WormMine: Gene WBGene00004271

• WormBase Gene ID: WBGene00004271
• Gene Name: rab-7
• Sequence Name: W03C9.3
• Brief Description: rab-7 encodes a Rab GTPase orthologous to the Rab7 GTPases of yeast, Drosophila, and vertebrates; RAB-7 is required for endosome and endosome to lysosome trafficking and thus, for proper yolk protein transport in oocytes and transport of endocytosed materials in coelomoyctes; RAB-7 is also required for apoptotic cell clearance, particularly for regulation of lysosome to phagosome fusion; RAB-7 activity is also required for normal embryogenesis, locomotion, and body morphology; RAB-7 localizes to late endosomes, lysosomes, and phagosomes; RAB-7 localization, and presumably function, at endosomes is positively regulated by SAND-1, a novel, conserved protein required for early to late endosome maturation and transport; rab-7 activity is upregulated by tub-1/tubby, a gene involved in obesity across species, suggesting that rab-7 may also be involved in a tub-1/tubby mediated endocytic pathway for regulation of fat storage.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTPase activity. Involved in several processes, including oocyte growth; positive regulation of early endosome to late endosome transport; and vesicle-mediated transport. Located in late endosome membrane; lysosome; and phagocytic vesicle membrane. Expressed in several structures, including oocyte. Used to study obesity. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 2B. Is an ortholog of human RAB7A (RAB7A, member RAS oncogene family).
• Biotype: SO:0001217
• Genetic Position: II :4.64486 ±0.24308
• Length (nt): 1409

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004271

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W03C9.3.1	W03C9.3.1	791	II: 11965523-11966931

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W03C9.3	W03C9.3	630	II: 11965655-11965741

75 RNAi Result

• WBRNAi00070445
• WBRNAi00101871
• WBRNAi00063274
• WBRNAi00091345
• WBRNAi00107763
• WBRNAi00093203
• WBRNAi00026466
• WBRNAi00009246
• WBRNAi00077456
• WBRNAi00074845
• WBRNAi00083903
• WBRNAi00097831
• WBRNAi00097840
• WBRNAi00097849
• WBRNAi00097859
• WBRNAi00097929
• WBRNAi00093799
• WBRNAi00090905
• WBRNAi00087672
• WBRNAi00076734
• WBRNAi00098557
• WBRNAi00097837
• WBRNAi00097853
• WBRNAi00083367
• WBRNAi00054664
• WBRNAi00102817
• WBRNAi00061379
• WBRNAi00097830
• WBRNAi00087663
• WBRNAi00087621

25 Allele

• gk963801
• gk963053
• gk962684
• gk963539
• otn289
• WBVar01440320
• tm3300
• gk806437
• WBVar00176402
• gk434106
• gk422795
• gk372118
• WBVar00176403
• gk667568
• ok511
• gk577632
• gk156332
• WBVar01312827
• gk156331
• WBVar01792302
• gk156333
• WBVar00106033
• WBVar01766521
• WBVar00106034
• WBVar02040617

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004271
• Start: 11965523
• End: 11966931
• 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_chrII_11965259..11965522
• Length (nt): 264
• Chromosome Location: II: 11965259-11965522
• Organism: Caenorhabditis elegans

104 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
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
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
	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
	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 that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	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
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
	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 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_upregulated_daf-16(mu86);glp-1(e2141)

11 Expression Patterns

• Primary Identifier: Expr4950
• Remark: Picture: Fig 3A.
• Pattern: RAB-7::GFP is expressed ubiquitously, including the amphid neurons where both TUB-1 and RBG-3 are expressed.

• Primary Identifier: Expr4524
• Subcellular Localization: In wild-type oocytes, RAB-7 appeared to be mostly membrane associated.

• Primary Identifier: Expr1032110
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8124
• Remark: Picture: Figure S1B.
• Subcellular Localization: In engulfing cells, GFP::RAB-7 was detected in the cytoplasm, and a portion of it is enriched on cytoplasmic puncta

• Primary Identifier: Expr8080
• Remark: No GO_term assigned. Picture: Fig. 1 i to l. Possible ced-1::yfp-rab-7.
• Subcellular Localization: YFP::RAB-7 localized around late-stage, highly refractile, apoptotic-cell corpses.

• Primary Identifier: Expr1021315
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1158205
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2015231
• 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: 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: Expr13492
• Subcellular Localization: GFP::RAB-7 is localized to both the cell body and the axon, but it is less enriched in synapses than GFP::RAB-3.

• Primary Identifier: Expr2033465
• 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).

22 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004271
• Start: 11965523
• End: 11966931
• Strand: -1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1409

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00035667
• WBStrain00048935

0 Upstream Intergenic Region