Human Gene RAB40B (uc002kft.3) Description and Page Index
  Description: Homo sapiens RAB40B, member RAS oncogene family (RAB40B), mRNA.
RefSeq Summary (NM_006822): 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]. ##Evidence-Data-START## Transcript exon combination :: SRR1660803.217315.1, SRR1803611.119876.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000571995.6/ ENSP00000461785.1 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr17:80,614,943-80,656,598 Size: 41,656 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr17:80,615,739-80,656,472 Size: 40,734 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:80,614,943-80,656,598)mRNA (may differ from genome)Protein (278 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RB40B_HUMAN
DESCRIPTION: RecName: Full=Ras-related protein Rab-40B; AltName: Full=SOCS box-containing protein RAR; Short=Protein Rar;
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 (By similarity).
PATHWAY: Protein modification; protein ubiquitination.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential).
DOMAIN: The SOCS box domain mediates the interaction with the Elongin BC complex, an adapter module in different E3 ubiquitin ligase complexes (By similarity).
SIMILARITY: Belongs to the small GTPase superfamily. Rab family.
SIMILARITY: Contains 1 SOCS box domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.83 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 463.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -78.00126-0.619 Picture PostScript Text
3' UTR -195.00796-0.245 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005225 - Small_GTP-bd_dom
IPR001806 - Small_GTPase
IPR003579 - Small_GTPase_Rab_type
IPR001496 - SOCS_C

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF07525 - SOCS box
PF08477 - Ras of Complex, Roc, domain of DAPkinase

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q12829
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005525 GTP binding

Biological Process:
GO:0016567 protein ubiquitination
GO:0035556 intracellular signal transduction
GO:0072659 protein localization to plasma membrane
GO:1990967 multi-organism toxin transport
GO:0006904 vesicle docking involved in exocytosis
GO:0009306 protein secretion
GO:0017157 regulation of exocytosis

Cellular Component:
GO:0005635 nuclear envelope
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030667 secretory granule membrane
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC035814 - Homo sapiens RAB40B, member RAS oncogene family, mRNA (cDNA clone IMAGE:5769997), with apparent retained intron.
AK095782 - Homo sapiens cDNA FLJ38463 fis, clone FEBRA2021134.
AK124376 - Homo sapiens cDNA FLJ42385 fis, clone UTERU2037577.
U05227 - Human Rar protein mRNA, complete cds.
JD303454 - Sequence 284478 from Patent EP1572962.
BC018039 - Homo sapiens RAB40B, member RAS oncogene family, mRNA (cDNA clone MGC:26251 IMAGE:4801271), complete cds.
AB209711 - Homo sapiens mRNA for RAB40B, member RAS oncogene family variant protein.
JD263493 - Sequence 244517 from Patent EP1572962.
KJ898322 - Synthetic construct Homo sapiens clone ccsbBroadEn_07716 RAB40B gene, encodes complete protein.
JD554771 - Sequence 535795 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q12829 (Reactome details) participates in the following event(s):

R-HSA-8870466 RGGT:CHM binds RABs
R-HSA-8870469 RGGT geranylgeranylates RAB proteins
R-HSA-8873719 RAB geranylgeranylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006822, NP_006813, Q12829, Q8WVG3, RB40B_HUMAN, SEC4L
UCSC ID: uc002kft.3
RefSeq Accession: NM_006822
Protein: Q12829 (aka RB40B_HUMAN or R40B_HUMAN)
CCDS: CCDS11816.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006822.2
exon count: 6CDS single in 3' UTR: no RNA size: 1776
ORF size: 837CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 1645.00frame shift in genome: no % Coverage: 99.04
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.