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] See more...

Aliases for RAB40B Gene

Aliases for RAB40B Gene

  • RAB40B, Member RAS Oncogene Family 2 3 5
  • SEC4L 2 3 4
  • SOCS Box-Containing Protein RAR 3 4
  • Ras-Related Protein Rab-40B 3 4
  • Protein Rar 3 4
  • RAR 2 3
  • GTP-Binding Protein Homologous To Saccharomyces Cerevisiae SEC4 3
  • RAB40B 5

External Ids for RAB40B Gene

Previous GeneCards Identifiers for RAB40B Gene

  • GC17M079683
  • GC17M083584
  • GC17M081144
  • GC17M081293
  • GC17M078208
  • GC17M080614
  • GC17M076014

Summaries for RAB40B Gene

Entrez Gene Summary for RAB40B Gene

  • 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]

GeneCards Summary for RAB40B Gene

RAB40B (RAB40B, Member RAS Oncogene Family) is a Protein Coding gene. Diseases associated with RAB40B include Epilepsy, Familial Temporal Lobe, 4. Among its related pathways are Metabolism of proteins and RAB geranylgeranylation. Gene Ontology (GO) annotations related to this gene include GTP binding and GTPase activity. An important paralog of this gene is RAB40AL.

UniProtKB/Swiss-Prot Summary for RAB40B Gene

  • May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAB40B Gene

Genomics for RAB40B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RAB40B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J082696 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 285.4 +0.4 401 3 SP1 ZNF600 ZNF10 ZSCAN16 ZIC2 ZBTB10 MXD4 NONO CHD2 BHLHE40 RAB40B lnc-WDR45B-6 TBCD OGFOD3 ENSG00000260563 ALYREF NARF-IT1 CSNK1D ENSG00000262652 ENSG00000263321
GH17J082686 Enhancer 1 Ensembl ENCODE dbSUPER 65.4 +11.3 11333 1.7 ATF2 YY1 FOXA2 RXRA ZBTB33 JUND NFE2 NFE2L2 BACH1 REST RAB40B lnc-WDR45B-6 lnc-WDR45B-4 WDR45B
GH17J082703 Enhancer 0.9 ENCODE dbSUPER 34.7 -5.7 -5676 1 BHLHE40 ZFP64 RXRA ZNF511 SAP130 RARA GABPB1 MAFK ZNF205 HNF4A HSALNG0119467 LOC105376791 RAB40B FN3KRP LOC101929552
GH17J082880 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 13.2 -189.2 -189160 13.9 MYC ZNF600 NCOR1 IKZF1 ZNF592 ATF2 KLF9 CEBPA NFIC ZIC2 FN3KRP FN3K RAB40B ZNF750 WDR45B LOC101929552 TBCD B3GNTL1 NARF CYBC1
GH17J082677 Enhancer 0.6 Ensembl ENCODE dbSUPER 41 +20.4 20371 1.9 ZNF664 lnc-WDR45B-4 RAB40B FN3KRP WDR45B FN3K lnc-FOXK2-2 lnc-WDR45B-6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB40B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAB40B

Top Transcription factor binding sites by QIAGEN in the RAB40B gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • NF-Y
  • NF-YA
  • NF-YB
  • NF-YC

Genomic Locations for RAB40B Gene

Latest Assembly
chr17:82,654,973-82,698,702
(GRCh38/hg38)
Size:
43,730 bases
Orientation:
Minus strand

Previous Assembly
chr17:80,612,849-80,656,574
(GRCh37/hg19 by Entrez Gene)
Size:
43,726 bases
Orientation:
Minus strand

chr17:80,612,849-80,656,604
(GRCh37/hg19 by Ensembl)
Size:
43,756 bases
Orientation:
Minus strand

Genomic View for RAB40B Gene

Genes around RAB40B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB40B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB40B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB40B Gene

Proteins for RAB40B Gene

  • Protein details for RAB40B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12829-RB40B_HUMAN
    Recommended name:
    Ras-related protein Rab-40B
    Protein Accession:
    Q12829
    Secondary Accessions:
    • Q8WVG3

    Protein attributes for RAB40B Gene

    Size:
    278 amino acids
    Molecular mass:
    30956 Da
    Quaternary structure:
    No Data Available

neXtProt entry for RAB40B Gene

Post-translational modifications for RAB40B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RAB40B Gene

Domains & Families for RAB40B Gene

Gene Families for RAB40B Gene

Protein Domains for RAB40B Gene

InterPro:
Blocks:
  • Transforming protein P21 RAS signature
  • SOCS protein, C-terminal

Suggested Antigen Peptide Sequences for RAB40B Gene

GenScript: Design optimal peptide antigens:
  • SOCS box-containing protein RAR (RB40B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q12829

UniProtKB/Swiss-Prot:

RB40B_HUMAN :
  • The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes.
  • Belongs to the small GTPase superfamily. Rab family.
Domain:
  • The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes.
Family:
  • Belongs to the small GTPase superfamily. Rab family.
genes like me logo Genes that share domains with RAB40B: view

Function for RAB40B Gene

Molecular function for RAB40B Gene

UniProtKB/Swiss-Prot Function:
May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.

Phenotypes From GWAS Catalog for RAB40B Gene

Gene Ontology (GO) - Molecular Function for RAB40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003924 GTPase activity IEA --
GO:0005515 protein binding IPI 32296183
GO:0005525 GTP binding IEA --
genes like me logo Genes that share ontologies with RAB40B: view
genes like me logo Genes that share phenotypes with RAB40B: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB40B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RAB40B Gene

Localization for RAB40B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB40B Gene

Cell membrane. Lipid-anchor. Cytoplasmic side.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RAB40B gene
Compartment Confidence
nucleus 4
plasma membrane 3
endosome 3
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
lysosome 1
golgi apparatus 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RAB40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005635 nuclear envelope IDA 22042847
GO:0005768 endosome IBA 21873635
GO:0005886 plasma membrane IBA 21873635
GO:0008021 synaptic vesicle IBA 21873635
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RAB40B: view

Pathways & Interactions for RAB40B Gene

genes like me logo Genes that share pathways with RAB40B: view

Pathways by source for RAB40B Gene

1 Sino Biological pathway for RAB40B Gene

UniProtKB/Swiss-Prot Q12829-RB40B_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RAB40B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
GO:0035556 intracellular signal transduction IEA --
GO:0072659 protein localization to plasma membrane IBA 21873635
GO:1901998 toxin transport IMP 22042847
genes like me logo Genes that share ontologies with RAB40B: view

No data available for SIGNOR curated interactions for RAB40B Gene

Drugs & Compounds for RAB40B Gene

No Compound Related Data Available

Transcripts for RAB40B Gene

mRNA/cDNA for RAB40B Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB40B

Alternative Splicing Database (ASD) splice patterns (SP) for RAB40B Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c
SP1: - - -
SP2: - - - -
SP3: -
SP4: -
SP5:

Relevant External Links for RAB40B Gene

GeneLoc Exon Structure for
RAB40B

Expression for RAB40B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAB40B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAB40B Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x4.5) and Brain - Nucleus accumbens (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for RAB40B Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RAB40B Gene



Protein tissue co-expression partners for RAB40B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAB40B

SOURCE GeneReport for Unigene cluster for RAB40B Gene:

Hs.484068

Evidence on tissue expression from TISSUES for RAB40B Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with RAB40B: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB40B Gene

Orthologs for RAB40B Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB40B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RAB40B 29 30
  • 99.76 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RAB40B 29 30
  • 88.37 (n)
OneToMany
Mouse
(Mus musculus)
Mammalia Rab40b 29 16 30
  • 87.41 (n)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Rab40b 29
  • 86.81 (n)
Dog
(Canis familiaris)
Mammalia -- 30
  • 62 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 5 (a)
OneToMany
Chicken
(Gallus gallus)
Aves RAB40B 29 30
  • 78.9 (n)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 81 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rab40b 29
  • 80.58 (n)
Str.14347 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.23887 29
Zebrafish
(Danio rerio)
Actinopterygii rab40b 29 30
  • 74.22 (n)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.595 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG1900 31
  • 60 (a)
Rab40 30
  • 59 (a)
OneToMany
Species where no ortholog for RAB40B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RAB40B Gene

ENSEMBL:
Gene Tree for RAB40B (if available)
TreeFam:
Gene Tree for RAB40B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAB40B: view image
Alliance of Genome Resources:
Additional Orthologs for RAB40B

Paralogs for RAB40B Gene

genes like me logo Genes that share paralogs with RAB40B: view

Variants for RAB40B Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAB40B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RAB40B Gene

Variant ID Type Subtype PubMed ID
dgv1832e59 CNV duplication 20981092
dgv5805n54 CNV loss 21841781
esv1007821 CNV deletion 20482838
esv1288593 CNV deletion 17803354
esv1330810 CNV insertion 17803354
esv1371613 CNV deletion 17803354
esv1463213 CNV deletion 17803354
esv1565279 CNV insertion 17803354
esv1664800 CNV insertion 17803354
esv1683901 CNV deletion 17803354
esv1706997 CNV deletion 17803354
esv21913 CNV gain+loss 19812545
esv2506580 CNV insertion 19546169
esv2716514 CNV deletion 23290073
esv2716515 CNV deletion 23290073
esv2716516 CNV deletion 23290073
esv2716517 CNV deletion 23290073
esv2716519 CNV deletion 23290073
esv2716520 CNV deletion 23290073
esv2716521 CNV deletion 23290073
esv2762577 CNV gain+loss 21179565
esv3380492 CNV duplication 20981092
esv3434025 CNV duplication 20981092
esv3554909 CNV deletion 23714750
esv3641436 CNV loss 21293372
esv3641437 CNV loss 21293372
esv5414 CNV loss 18987735
nsv1061637 CNV loss 25217958
nsv1062980 CNV gain 25217958
nsv1065226 CNV loss 25217958
nsv1067362 CNV gain 25217958
nsv1067553 CNV loss 25217958
nsv1111152 CNV tandem duplication 24896259
nsv1119460 CNV insertion 24896259
nsv1125644 CNV tandem duplication 24896259
nsv1133238 CNV tandem duplication 24896259
nsv1138588 CNV deletion 24896259
nsv1154011 CNV insertion 26484159
nsv428351 CNV gain 18775914
nsv509680 CNV insertion 20534489
nsv576208 CNV loss 21841781
nsv576209 CNV gain 21841781
nsv820798 CNV duplication 20802225
nsv833575 CNV loss 17160897
nsv952395 CNV deletion 24416366
nsv954911 CNV deletion 24416366

Variation tolerance for RAB40B Gene

Residual Variation Intolerance Score: 19.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.76; 78.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB40B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB40B
Leiden Open Variation Database (LOVD)
RAB40B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAB40B Gene

Disorders for RAB40B Gene

MalaCards: The human disease database

(1) MalaCards diseases for RAB40B Gene - From: COP

Disorder Aliases PubMed IDs
epilepsy, familial temporal lobe, 4
  • etl4
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RAB40B

genes like me logo Genes that share disorders with RAB40B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAB40B Gene

Publications for RAB40B Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  2. Evolution of the Rab family of small GTP-binding proteins. (PMID: 11697911) Pereira-Leal JB … Seabra MC (Journal of molecular biology 2001) 2 3
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for RAB40B Gene

Sources for RAB40B Gene