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    Six3os1 SIX homeobox 3, opposite strand 1 [ Mus musculus (house mouse) ]

    Gene ID: 100043902, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Six3os1provided by MGI
    Official Full Name
    SIX homeobox 3, opposite strand 1provided by MGI
    Primary source
    MGI:MGI:1925118
    See related
    Ensembl:ENSMUSG00000093460 AllianceGenome:MGI:1925118
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rncr1; Six3os; D17Mgi26; E130112H22Rik
    Summary
    Acts upstream of or within regulation of photoreceptor cell differentiation. Located in cytoplasm and nucleus. Is expressed in several structures, including alimentary system; brain; future brain; liver; and sensory organ. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in whole brain E14.5 (RPKM 4.1), CNS E14 (RPKM 3.8) and 2 other tissues See more
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    Genomic context

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    See Six3os1 in Genome Data Viewer
    Location:
    17 E4; 17 55.42 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (85909360..85925824, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (85601932..85618396, complement)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_43471 Neighboring gene ribosomal protein L31, pseudogene 16 Neighboring gene STARR-seq mESC enhancer starr_43472 Neighboring gene STARR-seq mESC enhancer starr_43473 Neighboring gene developmentally regulated GTP binding protein 2 pseudogene Neighboring gene sine oculis-related homeobox 3 Neighboring gene sine oculis-related homeobox 2 Neighboring gene Riken cDNA CJ186046 gene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Geng X, et al. Gene Expr Patterns, 2007 Jan. PMID 17084678, Free PMC Article
    2. Developmental constraint through negative pleiotropy in the zygomatic arch. Percival CJ, et al. Evodevo, 2018. PMID 29423138, Free PMC Article
    3. The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Rapicavoli NA, et al. Neural Dev, 2011 Sep 21. PMID 21936910, Free PMC Article
    4. Homeobox Gene Six3 is Required for the Differentiation of D2-Type Medium Spiny Neurons. Song X, et al. Neurosci Bull, 2021 Jul. PMID 34014554, Free PMC Article
    5. Natural antisense transcripts associated with genes involved in eye development. Alfano G, et al. Hum Mol Genet, 2005 Apr 1. PMID 15703187

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Other Names

    • Six3 antisense
    • Six3 opposite strand transcript 1

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within regulation of photoreceptor cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of photoreceptor cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    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_015385.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an additional segment in one region and lacks a segment in another region, compared to variant 1.
      Source sequence(s)
      AC166821, AK053722, AY590889

    2. NR_015386.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal segment, compared to variant 1.
      Source sequence(s)
      AC166821, AK053722, AY589790

    3. NR_015387.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) has an additional exon in the 5' region and lacks 3' two exons but has a shorter and different 3' exon, compared to variant 1.
      Source sequence(s)
      AK053722, AY589791

    4. NR_038082.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the longest transcript.
      Source sequence(s)
      AC166821, AK053722, CF737515, CV783894

    5. NR_038083.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal segment, compared to variant 1.
      Source sequence(s)
      AC166821, AK053722

    6. NR_038084.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has an additional segment in one region and lacks a segment in another region, compared to variant 1.
      Source sequence(s)
      AC166821, AK053722, AY590888

    7. NR_038085.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) has an alternate and much shorter 3' exon, compared to variant 1.
      Source sequence(s)
      AK053722, BF461098, CF731326, CF737925
      Related
      ENSMUST00000161146.10

    8. NR_038086.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) lacks an internal segment, compared to variant 1.
      Source sequence(s)
      AC166821, AK053722, CA527570

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000083.7 Reference GRCm39 C57BL/6J

      Range
      85909360..85925824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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