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    LARP6 La ribonucleoprotein 6, translational regulator [ Homo sapiens (human) ]

    Gene ID: 55323, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LARP6provided by HGNC
    Official Full Name
    La ribonucleoprotein 6, translational regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:24012
    See related
    Ensembl:ENSG00000166173 MIM:611300; AllianceGenome:HGNC:24012
    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
    ACHN
    Summary
    Enables RNA binding activity and myosin binding activity. Involved in positive regulation of collagen biosynthetic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 22.8), thyroid (RPKM 15.1) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LARP6 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (70829130..70854157, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (68652085..68677121, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (71121469..71146496, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uveal autoantigen with coiled-coil domains and ankyrin repeats Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71002570-71003070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71005595-71006134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71010983-71011484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6609 Neighboring gene ribosomal protein L29 pseudogene 30 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71145885-71146386 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71163033-71163588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71163589-71164146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9701 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:71170236-71170412 Neighboring gene leucine rich repeat containing 49 Neighboring gene keratin 8 pseudogene 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71184427-71185125 Neighboring gene THAP domain containing 10

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen. Chen L, et al. J Invest Dermatol, 2022 Sep. PMID 35176288
    2. Characterization of Sequence-Specific Binding of LARP6 to the 5' Stem-Loop of Type I Collagen mRNAs and Implications for Rational Design of Antifibrotic Drugs. Stefanovic L, et al. J Mol Biol, 2022 Jan 30. PMID 34896113, Free PMC Article
    3. Acheron, a Lupus antigen family member, regulates integrin expression, adhesion, and motility in differentiating myoblasts. Glenn HL, et al. Am J Physiol Cell Physiol, 2010 Jan. PMID 19889961, Free PMC Article
    4. Binding of LARP6 to the conserved 5' stem-loop regulates translation of mRNAs encoding type I collagen. Cai L, et al. J Mol Biol, 2010 Jan 15. PMID 19917293, Free PMC Article
    5. Tacrolimus (FK506) prevents early stages of ethanol induced hepatic fibrosis by targeting LARP6 dependent mechanism of collagen synthesis. Manojlovic Z, et al. PLoS One, 2013. PMID 23755290, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LARP6 suppresses colorectal cancer progression through ZNF267/SGMS2-mediated imbalance of sphingomyelin synthesis.
      Title: LARP6 suppresses colorectal cancer progression through ZNF267/SGMS2-mediated imbalance of sphingomyelin synthesis.
    2. LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen.
      Title: LARP6 Regulates Keloid Fibroblast Proliferation, Invasion, and Ability to Synthesize Collagen.
    3. Characterization of Sequence-Specific Binding of LARP6 to the 5' Stem-Loop of Type I Collagen mRNAs and Implications for Rational Design of Antifibrotic Drugs.
      Title: Characterization of Sequence-Specific Binding of LARP6 to the 5' Stem-Loop of Type I Collagen mRNAs and Implications for Rational Design of Antifibrotic Drugs.
    4. Study shows that mTORC1 phosphorylates La ribonucleoprotein domain family, member 6 to stimulate type I collagen expression.
      Title: mTORC1 phosphorylates LARP6 to stimulate type I collagen expression.
    5. A cytoplasmic isoform of La protein as well as LARPs 6, 4, and 1 function in mRNA metabolism and translation in distinct but similar ways, sometimes with the poly(A)-binding protein, and in some cases by direct binding to poly(A)-RNA.
      Title: The La and related RNA-binding proteins (LARPs): structures, functions, and evolving perspectives.
    6. Akt mediated phosphorylation of LARP6; critical step in biosynthesis of type I collagen
      Title: Akt mediated phosphorylation of LARP6; critical step in biosynthesis of type I collagen.
    7. We postulate that collagen mRNAs directly partition to the endoplasmic reticulum membrane prior to synthesis of the signal peptide and that LARP6 and nonmuscle myosin filaments mediate this process.
      Title: Role of LARP6 and nonmuscle myosin in partitioning of collagen mRNAs to the ER membrane.
    8. Data indicate that LA motif protein LARP6 binding to spliced leader RNA (5'SL) of collagen alpha2(I) mRNA is more stable than the binding to 5'SL of alpha1(I) mRNA.
      Title: Characterization of binding of LARP6 to the 5' stem-loop of collagen mRNAs: implications for synthesis of type I collagen.
    9. The study presents the structure of the La motif and RRM1 of human LARP6 uncovering in both cases considerable structural variation in comparison to the equivalent domains in La and revealing an unprecedented fold for the RRM1.
      Title: Synergic interplay of the La motif, RRM1 and the interdomain linker of LARP6 in the recognition of collagen mRNA expands the RNA binding repertoire of the La module.
    10. LARP6 is a critical mediator by which IGF-1 augments synthesis of collagen type I in vascular smooth muscle
      Title: Insulin-like growth factor-1 increases synthesis of collagen type I via induction of the mRNA-binding protein LARP6 expression and binding to the 5' stem-loop of COL1a1 and COL1a2 mRNA.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11196

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA stem-loop binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA stem-loop binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables mRNA 5'-UTR binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA 5'-UTR binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of collagen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    la-related protein 6
    Names
    La ribonucleoprotein domain family member 6
    acheron
    death-associated LA motif protein

    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_001286679.2 → NP_001273608.1  la-related protein 6 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks part of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009269, AC090868, AI376944, AL833876, DA715263
      UniProtKB/Swiss-Prot
      Q9BRS8
      Conserved Domains (2) summary
      cd12289
      Location:1 → 108
      RRM_LARP6; RNA recognition motif in La-related protein 6 (LARP6) and similar proteins
      pfam12901
      Location:284 → 298
      SUZ-C; SUZ-C motif

    2. NM_018357.4 → NP_060827.2  la-related protein 6 isoform 1

      See identical proteins and their annotated locations for NP_060827.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC009269, AI376944, AL833876, DN992782
      Consensus CDS
      CCDS32281.1
      UniProtKB/Swiss-Prot
      Q5XKE4, Q8N3N2, Q9BRS8, Q9NUR0
      Related
      ENSP00000299213.7, ENST00000299213.10
      Conserved Domains (3) summary
      cd08033
      Location:93 → 169
      LARP_6; La RNA-binding domain of La-related protein 6
      pfam12901
      Location:452 → 484
      SUZ-C; SUZ-C motif
      cd12289
      Location:184 → 292
      RRM_LARP6; RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins

    3. NM_197958.3 → NP_932062.1  la-related protein 6 isoform 2

      See identical proteins and their annotated locations for NP_932062.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several exons and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC039153, DN992782
      Consensus CDS
      CCDS10236.1
      UniProtKB/Swiss-Prot
      Q9BRS8
      Related
      ENSP00000343869.3, ENST00000344870.4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      70829130..70854157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      68652085..68677121 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRS8.1 GenPept UniProtKB/Swiss-Prot:Q9BRS8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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