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    Lrsam1 leucine rich repeat and sterile alpha motif containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311866, updated on 19-Jun-2024

    Summary

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    Official Symbol
    Lrsam1provided by RGD
    Official Full Name
    leucine rich repeat and sterile alpha motif containing 1provided by RGD
    Primary source
    RGD:1564403
    See related
    Ensembl:ENSRNOG00000022312 AllianceGenome:RGD:1564403
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1564403
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including positive regulation of macroautophagy; protein ubiquitination; and ubiquitin-dependent endocytosis. Predicted to be located in cytosol and membrane. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease axonal type 2P. Orthologous to human LRSAM1 (leucine rich repeat and sterile alpha motif containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 103.5), Brain (RPKM 53.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lrsam1 in Genome Data Viewer
    Location:
    3p11
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (36621042..36661932, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (16223367..16264261, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (11970401..12009463, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 157 Neighboring gene peptidyl-tRNA hydrolase 1 homolog Neighboring gene syntaxin binding protein 1 Neighboring gene uncharacterized LOC134486073 Neighboring gene niban apoptosis regulator 2 Neighboring gene small nucleolar RNA, H/ACA box 65 Neighboring gene ribosomal protein L12 Neighboring gene solute carrier family 2 member 8

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular Salmonella Typhimurium. Huett A, et al. Cell Host Microbe, 2012 Dec 13. PMID 23245322, Free PMC Article
    2. PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1. Wang Z, et al. Autophagy, 2014. PMID 25484098, Free PMC Article
    3. Regulation of Tsg101 expression by the steadiness box: a role of Tsg101-associated ligase. McDonald B, et al. Mol Biol Cell, 2008 Feb. PMID 18077552, Free PMC Article
    4. Tal, a Tsg101-specific E3 ubiquitin ligase, regulates receptor endocytosis and retrovirus budding. Amit I, et al. Genes Dev, 2004 Jul 15. PMID 15256501, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin-protein transferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of xenophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein autoubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein polyubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ubiquitin-dependent endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in viral budding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase LRSAM1
    NP_001101303.1
    XP_038961180.1
    XP_038961181.1
    XP_038961183.1
    XP_063140035.1
    XP_063140036.1

    NCBI Reference Sequences (RefSeq)

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    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_001107833.1 → NP_001101303.1  E3 ubiquitin-protein ligase LRSAM1

      See identical proteins and their annotated locations for NP_001101303.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474001
      UniProtKB/TrEMBL
      A0A8I6AEY5, A6JU95, D3ZI42
      Related
      ENSRNOP00000090773.1, ENSRNOT00000110767.1
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG1196
      Location:254 → 559
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:678 → 717
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      36621042..36661932 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063283965.1 → XP_063140035.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

      UniProtKB/TrEMBL
      D3ZI42

    2. XM_039105253.2 → XP_038961181.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AEY5, A6JU95, D3ZI42
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG1196
      Location:254 → 559
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:678 → 717
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins

    3. XM_039105255.2 → XP_038961183.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

      UniProtKB/TrEMBL
      D3ZI42
      Conserved Domains (5) summary
      cd09523
      Location:540 → 604
      SAM_TAL; SAM domain of TAL subfamily
      COG1196
      Location:243 → 519
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:651 → 690
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins

    4. XM_039105252.2 → XP_038961180.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AEY5, A6JU95, D3ZI42
      Conserved Domains (5) summary
      cd09523
      Location:567 → 631
      SAM_TAL; SAM domain of TAL subfamily
      COG1196
      Location:254 → 559
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      COG4886
      Location:65 → 181
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:33 → 54
      LRR_RI; leucine-rich repeat [structural motif]
      cd16515
      Location:678 → 717
      RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins

    5. XM_063283966.1 → XP_063140036.1  E3 ubiquitin-protein ligase LRSAM1 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version

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