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    SOX9-AS1 SOX9 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 400618, updated on 5-Feb-2024

    Summary

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    Official Symbol
    SOX9-AS1provided by HGNC
    Official Full Name
    SOX9 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:49321
    See related
    Ensembl:ENSG00000234899 AllianceGenome:HGNC:49321
    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 SOX9-AS1 in Genome Data Viewer
    Location:
    17q24.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72071042..72120793, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (72944219..72993997, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70067183..70116934, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:70025920-70026690 Neighboring gene uncharacterized LOC102723517 Neighboring gene long intergenic non-protein coding RNA 1152 Neighboring gene regulator of chondrogenesis RNA Neighboring gene long intergenic non-protein coding RNA 2097 Neighboring gene SOX9 enhancer E1 Neighboring gene SOX9 enhancer eALDI Neighboring gene TES enhancer upstream of SOX9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70113837-70114458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70115824-70116324 Neighboring gene SOX9 promoter region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70119336-70119859 Neighboring gene SRY-box transcription factor 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70181507-70182008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70201265-70201766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70201767-70202266 Neighboring gene SOX9 enhancer E7 Neighboring gene uncharacterized LOC124900392

    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. Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma. Wu L, et al. Clin Res Hepatol Gastroenterol, 2022 Nov. PMID 35870795
    2. A SOX9-AS1/miR-5590-3p/SOX9 positive feedback loop drives tumor growth and metastasis in hepatocellular carcinoma through the Wnt/β-catenin pathway. Zhang W, et al. Mol Oncol, 2019 Oct. PMID 31402556, Free PMC Article
    3. The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells. Barter MJ, et al. Development, 2017 Dec 15. PMID 29084806, Free PMC Article
    4. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Chambers JC, et al. Nat Genet, 2011 Oct 16. PMID 22001757, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer.
      Title: LncRNA SOX9-AS1 triggers a transcriptional program involved in lipid metabolic reprogramming, cell migration and invasion in triple-negative breast cancer.
    2. Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma.
      Title: Impact of lncRNA SOX9-AS1 overexpression on the prognosis and progression of intrahepatic cholangiocarcinoma.
    3. SOX9-AS1 aggravates Hepatocellular carcinoma (HCC) progression and metastasis in vitro and in vivo. We demonstrated that SOX9-AS1 sponges miR-5590-3p to elevate SOX9 expression, and that SOX9 in turn transcriptionally activates SOX9-AS1.
      Title: A SOX9-AS1/miR-5590-3p/SOX9 positive feedback loop drives tumor growth and metastasis in hepatocellular carcinoma through the Wnt/β-catenin pathway.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    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

    Clone Names

    • FLJ31667, FLJ37644, DKFZp313A2240

    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_103737.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple exons and contains alternate 5' and 3' exons, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC007461
      Related
      ENST00000533232.5

    2. NR_103738.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC007461
      Related
      ENST00000434703.5

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      72071042..72120793 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      72944219..72993997 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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

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    Research Materials