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SOX2-OT SOX2 overlapping transcript [ Homo sapiens (human) ]

Gene ID: 347689, updated on 23-Jan-2022

Summary

Official Symbol
SOX2-OTprovided by HGNC
Official Full Name
SOX2 overlapping transcriptprovided by HGNC
Primary source
HGNC:HGNC:20209
See related
Ensembl:ENSG00000242808 MIM:616338
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SOX2OT; NCRNA00043
Summary
This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]
Expression
Restricted expression toward brain (RPKM 80.2) See more
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Genomic context

See SOX2-OT in Genome Data Viewer
Location:
3q26.33
Exon count:
10
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (181056680..181742228)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (180774468..181460016)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FMR1 autosomal homolog 1 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene VISTA enhancer hs192 Neighboring gene RNA, U6 small nuclear 4, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15084 Neighboring gene FAU pseudogene 2 Neighboring gene uncharacterized LOC102724604 Neighboring gene ribosomal protein L7a pseudogene 25 Neighboring gene SOX2 5' regulatory region Neighboring gene SRR2 enhancer downstream of SOX2 Neighboring gene SRY-box transcription factor 2 Neighboring gene RNA, 7SL, cytoplasmic 703, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 150

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association study of anorexia nervosa.
EBI GWAS Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

General gene information

Markers

Other Names

  • SOX2 overlapping transcript (non-coding RNA)
  • SOX2 overlapping transcript (non-protein coding)

Clone Names

  • DKFZp761J1324

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_004053.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate exon in place of the first four exons compared to variant 1.
    Source sequence(s)
    AC117415, AK022826, DA366949, JN711430
    Related
    ENST00000657986.1
  2. NR_075089.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate in place of the first four exons and lacks an alternate 3' exon compared to variant 1.
    Source sequence(s)
    AC117415, DA366949, JN711430
    Related
    ENST00000665033.1
  3. NR_075090.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an alternate in place of the first four exons and lacks two alternate 3' exons compared to variant 1.
    Source sequence(s)
    AC117415, DA366949, JN882275
    Related
    ENST00000476964.6
  4. NR_075091.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC117415, DA281835, JQ408703
  5. NR_075092.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate 3' exon compared to variant 1.
    Source sequence(s)
    AC117415, DA281835, JN711430
  6. NR_075093.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate in place of the first two exons and lacks two alternate 3' exons compared to variant 1.
    Source sequence(s)
    AC117415, DA310380
    Related
    ENST00000646841.2

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    181056680..181742228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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