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

Gene ID: 100043902, updated on 8-Feb-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 central nervous system; future brain; maxillary process; and sensory organ. [provided by Alliance of Genome Resources, Apr 2022]
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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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. Natural antisense transcripts associated with genes involved in eye development. Alfano G, et al. Hum Mol Genet, 2005 Apr 1. PMID 15703187
  5. Tissue-Specific Actions of Pax6 on Proliferation and Differentiation Balance in Developing Forebrain Are Foxg1 Dependent. Quintana-Urzainqui I, et al. iScience, 2018 Dec 21. PMID 30529950, Free PMC Article

See all (17) 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

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