Human Gene RAB2A (uc003xud.2)
  Description: Homo sapiens RAB2A, member RAS oncogene family (RAB2A), transcript variant 1, mRNA.
RefSeq Summary (NM_002865): The protein encoded by this gene belongs to the Rab family, members of which are small molecular weight guanosine triphosphatases (GTPases) that contain highly conserved domains involved in GTP binding and hydrolysis. The Rabs are membrane-bound proteins, involved in vesicular fusion and trafficking. This protein is a resident of pre-Golgi intermediates, and is required for protein transport from the endoplasmic reticulum (ER) to the Golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011].
Transcript (Including UTRs)
   Position: hg19 chr8:61,429,469-61,536,203 Size: 106,735 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr8:61,429,767-61,533,328 Size: 103,562 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:61,429,469-61,536,203)mRNA (may differ from genome)Protein (212 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RAB2A_HUMAN
DESCRIPTION: RecName: Full=Ras-related protein Rab-2A;
FUNCTION: Required for protein transport from the endoplasmic reticulum to the Golgi complex.
SUBUNIT: Interacts with PRKCI.
SUBCELLULAR LOCATION: Endoplasmic reticulum-Golgi intermediate compartment membrane; Lipid-anchor. Melanosome. Endoplasmic reticulum membrane; Lipid-anchor (Potential). Golgi apparatus membrane; Lipid-anchor (Potential). Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
SIMILARITY: Belongs to the small GTPase superfamily. Rab family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RAB2A
CDC HuGE Published Literature: RAB2A
Positive Disease Associations: Cholesterol, HDL
Related Studies:
  1. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.

-  MalaCards Disease Associations
  MalaCards Gene Search: RAB2A
Diseases sorted by gene-association score: sezary's disease (10), warburg micro syndrome 4 (7), lipoblastoma (7), warburg micro syndrome (7), image syndrome (5)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 37.43 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1286.82 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -165.10298-0.554 Picture PostScript Text
3' UTR -679.522875-0.236 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

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF01926 - 50S ribosome-binding GTPase
PF04670 - Gtr1/RagA G protein conserved region
PF08477 - Ras of Complex, Roc, domain of DAPkinase

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1Z0A - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P61019
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019003 GDP binding

Biological Process:
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0007030 Golgi organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0042470 melanosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK297576 - Homo sapiens cDNA FLJ51998 complete cds, highly similar to Ras-related protein Rab-2A.
AK312344 - Homo sapiens cDNA, FLJ92663, Homo sapiens RAB2, member RAS oncogene family (RAB2), mRNA.
E02340 - cDNA sequence of human YRT-1 like gene.
X12953 - Human rab2 mRNA, YPT1-related and member of ras family.
BC008929 - Homo sapiens RAB2A, member RAS oncogene family, mRNA (cDNA clone MGC:1656 IMAGE:2966694), complete cds.
M28213 - Homo sapiens GTP-binding protein (RAB2) mRNA, complete cds.
AB528604 - Synthetic construct DNA, clone: pF1KB4347, Homo sapiens RAB2 gene for RAB2A, member RAS oncogene family, without stop codon, in Flexi system.
CU679191 - Synthetic construct Homo sapiens gateway clone IMAGE:100018591 5' read RAB2A mRNA.
HQ447940 - Synthetic construct Homo sapiens clone IMAGE:100071302; CCSB004478_01 RAB2A, member RAS oncogene family (RAB2A) gene, encodes complete protein.
BT019695 - Homo sapiens RAB2, member RAS oncogene family mRNA, complete cds.
AF498930 - Homo sapiens small GTP binding protein RAB2A (RAB2A) mRNA, complete cds.
X13899 - H.sapiens mRNA for ras-related Hrab2 protein.
JD409236 - Sequence 390260 from Patent EP1572962.
JD125439 - Sequence 106463 from Patent EP1572962.
JD186852 - Sequence 167876 from Patent EP1572962.
JD219092 - Sequence 200116 from Patent EP1572962.
DQ572175 - Homo sapiens piRNA piR-40287, complete sequence.
AF070629 - Homo sapiens clone 24484 RAB2 mRNA, partial cds.
JD023900 - Sequence 4924 from Patent EP1572962.
JD023901 - Sequence 4925 from Patent EP1572962.
JD035345 - Sequence 16369 from Patent EP1572962.
JD029118 - Sequence 10142 from Patent EP1572962.
JD200196 - Sequence 181220 from Patent EP1572962.
JD091624 - Sequence 72648 from Patent EP1572962.
S48723 - rab2=low molecular weight GTP-binding protein {3' region} [human, mRNA Partial, 103 nt].
AL137321 - Homo sapiens mRNA; cDNA DKFZp434P231 (from clone DKFZp434P231).
AY034106 - Homo sapiens bladder cancer-related protein (LHX) gene, partial 3'UTR sequence.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_rabPathway - Rab GTPases Mark Targets In The Endocytotic Machinery

Reactome (by CSHL, EBI, and GO)

Protein P61019 (Reactome details) participates in the following event(s):

R-HSA-2422927 MAPK3-3 or MAPK1 phosphorylate GORASP2
R-HSA-8870466 RGGT:CHM binds RABs
R-HSA-8870469 RGGT geranylgeranylates RAB proteins
R-HSA-162658 Golgi Cisternae Pericentriolar Stack Reorganization
R-HSA-8873719 RAB geranylgeranylation
R-HSA-68875 Mitotic Prophase
R-HSA-597592 Post-translational protein modification
R-HSA-68886 M Phase
R-HSA-392499 Metabolism of proteins
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5W8, B4DMQ5, NM_002865, NP_002856, P08886, P61019, RAB2, RAB2A_HUMAN
UCSC ID: uc003xud.2
RefSeq Accession: NM_002865
Protein: P61019 (aka RAB2A_HUMAN or RB2A_HUMAN)
CCDS: CCDS6175.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002865.2
exon count: 8CDS single in 3' UTR: no RNA size: 3812
ORF size: 639CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1478.00frame shift in genome: no % Coverage: 100.00
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.