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

Gene ID: 101928471, updated on 10-Oct-2023

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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (24223271..24237965)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (24094245..24108934)
105.20220307 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: 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. 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)

Genotypes

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_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
    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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