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    SOX5-AS1 SOX5 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 101928471, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SOX5-AS1provided by HGNC
    Official Full Name
    SOX5 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:53311
    See related
    Ensembl:ENSG00000256120 AllianceGenome:HGNC:53311
    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
    Restricted expression toward testis (RPKM 4.9) See more
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    Genomic context

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    See SOX5-AS1 in Genome Data Viewer
    Location:
    12p12.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (24223271..24237965)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (24094245..24108934)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (24376205..24390899)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369697 Neighboring gene Sharpr-MPRA regulatory region 8728 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:23793632-23794207 Neighboring gene SRY-box transcription factor 5 Neighboring gene NANOG hESC enhancer GRCh37_chr12:23909365-23909887 Neighboring gene MPRA-validated peak1610 silencer Neighboring gene MPRA-validated peak1611 silencer Neighboring gene MPRA-validated peak1613 silencer Neighboring gene Sharpr-MPRA regulatory region 3652 Neighboring gene Sharpr-MPRA regulatory region 12792 Neighboring gene VISTA enhancer hs895 Neighboring gene MPRA-validated peak1614 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:24369389-24370015 Neighboring gene Sharpr-MPRA regulatory region 6359 Neighboring gene microRNA 920 Neighboring gene NANOG hESC enhancer GRCh37_chr12:24744672-24745173 Neighboring gene uncharacterized LOC105369698 Neighboring gene long intergenic non-protein coding RNA 477 Neighboring gene lysine rich nucleolar protein 1 pseudogene 1 Neighboring gene ribosomal protein L21 pseudogene 102

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). Le Clerc S, et al. J Infect Dis, 2009 Oct 15. PMID 19754311
    2. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs. Adkins DE, et al. Mol Psychiatry, 2011 Mar. PMID 20195266, Free PMC Article
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    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
    Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03).
    EBI GWAS Catalog
    Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
    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)

    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_120472.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      BX106967, CR744081, DB076822

    2. NR_120473.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple 3' exons and its transcription extends past a splice site used in the variant 1, resulting in a shorter transcript than variant 1.
      Source sequence(s)
      BX106967
      Related
      ENST00000540733.1

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      24223271..24237965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      24094245..24108934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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