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

Gene ID: 10966, updated on 23-Nov-2023

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
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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 intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in toxin transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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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