Human Gene RAB1A (uc002sdm.3) Description and Page Index
  Description: Homo sapiens RAB1A, member RAS oncogene family (RAB1A), transcript variant 1, mRNA.
RefSeq Summary (NM_004161): This gene encodes a member of the Ras superfamily of GTPases. Members of the gene family cycle between inactive GDP-bound and active GTP-bound forms. This small GTPase controls vesicle traffic from the endoplasmic reticulum to the Golgi apparatus. Multiple alternatively spliced transcript variants have been identified for this gene which encode different protein isoforms. [provided by RefSeq, Oct 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:65,313,988-65,357,435 Size: 43,448 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr2:65,315,627-65,357,049 Size: 41,423 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:65,313,988-65,357,435)mRNA (may differ from genome)Protein (205 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RAB1A_HUMAN
DESCRIPTION: RecName: Full=Ras-related protein Rab-1A; AltName: Full=YPT1-related protein;
FUNCTION: Probably required for transit of protein from the ER through Golgi compartment. Binds GTP and GDP and possesses intrinsic GTPase activity.
SUBUNIT: May interact with YIPF5 (By similarity).
SUBCELLULAR LOCATION: Golgi apparatus. Endoplasmic reticulum.
PTM: Phosphorylated by CDK1 kinase during mitosis.
PTM: Phosphocholinated at Ser-79 by L.pneumophila AnkX, leading to displace GDP dissociation inhibitors (GDI). Both GDP-bound and GTP-bound forms can be phosphocholinated. Dephosphocholinated by L.pneumophila Lem3, restoring accessibility to L.pneumophila GTPase effector LepB.
SIMILARITY: Belongs to the small GTPase superfamily. Rab family.

-  MalaCards Disease Associations
  MalaCards Gene Search: RAB1A
Diseases sorted by gene-association score: hypotrichosis 3 (3), rectum adenocarcinoma (2)

-  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: 141.53 RPKM in Cells - Transformed fibroblasts
Total median expression: 3645.09 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 -180.90386-0.469 Picture PostScript Text
3' UTR -402.971639-0.246 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
PF09439 - Signal recognition particle receptor beta subunit

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2FOL
- X-ray MuPIT

2WWX
- X-ray MuPIT

3L0I
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3SFV - X-ray MuPIT 3TKL - X-ray MuPIT 4FMB - X-ray MuPIT
4FMC - X-ray MuPIT 4FMD - X-ray MuPIT 4FME - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P62820
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  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:0045296 cadherin binding

Biological Process:
GO:0000045 autophagosome assembly
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0006897 endocytosis
GO:0006914 autophagy
GO:0007030 Golgi organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016477 cell migration
GO:0019068 virion assembly
GO:0030252 growth hormone secretion
GO:0032402 melanosome transport
GO:0034446 substrate adhesion-dependent cell spreading
GO:0042742 defense response to bacterium
GO:0043687 post-translational protein modification
GO:0047496 vesicle transport along microtubule
GO:0048208 COPII vesicle coating
GO:0072606 interleukin-8 secretion
GO:0090110 cargo loading into COPII-coated vesicle
GO:1903020 positive regulation of glycoprotein metabolic process
GO:1904668 positive regulation of ubiquitin protein ligase activity
GO:0060271 cilium assembly
GO:0090557 establishment of endothelial intestinal barrier

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0030658 transport vesicle membrane
GO:0042470 melanosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF209009 - JP 2014500723-A/16512: Polycomb-Associated Non-Coding RNAs.
LF384714 - JP 2014500723-A/192217: Polycomb-Associated Non-Coding RNAs.
AK055927 - Homo sapiens cDNA FLJ31365 fis, clone NB9N41000135, highly similar to RAS-RELATED PROTEIN RAB-1A.
LP895407 - Sequence 271 from Patent EP3253886.
JD237617 - Sequence 218641 from Patent EP1572962.
LF325074 - JP 2014500723-A/132577: Polycomb-Associated Non-Coding RNAs.
JD453452 - Sequence 434476 from Patent EP1572962.
LF325073 - JP 2014500723-A/132576: Polycomb-Associated Non-Coding RNAs.
LF325072 - JP 2014500723-A/132575: Polycomb-Associated Non-Coding RNAs.
JD515710 - Sequence 496734 from Patent EP1572962.
BC000905 - Homo sapiens RAB1A, member RAS oncogene family, mRNA (cDNA clone MGC:5233 IMAGE:2900705), complete cds.
BX571747 - Homo sapiens mRNA; cDNA DKFZp686E08159 (from clone DKFZp686E08159).
AL050268 - Homo sapiens mRNA; cDNA DKFZp564B163 (from clone DKFZp564B163).
BC062594 - Homo sapiens cDNA clone IMAGE:5244515, **** WARNING: chimeric clone ****.
LF325071 - JP 2014500723-A/132574: Polycomb-Associated Non-Coding RNAs.
LF325070 - JP 2014500723-A/132573: Polycomb-Associated Non-Coding RNAs.
LF325069 - JP 2014500723-A/132572: Polycomb-Associated Non-Coding RNAs.
AF170935 - Homo sapiens GTP-binding protein (RAB1A) mRNA, 3' untranslated region.
AK303678 - Homo sapiens cDNA FLJ57768 complete cds, highly similar to Ras-related protein Rab-1A.
LF325068 - JP 2014500723-A/132571: Polycomb-Associated Non-Coding RNAs.
M28209 - Homo sapiens GTP-binding protein (RAB1) mRNA, complete cds.
JD565109 - Sequence 546133 from Patent EP1572962.
CR533479 - Homo sapiens full open reading frame cDNA clone RZPDo834D0817D for gene RAB1A, RAB1A, member RAS oncogene family; complete cds, incl. stopcodon.
AF498929 - Homo sapiens small GTP binding protein RAB1A (RAB1A) mRNA, complete cds.
CR536488 - Homo sapiens full open reading frame cDNA clone RZPDo834E0917D for gene RAB1A, RAB1A, member RAS oncogene family; complete cds, incl. stopcodon.
X13898 - H.sapiens mRNA for ras-related Hrab1A protein.
AK315495 - Homo sapiens cDNA, FLJ96558, Homo sapiens RAB1A, member RAS oncogene family (RAB1A), mRNA.
BT019528 - Homo sapiens RAB1A, member RAS oncogene family mRNA, complete cds.
BT019529 - Homo sapiens RAB1A, member RAS oncogene family mRNA, complete cds.
CU674450 - Synthetic construct Homo sapiens gateway clone IMAGE:100018017 5' read RAB1A mRNA.
EU831590 - Synthetic construct Homo sapiens clone HAIB:100066619; DKFZo007A0919 RAB1A, member RAS oncogene family protein (RAB1A) gene, encodes complete protein.
KJ891963 - Synthetic construct Homo sapiens clone ccsbBroadEn_01357 RAB1A gene, encodes complete protein.
DQ894084 - Synthetic construct Homo sapiens clone IMAGE:100008544; FLH167548.01L; RZPDo839C0289D RAB1A, member RAS oncogene family (RAB1A) gene, encodes complete protein.
AB464118 - Synthetic construct DNA, clone: pF1KB8320, Homo sapiens RAB1A gene for RAB1A, member RAS oncogene family, without stop codon, in Flexi system.
AB590355 - Synthetic construct DNA, clone: pFN21AB8024, Homo sapiens RAB1A gene for RAB1A, member RAS oncogene family, without stop codon, in Flexi system.
AM392684 - Synthetic construct Homo sapiens clone IMAGE:100002094 for hypothetical protein (RAB1A gene).
EU831675 - Synthetic construct Homo sapiens clone HAIB:100066704; DKFZo003A0920 RAB1A, member RAS oncogene family protein (RAB1A) gene, encodes complete protein.
LF325067 - JP 2014500723-A/132570: Polycomb-Associated Non-Coding RNAs.
LF325066 - JP 2014500723-A/132569: Polycomb-Associated Non-Coding RNAs.
LF383437 - JP 2014500723-A/190940: Polycomb-Associated Non-Coding RNAs.
AK123525 - Homo sapiens cDNA FLJ41531 fis, clone BRTHA2014997.
MA620291 - JP 2018138019-A/192217: Polycomb-Associated Non-Coding RNAs.
MA560651 - JP 2018138019-A/132577: Polycomb-Associated Non-Coding RNAs.
MA560650 - JP 2018138019-A/132576: Polycomb-Associated Non-Coding RNAs.
MA560649 - JP 2018138019-A/132575: Polycomb-Associated Non-Coding RNAs.
MA560648 - JP 2018138019-A/132574: Polycomb-Associated Non-Coding RNAs.
MA560647 - JP 2018138019-A/132573: Polycomb-Associated Non-Coding RNAs.
MA560646 - JP 2018138019-A/132572: Polycomb-Associated Non-Coding RNAs.
MA560645 - JP 2018138019-A/132571: Polycomb-Associated Non-Coding RNAs.
MA560644 - JP 2018138019-A/132570: Polycomb-Associated Non-Coding RNAs.
MA560643 - JP 2018138019-A/132569: Polycomb-Associated Non-Coding RNAs.
MA619014 - JP 2018138019-A/190940: Polycomb-Associated Non-Coding RNAs.
MA444586 - JP 2018138019-A/16512: Polycomb-Associated Non-Coding RNAs.

-  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 P62820 (Reactome details) participates in the following event(s):

R-HSA-6811415 RAB:GTP recruits GBF1 to the Golgi membrane
R-NUL-2422970 Phosphorylation of Gorasp1, Golga2 and RAB1A by CDK1:CCNB
R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-6814833 TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP
R-HSA-8870466 RGGT:CHM binds RABs
R-HSA-6807864 RAB1:GTP recruits GBF1 to the ERGIC
R-HSA-6814831 TBC1D20 binds RAB1:GTP
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-8877475 TRAPPC complexes exchange GTP for GDP on RAB1
R-HSA-2172183 Phosphorylation of GORASP1, GOLGA2 and RAB1A by CDK1:CCNB
R-HSA-6811411 GBF1 recruits ARF:GDP to the Golgi
R-HSA-2172194 Recruitment of PLK1 to phosphorylated GORASP1 (GRASP65)
R-HSA-2214351 PLK1 phosphorylates GORASP1
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-8870469 RGGT geranylgeranylates RAB proteins
R-HSA-6807866 GBF1 recruits ARF:GDP to the ERGIC
R-HSA-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-HSA-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-HSA-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-HSA-6811414 GBF1 stimulates nucleotide exchange on ARF
R-HSA-6811412 Active ARF recruits coatomer to the Golgi
R-HSA-6807868 GBF1 stimulates ARF nucleotide exchange
R-HSA-6807872 Active ARF recruits coatomer
R-HSA-6811417 ARFGAP, cargo, vSNARES and p24 proteins bind COPI vesicles at Golgi
R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-HSA-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-8873719 RAB geranylgeranylation
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-162658 Golgi Cisternae Pericentriolar Stack Reorganization
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-597592 Post-translational protein modification
R-HSA-9007101 Rab regulation of trafficking
R-HSA-68875 Mitotic Prophase
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-392499 Metabolism of proteins
R-HSA-68886 M Phase
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: NM_004161, NP_004152, P11476, P62820, Q6FIE7, Q96N61, Q9Y3T2, RAB1, RAB1A_HUMAN
UCSC ID: uc002sdm.3
RefSeq Accession: NM_004161
Protein: P62820 (aka RAB1A_HUMAN or RB1A_HUMAN)
CCDS: CCDS46306.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004161.4
exon count: 6CDS single in 3' UTR: no RNA size: 2648
ORF size: 618CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1313.00frame shift in genome: no % Coverage: 99.81
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.