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LRSAM1 leucine rich repeat and sterile alpha motif containing 1 [ Homo sapiens (human) ]

Gene ID: 90678, updated on 4-Nov-2018

Summary

Official Symbol
LRSAM1provided by HGNC
Official Full Name
leucine rich repeat and sterile alpha motif containing 1provided by HGNC
Primary source
HGNC:HGNC:25135
See related
Ensembl:ENSG00000148356 MIM:610933; Vega:OTTHUMG00000020701
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TAL; CMT2P; RIFLE
Summary
This gene encodes a ring finger protein involved in a variety of functions, including regulation of signaling pathways and cell adhesion, mediation of self-ubiquitylation, and involvement in cargo sorting during receptor endocytosis. Mutations in this gene have been associated with Charcot-Marie-Tooth disease. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jan 2012]
Expression
Ubiquitous expression in skin (RPKM 9.6), bone marrow (RPKM 7.7) and 24 other tissues See more
Orthologs

Genomic context

See LRSAM1 in Genome Data Viewer
Location:
9q33.3-q34.11
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (127451486..127503501)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130213765..130265780)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene zinc finger protein 79 Neighboring gene small nucleolar RNA, H/ACA box 65 Neighboring gene ribosomal protein L12 Neighboring gene family with sequence similarity 129 member B Neighboring gene uncharacterized LOC105376281 Neighboring gene FAM129B intron CAGE-defined low expression enhancer

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag TAL, a Tsg101-associated ligase, binds and ubiquitinates Tsg101; TAL-mediated binding and ubiquitination of Tsg101 cooperatively regulate release of HIV-1 Gag PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31641

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
negative regulation of endocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of xenophagy IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of xenophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
viral budding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase LRSAM1
Names
RING-type E3 ubiquitin transferase LRSAM1
Tsg101-associated ligase
NP_001005373.1
NP_001005374.1
NP_001177652.1
NP_612370.3
XP_006717379.1
XP_016870772.1
XP_016870773.1

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.

Genomic

  1. NG_032008.1 RefSeqGene

    Range
    5001..57016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_373

mRNA and Protein(s)

  1. NM_001005373.3NP_001005373.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_001005373.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AY358830, BC009239, DA165729, DB309230
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q6UWE0
    UniProtKB/TrEMBL
    A0A024R870
    Related
    ENSP00000300417.6, ENST00000300417.10
    Conserved Domains (8) summary
    cd09523
    Location:567631
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:571631
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:674716
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
  2. NM_001005374.3NP_001005374.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_001005374.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AI364608, AY358830, BC009239
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q6UWE0
    UniProtKB/TrEMBL
    A0A024R870
    Related
    ENSP00000362419.1, OTTHUMP00000022175, ENST00000373322.1, OTTHUMT00000054166
    Conserved Domains (8) summary
    cd09523
    Location:567631
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:571631
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:674716
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
  3. NM_001190723.2NP_001177652.1  E3 ubiquitin-protein ligase LRSAM1 isoform 2

    See identical proteins and their annotated locations for NP_001177652.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK056203, BC009239, DA165729, DB309230
    Consensus CDS
    CCDS55347.1
    UniProtKB/Swiss-Prot
    Q6UWE0
    Related
    ENSP00000362421.4, OTTHUMP00000022173, ENST00000373324.8, OTTHUMT00000054163
    Conserved Domains (8) summary
    cd09523
    Location:540604
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:544604
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:647689
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
  4. NM_138361.5NP_612370.3  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_612370.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AI364608, AK091589, BC009239, DA726792
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q6UWE0
    UniProtKB/TrEMBL
    A0A024R870
    Related
    ENSP00000322937.4, OTTHUMP00000022174, ENST00000323301.8, OTTHUMT00000054164
    Conserved Domains (8) summary
    cd09523
    Location:567631
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:571631
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:674716
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    127451486..127503501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017015283.1XP_016870772.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

    UniProtKB/Swiss-Prot
    Q6UWE0
    UniProtKB/TrEMBL
    A0A024R870
    Conserved Domains (8) summary
    cd09523
    Location:567631
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:571631
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:674716
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)
  2. XM_017015284.2XP_016870773.1  E3 ubiquitin-protein ligase LRSAM1 isoform X3

  3. XM_006717316.4XP_006717379.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

    Conserved Domains (9) summary
    cd09523
    Location:536598
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:538598
    SAM; Sterile alpha motif
    cd00116
    Location:67162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:3354
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127181
    LRR_8; Leucine rich repeat
    pfam13863
    Location:257359
    DUF4200; Domain of unknown function (DUF4200)
    pfam13920
    Location:641683
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)

RNA

  1. XR_929874.3 RNA Sequence

  2. XR_001746415.2 RNA Sequence

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