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

Gene ID: 311866, updated on 4-Jan-2025

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
EnsemblRapid:ENSRNOG00000022312 AllianceGenome:RGD:1564403
Gene type
protein coding
RefSeq status
VALIDATED
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, Jan 2025]
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
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_001107833.2 → NP_001101303.1  E3 ubiquitin-protein ligase LRSAM1 isoform a

    See identical proteins and their annotated locations for NP_001101303.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A0A8I6AEY5, A6JU95, D3ZI42
    Related
    ENSRNOP00000090773.1, ENSRNOT00000110767.2
    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

  2. NM_001434258.1 → NP_001421187.1  E3 ubiquitin-protein ligase LRSAM1 isoform a

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A0A8I6AEY5, A6JU95, D3ZI42

  3. NM_001434259.1 → NP_001421188.1  E3 ubiquitin-protein ligase LRSAM1 isoform a

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A0A8I6AEY5, A6JU95, D3ZI42

  4. NM_001434260.1 → NP_001421189.1  E3 ubiquitin-protein ligase LRSAM1 isoform b

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    D3ZI42

  5. NM_001434261.1 → NP_001421190.1  E3 ubiquitin-protein ligase LRSAM1 isoform b

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    D3ZI42

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

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

    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

    Related
    ENSRNOP00000103205.1, ENSRNOT00000124852.1
    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

    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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