals.	Fold change > 2, p-value < 0.05.	WBPaper00060911:prx-5(RNAi)_downregulated_protein

4 Expression Patterns

• Primary Identifier: Expr4683
• Pattern: hlh-29/hlh-28 mRNA is present at all developmental stages and does not vary significantly during later larval stages. Embryos and early L1-stage larvae produce significantly more hlh-29/hlh-28 RNA than later larvae. In separate assays from three independent cDNA samples, L1-stage larvae produced an average of 3 1/2 times more hlh-29 RNA than did L4 stage larvae and adults.

• Primary Identifier: Expr3506
• Pattern: Expressed in: early MS, E lineage.

• Primary Identifier: Expr1020647
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149877
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

5 GO Annotation

3 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001967
• Start: 17551055
• End: 17552202
• Strand: 1

5 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1148

1 Sequence Ontology Term