Human Gene LAMTOR2 (uc001fnb.3)
  Description: Homo sapiens late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 (LAMTOR2), transcript variant 1, mRNA.
RefSeq Summary (NM_014017): The product of this gene is highly conserved with a mouse protein associated with the cytoplasmic face of late endosomes and lysosomes. The mouse protein interacts with MAPK scaffold protein 1, a component of the mitogen-activated protein kinase pathway. In humans, a mutation in this gene has been associated with a primary immunodeficiency syndrome, and suggests a role for this protein in endosomal biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009].
Transcript (Including UTRs)
   Position: hg19 chr1:156,024,517-156,028,605 Size: 4,089 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:156,024,681-156,028,162 Size: 3,482 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:156,024,517-156,028,605)mRNA (may differ from genome)Protein (125 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ragulator complex protein LAMTOR2; AltName: Full=Endosomal adaptor protein p14; AltName: Full=Late endosomal/lysosomal Mp1-interacting protein; AltName: Full=Late endosomal/lysosomal adaptor and MAPK and MTOR activator 2; AltName: Full=Mitogen-activated protein-binding protein-interacting protein; AltName: Full=Roadblock domain-containing protein 3;
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. Adapter protein that enhances the efficiency of the MAP kinase cascade facilitating the activation of MAPK2.
SUBUNIT: Interacts with MAPK1 and MAP2K1 (By similarity). 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 LAMTOR1 and LAMTOR3; the interaction is direct.
INTERACTION: Q9UHA4:LAMTOR3; NbExp=3; IntAct=EBI-2643704, EBI-1038192;
SUBCELLULAR LOCATION: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Lysosome membrane; Peripheral membrane protein; Cytoplasmic side (By similarity).
DISEASE: Defects in LAMTOR2 are the cause of immunodeficiency due to defect in MAPBP-interacting protein (ID-MAPBPIP) [MIM:610798]. This form of primary immunodeficiency syndrome includes congenital neutropenia, partial albinism, short stature and B-cell and cytotoxic T-cell deficiency.
SIMILARITY: Belongs to the GAMAD family.
WEB RESOURCE: Name=MAPBPIPbase; Note=ROBLD3 mutation db; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: LAMTOR2
Diseases sorted by gene-association score: immunodeficiency due to defect in mapbp-interacting protein* (1369), t cell deficiency (8)
* = Manually curated disease association

-  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: 25.26 RPKM in Adrenal Gland
Total median expression: 830.58 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 -65.80164-0.401 Picture PostScript Text
3' UTR -153.70443-0.347 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
IPR004942 - Dynein_light-rel

Pfam Domains:
PF03259 - Roadblock/LC7 domain

SCOP Domains:
103196 - Roadblock/LC7 domain

ModBase Predicted Comparative 3D Structure on Q9Y2Q5
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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  Protein SequenceProtein SequenceProtein Sequence 

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

Biological Process:
GO:0000165 MAPK cascade
GO:0000186 activation of MAPKK activity
GO:0001558 regulation of cell growth
GO:0007050 cell cycle arrest
GO:0016241 regulation of macroautophagy
GO:0032008 positive regulation of TOR signaling
GO:0034613 cellular protein localization
GO:0043312 neutrophil degranulation
GO:0071230 cellular response to amino acid stimulus

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0031902 late endosome membrane
GO:0035579 specific granule membrane
GO:0070821 tertiary granule membrane
GO:0071986 Ragulator complex

-  Descriptions from all associated GenBank mRNAs
  AK307086 - Homo sapiens cDNA, FLJ97034.
AF070659 - Homo sapiens HSPC003 mRNA, complete cds.
BC024190 - Homo sapiens roadblock domain containing 3, mRNA (cDNA clone MGC:2685 IMAGE:2819969), complete cds.
CU692872 - Synthetic construct Homo sapiens gateway clone IMAGE:100021807 5' read MAPBPIP mRNA.
KJ893650 - Synthetic construct Homo sapiens clone ccsbBroadEn_03044 LAMTOR2 gene, encodes complete protein.
DQ896212 - Synthetic construct Homo sapiens clone IMAGE:100010672; FLH191223.01L; RZPDo839A1267D mitogen-activated protein-binding protein-interacting protein (MAPBPIP) gene, encodes complete protein.
DQ892965 - Synthetic construct clone IMAGE:100005595; FLH191227.01X; RZPDo839A1277D mitogen-activated protein-binding protein-interacting protein (MAPBPIP) gene, encodes complete protein.
JD024315 - Sequence 5339 from Patent EP1572962.
JD131455 - Sequence 112479 from Patent EP1572962.
JD208468 - Sequence 189492 from Patent EP1572962.
JD028041 - Sequence 9065 from Patent EP1572962.

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

Protein Q9Y2Q5 (Reactome details) participates in the following event(s):

R-HSA-5653936 Formation of ragulator
R-HSA-5653974 Ragulator binds Rag dimers
R-HSA-5674132 WDR83:LAMTOR2:LAMTOR3 binds MAPK components
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-6799350 Exocytosis of specific 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-5674135 MAP2K and MAPK activation
R-HSA-6798695 Neutrophil degranulation
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-168249 Innate Immune System
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-168256 Immune System
R-HSA-5683057 MAPK family signaling cascades
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: HSPC003, LTOR2_HUMAN, MAPBPIP, NM_014017, NP_054736, Q5VY97, Q5VY98, Q5VY99, Q9Y2Q5, ROBLD3
UCSC ID: uc001fnb.3
RefSeq Accession: NM_014017
Protein: Q9Y2Q5 (aka LTOR2_HUMAN)
CCDS: CCDS1128.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_014017.3
exon count: 4CDS single in 3' UTR: no RNA size: 699
ORF size: 378CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 956.00frame shift in genome: no % Coverage: 97.42
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.