WormMine: Gene WBGene00004268

• WormBase Gene ID: WBGene00004268
• Gene Name: rab-5
• Sequence Name: F26H9.6
• Brief Description: rab-5 encodes the C. elegans Rab5 GTPase ortholog; RAB-5 activity is required for receptor-mediated yolk endocytosis and for phagosome maturation involved in apoptotic cell clearance; rab-5 mutations also affect localization of P granules and PAR-2, as well as the cytoplasmic appearance of cells in the early embryo and larval development; RAB-5 localizes to early endosomes and maturing phagosomes.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTPase activating protein binding activity and GTPase activity. Involved in embryo development; protein localization; and vesicle-mediated transport. Located in several cellular components, including cholinergic synapse; cytoplasmic vesicle; and periciliary membrane compartment. Expressed in several structures, including ventral cord neurons. Is an ortholog of human RAB5B (RAB5B, member RAS oncogene family) and RAB5C (RAB5C, member RAS oncogene family).
• Biotype: SO:0001217
• Genetic Position: I :3.73499 ±0.001928
• Length (nt): 1780

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004268

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F26H9.6.1	F26H9.6.1	1081	I: 9308442-9310221

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F26H9.6	F26H9.6	627	I: 9308445-9308535

88 RNAi Result

• WBRNAi00113816
• WBRNAi00098330
• WBRNAi00107760
• WBRNAi00085166
• WBRNAi00066841
• WBRNAi00085387
• WBRNAi00071846
• WBRNAi00097524
• WBRNAi00097526
• WBRNAi00097525
• WBRNAi00085170
• WBRNAi00097848
• WBRNAi00097857
• WBRNAi00097930
• WBRNAi00098315
• WBRNAi00064976
• WBRNAi00090888
• WBRNAi00087668
• WBRNAi00098556
• WBRNAi00085177
• WBRNAi00097852
• WBRNAi00081348
• WBRNAi00000037
• WBRNAi00083343
• WBRNAi00091950
• WBRNAi00091949
• WBRNAi00061378
• WBRNAi00108427
• WBRNAi00087620
• WBRNAi00071038

25 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• gk964127
• WBVar00155725
• WBVar00155726
• udn12
• ok2605
• WBVar01817513
• udn10
• udn11
• udn13
• udn14
• gk816722
• gk369874
• gk865192
• gk855722
• gk118509
• gk118510
• WBVar01957495
• tm2456
• tm2471
• gk964128

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004268
• Start: 9308442
• End: 9310221
• 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_9310222..9310318
• Length (nt): 97
• Chromosome Location: I: 9310222-9310318
• Organism: Caenorhabditis elegans

108 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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
	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 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
	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 hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	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)
	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
	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
	Transcripts that showed significantly decreased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_downregulated
	Genes that showed significantly altered expression between N2 and npr-1(ur89) strains exposed to either the nematocidal B. thuringiensis B-18247, the pathogenic P. aeruginosa PA14, or the control E. coli OP50 for 12 or 24 hours.	Estimation of transcript abundance and significantly differentially expressed genes were identified by Cuffdiff using the quartile normalization method. Transcripts with a significant change between different conditions (adjusted p-value < 0.01 by the false discovery rate, FDR) were treated as signature for each comparison.	WBPaper00049498:npr-1(ur89)_regulated_3
	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
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
	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

13 Expression Patterns

• Primary Identifier: Expr1032107
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8079
• Remark: No GO_term assigned. Picture: Fig. 1 e to h. Possible ced-1::yfp-rab-5.
• Subcellular Localization: Yellow fluorescent protein (YFP)::RAB-5 preferentially localized around early, uncondensed cell corpses.

• Primary Identifier: Expr12618
• Pattern: The transcriptional expression pattern of the rab-5 and uev-3 operon was determined using 1.8 kb of the 5'upstream sequences of the operon to drive GFP expression. GFP is observed in all tissues and is noticeably present in ventral cord neurons.

• Primary Identifier: Expr9324
• Subcellular Localization: GFP::RAB-5 labels early endosomes.

• Primary Identifier: Expr10744
• Subcellular Localization: Early endosome component RAB-5 shows punctate GFP localization in the far distal dendrite region, immediately proximal to cilia. The distal extent of these endocytic protein pools overlapped with the CHE-13 pool at the ciliary base. These intraflagellar transport (IFT) pools correspond to the transitional fiber region below ciliary transition zones and thus precisely mark the junction between dendritic and ciliary compartments. GFP::RAB-5 fusion protein molecules, presumably associated with vesicles, frequently emerge from the far distal dendrite pools and translocate along dendrites toward the soma.

• Primary Identifier: Expr2015228
• 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: Expr3545
• Subcellular Localization: Synaptic expression, co-localized with SNB-1::RFP.

• Primary Identifier: Expr11649
• Subcellular Localization: In growing oocytes, GFP-RAB-5 and mRFP- RAB-7 localized on small cortical puncta; their localization only partially overlapped. After fertilization, the size of the endosomes increased, and GFP-RAB-5 and mRFP-RAB-7 localized on the same enlarged endosomes, although in a mosaic pattern on the membrane.

• Primary Identifier: Expr1149621
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr14419
• Subcellular Localization: In wild-type worms, GFP::RAB-5 localises at the PCMC.

• Primary Identifier: Expr2033462
• 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: Expr1015318
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr11827
• Subcellular Localization: GFP::RAB-5, which is expressed in the phagocytes including gonadal sheath cells, was enriched on residual bodies-containing phagosomes.

35 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004268
• Start: 9308442
• End: 9310221
• Strand: 1

35 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1780

1 Sequence Ontology Term