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    SOX1-OT SOX1 overlapping transcript [ Homo sapiens (human) ]

    Gene ID: 100505996, updated on 10-Oct-2023

    Summary

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    Official Symbol
    SOX1-OTprovided by HGNC
    Official Full Name
    SOX1 overlapping transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:42733
    See related
    Ensembl:ENSG00000224243 AllianceGenome:HGNC:42733
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LINC00403
    Expression
    Biased expression in brain (RPKM 2.9), salivary gland (RPKM 0.8) and 1 other tissue See more
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    Genomic context

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    See SOX1-OT in Genome Data Viewer
    Location:
    13q34
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (111972310..112108015)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (111215906..111351585)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (112626624..112762329)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112506195-112507184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112507185-112508174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112513428-112514170 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:112514171-112514912 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112547335-112548032 Neighboring gene long intergenic non-protein coding RNA 354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112666027-112666570 Neighboring gene uncharacterized LOC105378193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112682419-112682919 Neighboring gene small nucleolar RNA SNORD44 Neighboring gene MPRA-validated peak2105 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112710313-112711042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112728639-112729419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112727858-112728638 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112757992-112758611 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112760473-112761092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112761713-112762331 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:112766326-112767525 Neighboring gene SRY-box transcription factor 1 Neighboring gene long intergenic non-protein coding RNA 404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112805199-112805774 Neighboring gene uncharacterized LOC100506016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112813701-112814406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112814407-112815111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112817596-112818292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:112818293-112818987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112826532-112827032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:112827033-112827533 Neighboring gene uncharacterized LOC105370370 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:112837781-112838980 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:112843656-112844855

    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. LncRNA SOX1-OT V1 acts as a decoy of HDAC10 to promote SOX1-dependent hESC neuronal differentiation. Xi J, et al. EMBO Rep, 2022 Feb 3. PMID 34927789, Free PMC Article
    2. Expression of a SOX1 overlapping transcript in neural differentiation and cancer models. Ahmad A, et al. Cell Mol Life Sci, 2017 Nov. PMID 28674729, 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
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    5. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA SOX1-OT V1 acts as a decoy of HDAC10 to promote SOX1-dependent hESC neuronal differentiation.
      Title: LncRNA SOX1-OT V1 acts as a decoy of HDAC10 to promote SOX1-dependent hESC neuronal differentiation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    Other Names

    • long intergenic non-protein coding RNA 403

    Clone Names

    • FLJ30583, FLJ33739

    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_120392.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AI693652, BQ184460, DA195709

    2. NR_120394.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks multiple 5' exons and contains an alternate 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AL356961
      Related
      ENST00000421423.1

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      111972310..112108015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      111215906..111351585
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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