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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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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

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