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    LRRC47 leucine rich repeat containing 47 [ Homo sapiens (human) ]

    Gene ID: 57470, updated on 3-Nov-2024

    Summary

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    Official Symbol
    LRRC47provided by HGNC
    Official Full Name
    leucine rich repeat containing 47provided by HGNC
    Primary source
    HGNC:HGNC:29207
    See related
    Ensembl:ENSG00000130764 MIM:619154; AllianceGenome:HGNC:29207
    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
    Summary
    Enables RNA binding activity. Predicted to be involved in phenylalanyl-tRNA aminoacylation. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 13.4), prostate (RPKM 12.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC47 in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3778559..3796498, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (3290152..3308095, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (3695123..3713062, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3678785-3679286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3679287-3679786 Neighboring gene coiled-coil domain containing 27 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3687696-3688374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3689661-3690176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3690177-3690692 Neighboring gene MPRA functional variant 1:3691528:A:G red blood cell enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3691725-3692240 Neighboring gene small integral membrane protein 1 (Vel blood group) Neighboring gene RNA, 7SL, cytoplasmic 574, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:3709930-3710608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 125 Neighboring gene Sharpr-MPRA regulatory region 1968 Neighboring gene centrosomal protein 104 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3745882-3747081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3747165-3748364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:3755401-3755900 Neighboring gene uncharacterized LOC124903829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3767162-3767662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 67 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 127 Neighboring gene Sharpr-MPRA regulatory region 4254 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:3787529-3787731 Neighboring gene DNA fragmentation factor subunit beta

    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. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Schmidt N, et al. Cell, 2023 Oct 26. PMID 37794589, Free PMC Article
    2. The MAP3K13-TRIM25-FBXW7α axis affects c-Myc protein stability and tumor development. Zhang Q, et al. Cell Death Differ, 2020 Feb. PMID 31186535, Free PMC Article
    3. Genome-wide association study identifies loci affecting blood copper, selenium and zinc. Evans DM, et al. Hum Mol Genet, 2013 Oct 1. PMID 23720494, Free PMC Article
    4. EIF3H Orchestrates Hippo Pathway-Mediated Oncogenesis via Catalytic Control of YAP Stability. Zhou Z, et al. Cancer Res, 2020 Jun 15. PMID 32269044, Free PMC Article
    5. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. Hirosawa M, et al. DNA Res, 1999 Oct 29. PMID 10574461

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    nucleocapsid gag HIV-1 NC is identified to have a physical interaction with leucine rich repeat containing 47 (LRRC47) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1185

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    contributes_to phenylalanine-tRNA ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in phenylalanyl-tRNA aminoacylation IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 47

    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_020710.3 → NP_065761.1  leucine-rich repeat-containing protein 47

      See identical proteins and their annotated locations for NP_065761.1

      Status: VALIDATED

      Source sequence(s)
      AB033011, AL365330, BC031301
      Consensus CDS
      CCDS51.1
      UniProtKB/Swiss-Prot
      Q8N1G4, Q9ULN5
      Related
      ENSP00000367498.1, ENST00000378251.3
      Conserved Domains (3) summary
      COG4886
      Location:44 → 239
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      PRK09616
      Location:317 → 507
      pheT; phenylalanine--tRNA ligase subunit beta
      sd00033
      Location:52 → 76
      LRR_RI; leucine-rich repeat [structural motif]

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      3778559..3796498 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      3290152..3308095 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N1G4.1 GenPept UniProtKB/Swiss-Prot:Q8N1G4

    Gene LinkOut

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

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