Human Gene LAMTOR4 (ENST00000341942.10_3) from GENCODE V47lift37
  Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 4, transcript variant 7 (from RefSeq NR_134529.3)
Gencode Transcript: ENST00000341942.10_3
Gencode Gene: ENSG00000188186.11_8
Transcript (Including UTRs)
   Position: hg19 chr7:99,746,541-99,751,826 Size: 5,286 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr7:99,746,596-99,751,587 Size: 4,992 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:99,746,541-99,751,826)mRNA (may differ from genome)Protein (99 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LTOR4_HUMAN
DESCRIPTION: RecName: Full=Ragulator complex protein LAMTOR4; AltName: Full=Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4;
FUNCTION: As part of the Ragulator complex it is involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids. Activated by amino acids through a mechanism involving the lysosomal V-ATPase, the Ragulator functions as a guanine nucleotide exchange factor activating the small GTPases Rag. Activated Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated.
SUBUNIT: Part of the Ragulator complex composed of LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5. LAMTOR4 and LAMTOR5 form an heterodimer that interacts, through LAMTOR1, with a LAMTOR2, LAMTOR3 heterodimer. The Ragulator complex interacts with both the mTORC1 complex and heterodimers constituted of the Rag GTPases RRAGA, RRAGB, RRAGC and RRAGD; regulated by amino acid availability.
SUBCELLULAR LOCATION: Lysosome.
SIMILARITY: Belongs to the LAMTOR4 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


-  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: 130.08 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 2390.78 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.4055-0.244 Picture PostScript Text
3' UTR -96.10239-0.402 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
  SCOP Domains:
103196 - Roadblock/LC7 domain

ModBase Predicted Comparative 3D Structure on Q0VGL1
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 Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0032947 protein complex scaffold

Biological Process:
GO:0007050 cell cycle arrest
GO:0008361 regulation of cell size
GO:0016241 regulation of macroautophagy
GO:0032008 positive regulation of TOR signaling
GO:0061462 protein localization to lysosome
GO:0071230 cellular response to amino acid stimulus

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0071986 Ragulator complex


-  Descriptions from all associated GenBank mRNAs
  KJ900707 - Synthetic construct Homo sapiens clone ccsbBroadEn_10101 C7orf59 gene, encodes complete protein.
BC105609 - Homo sapiens chromosome 7 open reading frame 59, mRNA (cDNA clone MGC:104465 IMAGE:30321610), complete cds.
BC063401 - Homo sapiens chromosome 7 open reading frame 59, mRNA (cDNA clone MGC:71073 IMAGE:5194116), complete cds.
BC130553 - Homo sapiens chromosome 7 open reading frame 59, mRNA (cDNA clone MGC:163425 IMAGE:40146584), complete cds.
BC130559 - Homo sapiens chromosome 7 open reading frame 59, mRNA (cDNA clone MGC:163431 IMAGE:40146590), complete cds.
HQ258033 - Synthetic construct Homo sapiens clone IMAGE:100072342 chromosome 7 open reading frame 59 (C7orf59) (C7orf59) gene, encodes complete protein.
JD066212 - Sequence 47236 from Patent EP1572962.
JD437023 - Sequence 418047 from Patent EP1572962.
JD533127 - Sequence 514151 from Patent EP1572962.
JD411677 - Sequence 392701 from Patent EP1572962.
JD240158 - Sequence 221182 from Patent EP1572962.
JD216533 - Sequence 197557 from Patent EP1572962.
JD566274 - Sequence 547298 from Patent EP1572962.

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

Protein Q0VGL1 (Reactome details) participates in the following event(s):

R-HSA-5653936 Formation of ragulator
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: C7orf59 , ENST00000341942.1, ENST00000341942.2, ENST00000341942.3, ENST00000341942.4, ENST00000341942.5, ENST00000341942.6, ENST00000341942.7, ENST00000341942.8, ENST00000341942.9, LAMTOR4 , LTOR4_HUMAN, NR_134529, Q0VGL1, uc317wel.1, uc317wel.2
UCSC ID: ENST00000341942.10_3
RefSeq Accession: NM_001008395.4
Protein: Q0VGL1 (aka LTOR4_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.