Human Gene LAMTOR1 (uc001ort.3) Description and Page Index
  Description: Homo sapiens late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 (LAMTOR1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr11:71,808,338-71,814,433 Size: 6,096 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr11:71,808,868-71,814,270 Size: 5,403 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:71,808,338-71,814,433)mRNA (may differ from genome)Protein (161 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ragulator complex protein LAMTOR1; AltName: Full=Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1; AltName: Full=Lipid raft adaptor protein p18; AltName: Full=Protein associated with DRMs and endosomes; AltName: Full=p27Kip1-releasing factor from RhoA; Short=p27RF-Rho;
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. LAMTOR1 is directly responsible for anchoring the Ragulator complex to membranes. Also required for late endosomes/lysosomes biogenesis it may regulate both the recycling of receptors through endosomes and the MAPK signaling pathway through recruitment of some of its components to late endosomes. May be involved in cholesterol homeostasis regulating LDL uptake and cholesterol release from late endosomes/lysosomes. May also play a role in RHOA activation.
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. Interacts with LAMTOR2 and LAMTOR3; the interaction is direct. Interacts with RRAGB and RRAGD; the interaction is direct indicating that it probably constitutes the main RAG- interacting subunit of the Ragulator complex. Interacts with MMP14. Interacts with CDKN1B; prevents the interaction of CDKN1B with RHOA leaving RHOA in a form accessible to activation by ARHGEF2.
SUBCELLULAR LOCATION: Late endosome membrane; Lipid-anchor; Cytoplasmic side. Lysosome membrane; Lipid-anchor; Cytoplasmic side. Cell membrane.
INDUCTION: Down-regulated by cholesterol (at protein level).
SIMILARITY: Belongs to the LAMTOR1 family.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 50.24 RPKM in Spleen
Total median expression: 1581.35 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 -87.50163-0.537 Picture PostScript Text
3' UTR -205.60530-0.388 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
IPR026310 - LAMTOR1

Pfam Domains:
PF15454 - Late endosomal/lysosomal adaptor and MAPK and MTOR activator

ModBase Predicted Comparative 3D Structure on Q6IAA8
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 BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 Protein SequenceProtein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0051020 GTPase binding
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0032947 protein complex scaffold

Biological Process:
GO:0001558 regulation of cell growth
GO:0001919 regulation of receptor recycling
GO:0007032 endosome organization
GO:0007040 lysosome organization
GO:0007050 cell cycle arrest
GO:0010872 regulation of cholesterol esterification
GO:0010874 regulation of cholesterol efflux
GO:0016197 endosomal transport
GO:0016241 regulation of macroautophagy
GO:0032008 positive regulation of TOR signaling
GO:0032418 lysosome localization
GO:0034613 cellular protein localization
GO:0042632 cholesterol homeostasis
GO:0043312 neutrophil degranulation
GO:0043410 positive regulation of MAPK cascade
GO:0060620 regulation of cholesterol import
GO:0071230 cellular response to amino acid stimulus

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0031902 late endosome membrane
GO:0035577 azurophil granule membrane
GO:0035579 specific granule membrane
GO:0045121 membrane raft
GO:0070062 extracellular exosome
GO:0071986 Ragulator complex
GO:0101003 ficolin-1-rich granule membrane

-  Descriptions from all associated GenBank mRNAs
  BC001706 - Homo sapiens chromosome 11 open reading frame 59, mRNA (cDNA clone MGC:1015 IMAGE:3544000), complete cds.
AK000632 - Homo sapiens cDNA FLJ20625 fis, clone KAT04008.
AF289583 - Homo sapiens clone pp7157 unknown mRNA.
JD296253 - Sequence 277277 from Patent EP1572962.
AK300681 - Homo sapiens cDNA FLJ51311 complete cds.
JD418518 - Sequence 399542 from Patent EP1572962.
JD253727 - Sequence 234751 from Patent EP1572962.
JD447921 - Sequence 428945 from Patent EP1572962.
JD332124 - Sequence 313148 from Patent EP1572962.
LF383519 - JP 2014500723-A/191022: Polycomb-Associated Non-Coding RNAs.
LF206745 - JP 2014500723-A/14248: Polycomb-Associated Non-Coding RNAs.
LF357506 - JP 2014500723-A/165009: Polycomb-Associated Non-Coding RNAs.
JD301455 - Sequence 282479 from Patent EP1572962.
LF206746 - JP 2014500723-A/14249: Polycomb-Associated Non-Coding RNAs.
JD338407 - Sequence 319431 from Patent EP1572962.
JD559975 - Sequence 540999 from Patent EP1572962.
JD109812 - Sequence 90836 from Patent EP1572962.
KJ894113 - Synthetic construct Homo sapiens clone ccsbBroadEn_03507 LAMTOR1 gene, encodes complete protein.
CR457247 - Homo sapiens full open reading frame cDNA clone RZPDo834B089D for gene FLJ20625, hypothetical protein FLJ20625; complete cds, incl. stopcodon.
LF357507 - JP 2014500723-A/165010: Polycomb-Associated Non-Coding RNAs.
JD478344 - Sequence 459368 from Patent EP1572962.
MA619096 - JP 2018138019-A/191022: Polycomb-Associated Non-Coding RNAs.
MA442322 - JP 2018138019-A/14248: Polycomb-Associated Non-Coding RNAs.
MA593083 - JP 2018138019-A/165009: Polycomb-Associated Non-Coding RNAs.
MA442323 - JP 2018138019-A/14249: Polycomb-Associated Non-Coding RNAs.
MA593084 - JP 2018138019-A/165010: Polycomb-Associated Non-Coding RNAs.

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

Protein Q6IAA8 (Reactome details) participates in the following event(s):

R-HSA-5653936 Formation of ragulator
R-HSA-5653974 Ragulator binds Rag dimers
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-6800426 Exocytosis of ficolin-rich granule membrane proteins
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-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System
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: C11orf59, LTOR1_HUMAN, NM_017907, NP_060377, PDRO, PP7157, Q6IAA8, Q8WZ09, Q9NWT0
UCSC ID: uc001ort.3
RefSeq Accession: NM_017907
Protein: Q6IAA8 (aka LTOR1_HUMAN)
CCDS: CCDS8209.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_017907.2
exon count: 5CDS single in 3' UTR: no RNA size: 1198
ORF size: 486CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1166.00frame shift in genome: no % Coverage: 98.41
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
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-  Methods, Credits, and Use Restrictions
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