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    LOC643339 uncharacterized LOC643339 [ Homo sapiens (human) ]

    Gene ID: 643339, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC643339
    Gene description
    uncharacterized LOC643339
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LOC643339 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (93003758..93377736, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (92984622..93358710, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (93397534..93771512, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene early endosome antigen 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 50 Neighboring gene MPRA-validated peak1889 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6755 Neighboring gene NANOG hESC enhancer GRCh37_chr12:93358015-93358572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6757 Neighboring gene MPRA-validated peak1891 silencer Neighboring gene RNA, U6 small nuclear 1329, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6760 Neighboring gene long intergenic non-protein coding RNA 2413 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:93431350-93431527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6761 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:93467941-93468861 Neighboring gene DPPA3 pseudogene 5 Neighboring gene uncharacterized LOC105369908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6762 Neighboring gene ribosomal protein L41 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6763 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:93535709-93535869 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:93561467-93562016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6764 Neighboring gene long intergenic non-protein coding RNA 2412 Neighboring gene MPRA-validated peak1892 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6765 Neighboring gene MPRA-validated peak1893 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene small nucleolar RNA SNORD74 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6767 Neighboring gene HNF4 motif-containing MPRA enhancer 125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93729207-93729708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93729709-93730208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93731209-93731709 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:93741082-93741250 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4704 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93764071-93765034 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:93771297-93772236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4709 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93835621-93836258 Neighboring gene nudix hydrolase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6770 Neighboring gene ubiquitin conjugating enzyme E2 N Neighboring gene mitochondrial ribosomal protein L42 Neighboring gene RNA, 7SL, cytoplasmic 737, pseudogene

    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
    • 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. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. Chalasani N, et al. Gastroenterology, 2010 Nov. PMID 20708005, Free PMC Article
    2. Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations. Xie T, et al. Neurobiol Aging, 2014 Jul. PMID 24529757

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    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

    General gene information

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    Markers

    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.

    RNA

    1. NR_040096.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC021646, AC124947, AC126172

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      93003758..93377736 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      92984622..93358710 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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    Molecular Biology Databases