Human Gene RRAGD (ENST00000369415.9_7) from GENCODE V47lift37
  Description: Ras related GTP binding D (from RefSeq NM_021244.5)
Gencode Transcript: ENST00000369415.9_7
Gencode Gene: ENSG00000025039.15_9
Transcript (Including UTRs)
   Position: hg19 chr6:90,074,335-90,121,992 Size: 47,658 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr6:90,077,775-90,121,712 Size: 43,938 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:90,074,335-90,121,992)mRNA (may differ from genome)Protein (400 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RRAGD_HUMAN
DESCRIPTION: RecName: Full=Ras-related GTP-binding protein D; Short=Rag D; Short=RagD;
FUNCTION: Has guanine nucleotide-binding activity but lacks intrinsic GTPase activity. Probably required for the amino acid- induced relocalization of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB. This is a crucial step in the activation of the TOR signaling cascade by amino acids.
SUBUNIT: Binds GTP. Forms a heterodimer with RRAGA in a sequence- independent manner and RRAGB. Heterodimerization stabilizes PPAG proteins. In complex with RRAGB, interacts with RPTOR; this interaction is particularly efficient with GTP-loaded RRAGB and GDP-loaded RRAGC. Interacts with NOL8.
INTERACTION: Q9P2J5:LARS; NbExp=13; IntAct=EBI-992949, EBI-356077; Q7L523:RRAGA; NbExp=7; IntAct=EBI-992949, EBI-752376; Q5VZM2:RRAGB; NbExp=7; IntAct=EBI-992949, EBI-993049;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Lysosome. Note=Predominantly cytoplasmic. May shuttle between the cytoplasm and nucleus, depending on the bound nucleotide state of associated RRAGA.
SIMILARITY: Belongs to the GTR/RAG GTP-binding protein family.
SEQUENCE CAUTION: Sequence=AAH03088.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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


-  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: 25.16 RPKM in Muscle - Skeletal
Total median expression: 358.89 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 -155.30280-0.555 Picture PostScript Text
3' UTR -882.103440-0.256 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
IPR006762 - Gtr1_RagA

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF04670 - Gtr1/RagA G protein conserved region
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
2Q3F - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NQL2
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  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
GO:0046982 protein heterodimerization activity
GO:0051020 GTPase binding

Biological Process:
GO:0007050 cell cycle arrest
GO:0010506 regulation of autophagy
GO:0016241 regulation of macroautophagy
GO:0032008 positive regulation of TOR signaling
GO:0034613 cellular protein localization
GO:0071230 cellular response to amino acid stimulus
GO:0071233 cellular response to leucine
GO:1904263 positive regulation of TORC1 signaling
GO:1990253 cellular response to leucine starvation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005813 centrosome
GO:0005829 cytosol
GO:0034448 EGO complex
GO:1990131 Gtr1-Gtr2 GTPase complex


-  Descriptions from all associated GenBank mRNAs
  JF432487 - Synthetic construct Homo sapiens clone IMAGE:100073708 Ras-related GTP binding D (RRAGD) gene, encodes complete protein.
KJ903026 - Synthetic construct Homo sapiens clone ccsbBroadEn_12420 RRAGD gene, encodes complete protein.
LP895562 - Sequence 426 from Patent EP3253886.
AJ420486 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1894669.
AL137502 - Homo sapiens mRNA; cDNA DKFZp761H171 (from clone DKFZp761H171).
BC003088 - Homo sapiens Ras-related GTP binding D, mRNA (cDNA clone MGC:1129 IMAGE:3536088), complete cds.
AK126164 - Homo sapiens cDNA FLJ44176 fis, clone THYMU2036604.
AF272036 - Homo sapiens Rag D mRNA, complete cds.
AK289799 - Homo sapiens cDNA FLJ75246 complete cds, highly similar to Homo sapiens Rag D mRNA.
JD085719 - Sequence 66743 from Patent EP1572962.
JD510305 - Sequence 491329 from Patent EP1572962.
LF211944 - JP 2014500723-A/19447: Polycomb-Associated Non-Coding RNAs.
DL492338 - Novel nucleic acids.
DL490827 - Novel nucleic acids.
MA447521 - JP 2018138019-A/19447: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9NQL2 (Reactome details) participates in the following event(s):

R-HSA-5653957 Rag dimer formation
R-HSA-5653974 Ragulator binds Rag dimers
R-HSA-8952716 SLC38A9 binds Ragulator:Rag dimers
R-HSA-5653968 Ragulator:Rag dimers:SLC38A9 bind mTORC1
R-HSA-165680 Formation of active mTORC1 complex
R-HSA-8952726 SLC38A9 transports L-Arg from lysosomal lumen to cytosol
R-HSA-380979 RHEB in mTORC1:RHEB:GTP hydrolyses GTP
R-HSA-447074 AMPK phosphorylates Raptor in the mTORC1 complex
R-HSA-5672843 AKT1S1 (PRAS40) binds mTORC1
R-HSA-5672017 Rheb in the mTORC1 complex hydrolyses GTP
R-HSA-5672817 Active mTORC1 binds the ULK1 complex
R-HSA-5675790 mTORC1 dissociates from ULK complex
R-HSA-5672824 Phosphorylated AKT1S1:mTORC1 binds YWHAB
R-HSA-377186 Activated Akt1 phosphorylates AKT1S1 (PRAS40)
R-HSA-165692 Phosphorylation of 4E-BP1 by activated mTORC1
R-HSA-165718 mTORC1 phosphorylation of RPS6KB1 (S6K)
R-HSA-5672010 Active mTORC1 phosphorylates ULK1
R-HSA-5673768 p-AMPK:AMP phosphorylates Raptor in the mTORC1 complex
R-HSA-8944454 mTORC1 phosphorylates MAF1
R-HSA-5672828 mTORC1 phosphorylates AKT1S1
R-HSA-165159 mTOR signalling
R-HSA-162582 Signal Transduction
R-HSA-380972 Energy dependent regulation of mTOR by LKB1-AMPK
R-HSA-5628897 TP53 Regulates Metabolic Genes
R-HSA-1632852 Macroautophagy
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-166208 mTORC1-mediated signalling
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-212436 Generic Transcription Pathway
R-HSA-6807070 PTEN Regulation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-74160 Gene expression (Transcription)
R-HSA-9006925 Intracellular signaling by second messengers

-  Other Names for This Gene
  Alternate Gene Symbols: A8K184, ENST00000369415.1, ENST00000369415.2, ENST00000369415.3, ENST00000369415.4, ENST00000369415.5, ENST00000369415.6, ENST00000369415.7, ENST00000369415.8, NM_021244, Q7L8F9, Q9NPG0, Q9NQL2, RRAGD , RRAGD_HUMAN, uc318hoe.1, uc318hoe.2
UCSC ID: ENST00000369415.9_7
RefSeq Accession: NM_021244.5
Protein: Q9NQL2 (aka RRAGD_HUMAN)

-  Gene Model Information
  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.