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

    Gene ID: 389541, updated on 17-Jun-2024

    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 MIM:618834; AllianceGenome:HGNC:33772
    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
    Summary
    Contributes to guanyl-nucleotide exchange factor activity and molecular adaptor activity. Involved in several processes, including cellular response to amino acid stimulus; positive regulation of TOR signaling; and protein localization to lysosome. Located in lysosome. Part of Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 36.0), spleen (RPKM 29.2) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See LAMTOR4 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100148918..100154203)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101379971..101393996)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99746541..99751826)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene TATA-box binding protein associated factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18417 Neighboring gene metallo-beta-lactamase domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26341 Neighboring gene ribosomal protein L7 pseudogene 60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99745544-99746156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99746769-99747381 Neighboring gene trafficking protein particle complex subunit 14 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99755453-99755629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99757927-99758426 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

    Bibliography

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of FNIP-folliculin RagC/D GAP IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of Ragulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of Ragulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of Ragulator complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in late endosome membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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, ENST00000341942.10
    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
    4. NM_001394587.1NP_001381516.1  ragulator complex protein LAMTOR4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC073842
    5. NM_001394588.1NP_001381517.1  ragulator complex protein LAMTOR4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC073842
    6. NM_001394589.1NP_001381518.1  ragulator complex protein LAMTOR4 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC073842

    RNA

    1. NR_134526.2 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_134527.2 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, BC063401, BG819624, CU450474
    3. NR_134529.3 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)
      AC073842
      Related
      ENST00000468582.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100148918..100154203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      101379971..101393996
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358187.1XP_054214162.1  ragulator complex protein LAMTOR4 isoform X2

      UniProtKB/TrEMBL
      A0A087WV46
    2. XM_054358186.1XP_054214161.1  ragulator complex protein LAMTOR4 isoform X1

      UniProtKB/Swiss-Prot
      Q0VGL1