WormMine: Gene WBGene00006795

• WormBase Gene ID: WBGene00006795
• Gene Name: unc-61
• Sequence Name: Y50E8A.4
• Brief Description: unc-61, by alternative splicing, encodes two septin isoforms required (like the septin UNC-59) for normal axonal migration, distal tip cell migration, and postembryonic cytokinesis (at the cellular level) and for normal locomotion and formation of the postembryonic vulva, somatic gonad, and male tail (at the organismal level); both UNC-61A/B and UNC-59 are dispensable for embryonic cytokinesis and development, but are thought to be required for all postembryonic cytokinesis; UNC-61A/B and UNC-59 depend on each other for localization to the cytokinetic furrow.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable GTPase activity and molecular adaptor activity. Predicted to be involved in cytoskeleton-dependent cytokinesis and protein localization. Located in cleavage furrow and midbody. Expressed in anterior distal tip cell; nerve ring; posterior distal tip cell; and ventral cord neurons. Human ortholog(s) of this gene implicated in Parkinson's disease. Is an ortholog of human SEPTIN11 (septin 11) and SEPTIN8 (septin 8).
• Biotype: SO:0001217
• Genetic Position: V :6.74673 ±0.006359
• Length (nt): 3174

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006795

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y50E8A.4a.1	Y50E8A.4a.1	2010	V: 14731064-14734237
Transcript:Y50E8A.4b.1	Y50E8A.4b.1	1800	V: 14731095-14733877
Transcript:Y50E8A.4c.1	Y50E8A.4c.1	1814	V: 14731095-14733879

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y50E8A.4a	Y50E8A.4a	1593	V: 14731476-14731718
CDS:Y50E8A.4b	Y50E8A.4b	1386	V: 14731476-14731718
CDS:Y50E8A.4c	Y50E8A.4c	1398	V: 14731476-14731730

14 RNAi Result

• WBRNAi00089740
• WBRNAi00064057
• WBRNAi00080626
• WBRNAi00057105
• WBRNAi00020839
• WBRNAi00037335
• WBRNAi00089971
• WBRNAi00090131
• WBRNAi00090289
• WBRNAi00090375
• WBRNAi00090422
• WBRNAi00090469
• WBRNAi00090516
• WBRNAi00101883

46 Allele

• gk963271
• gk963706
• gk963301
• gk964458
• gk964459
• gk963796
• WBVar01975516
• WBVar02024654
• ok616
• gk954096
• cxTi10396
• e228
• gk789768
• gk495584
• WBVar01843116
• WBVar01775460
• gk873203
• WBVar01843115
• WBVar00591064
• gk931764
• WBVar01843114
• gk353965
• gk849591
• WBVar01775461
• gk469003
• WBVar01775462
• gk753309
• WBVar00017035
• gk254306
• WBVar02043723

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006795
• Start: 14731064
• End: 14734237
• 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

150 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 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
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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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
	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 that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
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
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:coelomocytes_L2-larva_expressed
	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 detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	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 significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	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

8 Expression Patterns

• Primary Identifier: Expr2036030
• 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: Expr1032865
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2689
• Remark: UNC-61 localization in early embryonic stages was described in Expr2319.
• Pattern: UNC-61 localized in embryos of later developmental stages. UNC-61 was enriched in the developing nervous system. In 1.5-fold embryos, localization to the developing nerve ring (not yet a complete ring) was apparent, with faint staining also seen in the ventral cord. In 3-fold embryos, enrichment was seen in the now completely ring-shaped nerve ring, and in some associated neuronal processes.

• Primary Identifier: Expr2690
• Pattern: Strong expression of the UNC-61 septin-GFP chimeras was observed in distal tip cells. UNC-61::GFP expression was continuous throughout larval development, its expression can be detected at least as early as the second larval stage. UNC-61::GFP was found in 2- and 3-fold embryos in the developing nerve ring, and in the cell bodies of the neurons that project into the nerve ring, and the ventral cord. In newly hatched larvae, expression of UNC-61::GFP was seen in the ventral cord neurons, and this expression was seen again in the second larval stage at the time when processes are extending from the neuronal cell bodies following their birth during the L1 molt. Most neurons, including those of the nerve ring ganglia and the ventral cord, only expressed UNC-61::GFP transiently in embryonic and/or early larval stages. Expression was not observed in any other tissues.
• Subcellular Localization: Developmentally regulated expression of UNC-61::GFP was observed in neuronal cytoplasm in cell bodies and axons, but was clearly excluded from nuclei. GFP were excluded from the distal tip cell nuclei, and in late L4 larvae and young adults, GFP appeared as fine puncta in the distal tip cell processes.

• Primary Identifier: Expr2017894
• 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: Expr1013797
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1160551
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2319
• Subcellular Localization: UNC-61 and non-muscle myosin II (NMY-II) prominently co-localize to the leading edge of the furrow. UNC-61 and NMY-II eventually also became localized to the midbody region. UNC-61 also co-localizes with actin in the cleavage furrow. Actin filaments began to aggregate at the cleavage furrow as cells underwent cytokinesis. Eventually, actin filaments concentrated at the boundary of two newly divided cells.

17 GO Annotation

24 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006795
• Start: 14731064
• End: 14734237
• Strand: -1

17 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3174

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00022737
• WBStrain00022738
• WBStrain00022749
• WBStrain00029194
• WBStrain00040370
• WBStrain00004131

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_14734238..14734651
• Length (nt): 414
• Chromosome Location: V: 14734238-14734651
• Organism: Caenorhabditis elegans