WormMine: Gene WBGene00006778

• WormBase Gene ID: WBGene00006778
• Gene Name: unc-42
• Sequence Name: F58E6.10
• Brief Description: unc-42 encodes a paired-like homeodomain protein of the Q50 class; UNC-42 is required to specify the fate of ASH sensory neurons, AVA, AVD, and AVE interneurons, and a subset of motor neurons; unc-42 mutants fail to express cell-surface receptors required for differentiated neuronal function (sra-6, srb-6, glr-1, glr-5, and glr-6); UNC-42 is also required for AVKR and HSNL growth cones to follow the PVPR and PVQL pioneer axons, for axonal outgrowth in the backward command interneurons AVA, AVD, and AVE, and for inhibition of ectopic FMRFamide-positive and GABAergic axons; unc-42 mutants are defective in mechanosensation, backward motion, and regulation of egg-laying.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including larval locomotory behavior; neuron differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Expressed in hypodermis; nerve ring; and neurons. Human ortholog(s) of this gene implicated in hypogonadism and panhypopituitarism. Is an ortholog of several human genes including ESX1 (ESX homeobox 1); PROP1 (PROP paired-like homeobox 1); and RHOXF2 (Rhox homeobox family member 2).
• Biotype: SO:0001217
• Genetic Position: V :2.1654 ±0.007367
• Length (nt): 4858

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006778

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F58E6.10b.1	F58E6.10b.1	1038	V: 9764534-9769356
Transcript:F58E6.10d.1	F58E6.10d.1	808	V: 9764534-9767734
Transcript:F58E6.10a.1	F58E6.10a.1	1028	V: 9764534-9769391
Transcript:F58E6.10e.1	F58E6.10e.1	871	V: 9764534-9767752
Transcript:F58E6.10c.1	F58E6.10c.1	300	V: 9764645-9764990

Other

5 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F58E6.10a	F58E6.10a	795	V: 9764645-9764816
CDS:F58E6.10b	F58E6.10b	840	V: 9764645-9764816
CDS:F58E6.10d	F58E6.10d	642	V: 9764645-9764816
CDS:F58E6.10c	F58E6.10c	300	V: 9764645-9764816
CDS:F58E6.10e	F58E6.10e	687	V: 9764645-9764816

13 RNAi Result

• WBRNAi00089722
• WBRNAi00049008
• WBRNAi00025750
• WBRNAi00027375
• WBRNAi00015983
• WBRNAi00033103
• WBRNAi00089933
• WBRNAi00090093
• WBRNAi00090251
• WBRNAi00090374
• WBRNAi00090421
• WBRNAi00090468
• WBRNAi00090515

90 Allele

• gk963301
• gk964351
• gk962860
• gk963365
• gk963364
• WBVar01863652
• WBVar01863653
• WBVar01863650
• WBVar01863651
• WBVar01863654
• e2700
• WBVar02024182
• gk244032
• gk244033
• gk244030
• gk244031
• gk244036
• gk244034
• gk244035
• gk244029
• gk244039
• gk244040
• gk244037
• gk244038
• tm4775
• otn2079
• h3647
• h11742
• h11556
• h3646

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006778
• Start: 9764534
• End: 9769391
• 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_chrV_9759085..9764533
• Length (nt): 5449
• Chromosome Location: V: 9759085-9764533
• Organism: Caenorhabditis elegans

178 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 of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	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
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	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 infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis 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:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	Transcripts that showed significantly increased expression in hsf-1(sy441) vs. in N2 day 1 adults without heat shock.	edgeR, fold change > 2, FDR < 0.05	WBPaper00066900:hsf-1(sy441)_upregulated
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	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 sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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 that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition.	Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed.	WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	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
	Transcripts that showed significantly decreased expression in set-2(tm1630) 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(tm1630)_downregulated
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	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 unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched
	Transcripts that showed significantly increased expression in lin-29(n333) comparing to in N2 at day 1 adult stage.	DESeq2, FDR < 0.01, fold change > 2.	WBPaper00066970:lin-29(n333)_upregulated

12 Expression Patterns

• Primary Identifier: Expr7591
• Remark: Clone: pUL#JRH/AD7. Other strains: UL1829, UL1830.
• Pattern: Expression is seen in 6 to 8 nerve cells in the nerve ring, from late embryo to adult.

• Primary Identifier: Expr1329
• Pattern: UNC-42 expression was detected with a mouse antiserum in several cells as early as 260 minutes of embryogenesis and in neurons at high levels in the head by comma stage, the time when these neurons extend axons and establish connections. Expression in head neurons continues into adulthood. UNC-42 was strongly expressed in at least 20 pairs of neurons of the head, including the AVA, AVD and AVE interneurons, ASH sensory neurons, and RMD and SMB motor neurons. Other neurons that express high levels of UNC-42 include the AIN, AVH, AVJ, AVK, RIV, SAA and SIB interneurons. The same expression pattern in the head was detected in animals that carry a transgene that encodes an UNC-42 protein tagged at its C terminus with GFP(gmEx186). Antiserum to UNC-42 and the gmEx104 GFP reporter gene revealed low levels of unc-42 expression in hypodermis and additional neurons in the head. Transient expression of UNC-42 protein was also detected in the DD motor neurons at hatching and at low levels in postembryonic ventral cord motor neurons derived from P11. UNC-42 protein was not detected in descendants of P2-P10 or P12. In the tail, unc-42-gfp (gmEx104) is strongly expressed in PVT.

• Primary Identifier: Expr16145
• Pattern: We found that in the adult nervous system unc-42 is strongly and consistently expressed in 40 neurons located in the head of the worm that fall into 15 anatomically distinct neuron classes. At the first larval stage, expression is detected in the same set of neuron classes as observed in the adult, with the addition of very weak and inconsistent expression in AVJ and SIA that disappears by the adult stage. In the embryo, expression is first observed in a few neuroblasts before the bean stage. At the bean stage, when most neurons have terminally divided, unc-42 expression commences and reaches the full complement of unc-42(+) cells at the 1.5-fold stage. The cellular sites of expression in the embryonic nervous system appear to be the same as observed post-embryonically, a notion further supported by recent scRNA data (Packer et al., 2019). No expression is observed outside the nervous system.

• Primary Identifier: Expr15658

• Primary Identifier: Expr12723

• Primary Identifier: Expr2036011
• 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: Expr1032850
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15440

• Primary Identifier: Expr1200033
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1022022
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1152746
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2017875
• 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).

18 GO Annotation

34 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006778
• Start: 9764534
• End: 9769391
• Strand: -1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4858

1 Sequence Ontology Term

• Name: gene

72 Strains

• WBStrain00022601
• WBStrain00022471
• WBStrain00022478
• WBStrain00023884
• WBStrain00023813
• WBStrain00023814
• WBStrain00026963
• WBStrain00026843
• WBStrain00026872
• WBStrain00027355
• WBStrain00027090
• WBStrain00029639
• WBStrain00030042
• WBStrain00034099
• WBStrain00035107
• WBStrain00035113
• WBStrain00036602
• WBStrain00047490
• WBStrain00047473
• WBStrain00047477
• WBStrain00047461
• WBStrain00047466
• WBStrain00049462
• WBStrain00049415
• WBStrain00049401
• WBStrain00049405
• WBStrain00049330
• WBStrain00049344
• WBStrain00049351
• WBStrain00049350

0 Upstream Intergenic Region