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    RAB40B RAB40B, member RAS oncogene family [ Homo sapiens (human) ]

    Gene ID: 10966, updated on 17-Jun-2024

    Summary

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    Official Symbol
    RAB40Bprovided by HGNC
    Official Full Name
    RAB40B, member RAS oncogene familyprovided by HGNC
    Primary source
    HGNC:HGNC:18284
    See related
    Ensembl:ENSG00000141542 MIM:619550; AllianceGenome:HGNC:18284
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RAR; SEC4L
    Summary
    The protein encoded by this gene has similarity to a yeast protein which suggests a role of the gene product in regulating secretory vesicles. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 11.7), kidney (RPKM 5.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAB40B in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82654973..82698698, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83529323..83573130, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80612849..80656574, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene forkhead box K2 Neighboring gene uncharacterized LOC105371942 Neighboring gene uncharacterized LOC124904132 Neighboring gene MPRA-validated peak3032 silencer Neighboring gene Sharpr-MPRA regulatory region 15512 Neighboring gene MPRA-validated peak3033 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9219 Neighboring gene WD repeat domain 45B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9221 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:80605965-80606464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80622218-80622718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80637586-80638111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80638112-80638636 Neighboring gene microRNA 4525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9224 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:80660456-80661655 Neighboring gene uncharacterized LOC124904093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80661763-80662564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80671133-80671632 Neighboring gene uncharacterized LOC101929552

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Rab40b upregulation correlates with the prognosis of gastric cancer by promoting migration, invasion, and metastasis. Li Y, et al. Med Oncol, 2015 Apr. PMID 25790780
    2. The role and regulation of Rab40b-Tks5 complex during invadopodia formation and cancer cell invasion. Jacob A, et al. J Cell Sci, 2016 Dec 1. PMID 27789576, Free PMC Article
    3. Rab40b regulates trafficking of MMP2 and MMP9 during invadopodia formation and invasion of breast cancer cells. Jacob A, et al. J Cell Sci, 2013 Oct 15. PMID 23902685, Free PMC Article
    4. Ubiquitylation by Rab40b/Cul5 regulates Rap2 localization and activity during cell migration. Duncan ED, et al. J Cell Biol, 2022 Apr 4. PMID 35293963, Free PMC Article
    5. Methods to Study the Unique SOCS Box Domain of the Rab40 Small GTPase Subfamily. Duncan ED, et al. Methods Mol Biol, 2021. PMID 34453716, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ubiquitylation by Rab40b/Cul5 regulates Rap2 localization and activity during cell migration.
      Title: Ubiquitylation by Rab40b/Cul5 regulates Rap2 localization and activity during cell migration.
    2. Rab40-Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration.
      Title: Rab40-Cullin5 complex regulates EPLIN and actin cytoskeleton dynamics during cell migration.
    3. This is the first study that identifies a new Rab40b-Tks5- and miR-204-dependent invadopodia transport pathway that regulates MMP2 and MMP9 secretion, and extracellular matrix remodeling during cancer progression.
      Title: Rab40b and Tks5 interact at invadopodia during metastasis.
    4. This is the first study that identifies a new Rab40b-Tks5- and miR-204-dependent invadopodia transport pathway that regulates MMP2 and MMP9 secretion, and extracellular matrix remodeling during cancer progression.
      Title: The role and regulation of Rab40b-Tks5 complex during invadopodia formation and cancer cell invasion.
    5. High expression level of Rab40b was significantly correlated with gastric cancer invasion and lymph node metastasis.
      Title: Rab40b upregulation correlates with the prognosis of gastric cancer by promoting migration, invasion, and metastasis.
    6. Rab40b mediates trafficking of MMP2/9 during invadopodia formation and metastasis of breast cancer cells.
      Title: Rab40b regulates trafficking of MMP2 and MMP9 during invadopodia formation and invasion of breast cancer cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42385

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular detoxification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein secretion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synaptic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ras-related protein Rab-40B
    Names
    GTP-binding protein homologous to Saccharomyces cerevisiae SEC4
    SOCS box-containing protein RAR
    protein Rar

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_006822.3 → NP_006813.1  ras-related protein Rab-40B

      See identical proteins and their annotated locations for NP_006813.1

      Status: REVIEWED

      Source sequence(s)
      AC024361
      Consensus CDS
      CCDS11816.1
      UniProtKB/Swiss-Prot
      Q12829, Q8WVG3
      Related
      ENSP00000461785.1, ENST00000571995.6
      Conserved Domains (2) summary
      cd04121
      Location:9 → 278
      Rab40; Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c
      cd03742
      Location:187 → 229
      SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      82654973..82698698 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017024042.2 → XP_016879531.1  ras-related protein Rab-40B isoform X3

      Conserved Domains (2) summary
      cd03742
      Location:127 → 169
      SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...
      cl21455
      Location:9 → 218
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. XM_006722271.4 → XP_006722334.1  ras-related protein Rab-40B isoform X2

      Conserved Domains (2) summary
      cd03742
      Location:147 → 189
      SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...
      cl21455
      Location:8 → 238
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    3. XM_011523528.3 → XP_011521830.1  ras-related protein Rab-40B isoform X1

      Conserved Domains (3) summary
      smart00175
      Location:13 → 160
      RAB; Rab subfamily of small GTPases
      cd03742
      Location:170 → 212
      SOCS_Rab40; SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as ...
      cl21455
      Location:30 → 261
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. XM_047435172.1 → XP_047291128.1  ras-related protein Rab-40B isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      83529323..83573130 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314774.1 → XP_054170749.1  ras-related protein Rab-40B isoform X3

    2. XM_054314773.1 → XP_054170748.1  ras-related protein Rab-40B isoform X2

    3. XM_054314772.1 → XP_054170747.1  ras-related protein Rab-40B isoform X1

    4. XM_054314775.1 → XP_054170750.1  ras-related protein Rab-40B isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12829.1 GenPept UniProtKB/Swiss-Prot:Q12829

    Gene LinkOut

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