Alternative titles; symbols
HGNC Approved Gene Symbol: SOX2-OT
Cytogenetic location: 3q26.33 Genomic coordinates (GRCh38): 3:181,056,680-181,742,228 (from NCBI)
Long noncoding RNAs (lncRNAs), like SOX2OT, contain over 200 nucleotides and are frequently spliced, capped, and polyadenylated. LncRNAs modulate gene expression through regulation of chromatin structure, transcription, mRNA processing, and translation. SOX2OT is host to the single-exon SOX2 gene (184429), which lies within an intron of SOX2OT and is transcribed in the same orientation (summary by Amaral et al., 2009).
Fantes et al. (2003) determined that SOX2OT is a noncoding gene with no open reading frame encoding a peptide of more than 70 amino acids. It produces a 3.4-kb mRNA from the same strand as SOX2, and human SOX2OT shares 88% identity with mouse Sox2ot. The genomic region encompassing SOX2OT is highly conserved. The authors suggested that SOX2OT may be involved in transcriptional regulation of SOX2.
By database analysis, Amaral et al. (2009) identified several splice variants of mouse and human SOX2OT, including transcripts with alternative transcriptional start sites. They also identified Sox2ot splice variants in chicken, frog, and zebrafish, and some splice sites appeared to be species specific. Comparison of orthologs from different species revealed 7 highly conserved elements. Northern blot analysis of adult mouse brain detected a major 3-kb Sox2ot transcript and minor transcripts of approximately 1, 4, 6, and greater than 10 kb. Quantitative RT-PCR of human tissues detected high SOX2OT expression in brain, with moderate expression in testis, kidney, ovary, lung, colon, skeletal muscle, and thymus, and no expression in liver and placenta. EST database analysis suggested high SOX2OT expression in human lens, specific brain regions, and kidney tumor. Quantitative RT-PCR of mouse tissues revealed coexpression of Sox2 with 3 different Sox2ot splice variants in adult brain, embryonic stem cells, embryo, and newborn. However, 2 of the Sox2ot variants were also variably expressed in colon, muscle, testis, lung, and/or heart. Sox2ot expression appeared to be dynamically regulated during development in chicken and zebrafish.
Fantes et al. (2003) determined that the SOX2OT gene contains at least 5 exons and spans 40 kb. Intron 3 harbors the single-exon SOX2 gene.
Amaral et al. (2009) determined that the SOX2OT gene is complex, with multiple alternatively spliced exons and at least 6 alternative transcriptional start sites. The gene spans approximately 850 kb.
By genomic sequence analysis, Fantes et al. (2003) mapped the SOX2OT gene to chromosome 3q26.3-q27.
Hartz (2015) mapped the SOX2OT gene to chromosome 3q26.33 based on an alignment of the SOX2OT sequence (GenBank AK022826) with the genomic sequence (GRCh38).
Amaral, P. P., Neyt, C., Wilkins, S. J., Askarian-Amiri, M. E., Sunkin, S. M., Perkins, A. C., Mattick, J. S. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 15: 2013-2027, 2009. [PubMed: 19767420] [Full Text: https://doi.org/10.1261/rna.1705309]
Fantes, J., Ragge, N. K., Lynch, S.-A., McGill, N. I., Collin, J. R. O., Howard-Peebles, P. N., Hayward, C., Vivian, A. J., Williamson, K., van Heyningen, V., FitzPatrick, D. R. Mutations in SOX2 cause anophthalmia. Nature Genet. 33: 461-462, 2003. [PubMed: 12612584] [Full Text: https://doi.org/10.1038/ng1120]
Hartz, P. A. Personal Communication. Baltimore, Md. 4/29/2015.