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)
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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
 

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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

+  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
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-  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
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-  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 
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 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.