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LAMTOR4 late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [ Homo sapiens (human) ]

Gene ID: 389541, updated on 17-Jun-2019

Summary

Official Symbol
LAMTOR4provided by HGNC
Official Full Name
late endosomal/lysosomal adaptor, MAPK and MTOR activator 4provided by HGNC
Primary source
HGNC:HGNC:33772
See related
Ensembl:ENSG00000188186
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C7orf59
Expression
Ubiquitous expression in skin (RPKM 36.0), spleen (RPKM 29.2) and 25 other tissues See more
Orthologs

Genomic context

See LAMTOR4 in Genome Data Viewer
Location:
7q22.1
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (100140177..100154212)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99746530..99751833)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene TATA-box binding protein associated factor 6 Neighboring gene canopy FGF signaling regulator 4 Neighboring gene metallo-beta-lactamase domain containing 1 Neighboring gene ribosomal protein L7 pseudogene 60 Neighboring gene microtubule associated protein 11 Neighboring gene microRNA 4658 Neighboring gene galactose-3-O-sulfotransferase 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Pathways from BioSystems

  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Energy dependent regulation of mTOR by LKB1-AMPK, organism-specific biosystem (from REACTOME)
    Energy dependent regulation of mTOR by LKB1-AMPK, organism-specific biosystemUpon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. This phosphorylation is immediately removed in basal conditions by PP2C, but if the cellular AMP:ATP rati...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • IGF1R signaling cascade, organism-specific biosystem (from REACTOME)
    IGF1R signaling cascade, organism-specific biosystemAfter autophosphorylation the type 1 insulin-like growth factor receptor (IGF1R) binds and phosphorylates scaffold proteins, IRS1/2/4 and SHC1, which in turn bind effectors possessing enzymatic activ...
  • IRS-mediated signalling, organism-specific biosystem (from REACTOME)
    IRS-mediated signalling, organism-specific biosystemRelease of phospho-IRS from the insulin receptor triggers a cascade of signalling events via PI3K, SOS, RAF and the MAP kinases.
  • IRS-related events triggered by IGF1R, organism-specific biosystem (from REACTOME)
    IRS-related events triggered by IGF1R, organism-specific biosystemThe phosphorylated type 1 insulin-like growth factor receptor phosphorylates IR1, IRS2, IRS4 and possibly other IRS/DOK family members (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et a...
  • Insulin receptor signalling cascade, organism-specific biosystem (from REACTOME)
    Insulin receptor signalling cascade, organism-specific biosystemAutophosphorylation of the insulin receptor triggers a series of signalling events, mediated by SHC or IRS, and resulting in activation of the Ras/RAF and MAP kinase cascades. A second effect of the ...
  • Macroautophagy, organism-specific biosystem (from REACTOME)
    Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
  • PI3K Cascade, organism-specific biosystem (from REACTOME)
    PI3K Cascade, organism-specific biosystem
    PI3K Cascade
  • PKB-mediated events, organism-specific biosystem (from REACTOME)
    PKB-mediated events, organism-specific biosystemPKB and PDK1 are activated via membrane-bound PIP3. Activated PDK1 phosphorylates PKB, which in turn phosphorylates PDE3B. The latter hydrolyses cAMP to 5'AMP, depleting cAMP pools.
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Insulin receptor, organism-specific biosystem (from REACTOME)
    Signaling by Insulin receptor, organism-specific biosystemInsulin binding to its receptor results in receptor autophosphorylation on tyrosine residues and the tyrosine phosphorylation of insulin receptor substrates (e.g. IRS and Shc) by the insulin receptor...
  • Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R), organism-specific biosystem (from REACTOME)
    Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R), organism-specific biosystemBinding of IGF1 (IGF-I) or IGF2 (IGF-II) to the extracellular alpha peptides of the type 1 insulin-like growth factor receptor (IGF1R) triggers the activation of two major signaling pathways: the SOS...
  • TP53 Regulates Metabolic Genes, organism-specific biosystem (from REACTOME)
    TP53 Regulates Metabolic Genes, organism-specific biosystemWhile the p53 tumor suppressor protein (TP53) is known to inhibit cell growth by inducing apoptosis, senescence and cell cycle arrest, recent studies have found that p53 is also able to influence cel...
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...
  • mTOR signaling pathway, organism-specific biosystem (from KEGG)
    mTOR signaling pathway, organism-specific biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...
  • mTOR signaling pathway, conserved biosystem (from KEGG)
    mTOR signaling pathway, conserved biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...
  • mTOR signalling, organism-specific biosystem (from REACTOME)
    mTOR signalling, organism-specific biosystemTarget of rapamycin (mTOR) is a highly-conserved serine/threonine kinase that regulates cell growth and division in response to energy levels, growth signals, and nutrients (Zoncu et al. 2011). Contr...
  • mTORC1-mediated signalling, organism-specific biosystem (from REACTOME)
    mTORC1-mediated signalling, organism-specific biosystemmTORC1 integrates four major signals ? growth factors, energy status, oxygen and amino acids ? to regulate many processes that are involved in the promotion of cell growth. Growth factors stimulate m...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC163425, MGC163431

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to molecular adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell cycle arrest TAS
Traceable Author Statement
more info
 
cellular response to amino acid stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to amino acid stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to lysosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell size IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of macroautophagy TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Ragulator complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Ragulator complex IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lysosomal membrane TAS
Traceable Author Statement
more info
 
lysosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ragulator complex protein LAMTOR4
Names
UPF0539 protein C7orf59
late endosomal/lysosomal adaptor and MAPK and MTOR activator 4

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001008395.4NP_001008396.1  ragulator complex protein LAMTOR4 isoform 1

    See identical proteins and their annotated locations for NP_001008396.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BI598677, CU450474
    Consensus CDS
    CCDS34702.1
    UniProtKB/Swiss-Prot
    Q0VGL1
    Related
    ENSP00000343118.5, ENST00000341942.9
  2. NM_001318236.2NP_001305165.1  ragulator complex protein LAMTOR4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which introduces a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AA772120, BG706819, CU450474
    Consensus CDS
    CCDS83210.1
    UniProtKB/TrEMBL
    A0A087WV46
    Related
    ENSP00000479176.1, ENST00000460732.5
  3. NM_001318237.2NP_001305166.1  ragulator complex protein LAMTOR4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    BI771662, CU450474
    Consensus CDS
    CCDS83211.1
    UniProtKB/TrEMBL
    A0A087WT92
    Related
    ENSP00000477680.1, ENST00000474141.5

RNA

  1. NR_134526.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in a 5' exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AA772120, CU450474, DB539334
    Related
    ENST00000474831.5
  2. NR_134527.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AA419348, AA772120, BC063401, BG819624, CU450474
  3. NR_134528.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate 5'-terminal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AA772120, BF978089, BI598677
    Related
    ENST00000468582.5
  4. NR_134529.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses an alternate 5'-terminal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AA772120, AJ714519, BC063401, BC130553, BF978089
  5. NR_134530.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) uses an alternate 5'-terminal exon and an alternate splice site in the 3'-terminal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AA772120, BC130553, BF978089, DB498044
    Related
    ENST00000488241.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    100140177..100154212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446761.1XP_024302529.1  ragulator complex protein LAMTOR4 isoform X2

  2. XM_024446760.1XP_024302528.1  ragulator complex protein LAMTOR4 isoform X1

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