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    SIX3-AS1 SIX3 antisense RNA 1 [ Homo sapiens (human) ]

    Gene ID: 100506108, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SIX3-AS1provided by HGNC
    Official Full Name
    SIX3 antisense RNA 1provided by HGNC
    Primary source
    HGNC:HGNC:40532
    See related
    Ensembl:ENSG00000236502 AllianceGenome:HGNC:40532
    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
    SIX3OS
    Summary
    Predicted to be involved in regulation of gene expression. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See SIX3-AS1 in Genome Data Viewer
    Location:
    2p21
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44940154..44941878, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44945419..44947143, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45167293..45169017, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15686 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45089860-45089961 Neighboring gene VISTA enhancer hs149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:45153974-45154534 Neighboring gene long intergenic non-protein coding RNA 1833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164020-45164553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45164554-45165086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45166505-45167006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45167007-45167506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45168275-45168801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45169884-45170608 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45172898-45173404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45182266-45182972 Neighboring gene SIX homeobox 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45199471-45200338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45202291-45203066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45203067-45203842 Neighboring gene keratinocyte-associated protein 2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45227219-45228192 Neighboring gene KRTCAP2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45232925-45233468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45233469-45234012 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45235286-45236059 Neighboring gene SIX homeobox 2

    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. Natural antisense transcripts associated with genes involved in eye development. Alfano G, et al. Hum Mol Genet, 2005 Apr 1. PMID 15703187
    2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    GeneRIFs: Gene References Into Functions

    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)

    General gene information

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    Markers

    Other Names

    • SIX3 antisense RNA 1 (non-protein coding)

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  

    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_103785.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC012354
      Related
      ENST00000456467.3

    2. NR_103786.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks the 5' exon and contains an alternate 5' exon, resulting in a shorter transcript, compared to variant 1.
      Source sequence(s)
      AC012354
      Related
      ENST00000760562.1

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      44940154..44941878 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      44945419..44947143 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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    Research Materials