SOX2-OT

From LncRNAWiki
Revision as of 15:31, 8 December 2017 by Lin Liu (talk | contribs)
Jump to: navigation, search

Annotated Information

Genomic organization of Sox2ot locus in mouse.[1]
SOX2-OT dynamic expression in mouse adult neurogenesis.[1]
Expression of Sox2ot orthologs in different vertebrate species.[1]

Approved Symbol

SOX2-OT (SOX2 overlapping transcript)

Previous Symbols

SOX2OT

Synonyms

DKFZp761J1324, NCRNA00043

Chromosome

3q26.33

RefSeq ID

NR_004053

OMIM ID

616338

Ensembl ID

ENSG00000242808

Disease

Esophageal squamous cell cancer, Alzheimer's disease,Neurodevelopmental syndromes associated with the SOX2 locus

Characteristics

SOX2OT is originally reported as a spliced ncRNA mapping to human chromosome 3q26.3-q27, with an intron overlapping the SOX2 gene in the same transcriptional orientation.[1] SOX2OT is transcribed by RNA polymerase II (RNAP II), and therefore represents a putative “mRNA-like” ncRNA.[1]

Expression

SOX2-OT is dynamically expressed in different developmental processes.[1] SOX2-OT is expressed in pluripotent ES cells and is initially down-regulated upon EB differentiation.[1] SOX2-OT is highly enriched in the human brain and its expression is spatially regulated.[1]

Function

The expression profiles of SOX2-OT, as well as its evolutionarily preserved genomic association with Sox2, suggest that it has conserved functions in vertebrate development, and that it may participate in the regulation of Sox2 or related processes.[1]

Labs working on this lncRNA

  • ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia,QLD 4072, Australia.

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,Mattick JS. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA. 2009 Nov;15(11):2013-27. doi:10.1261/rna.1705309. Epub 2009 Sep 18.

Sequence

>gi|449020153|ref|NR_004053.3| Homo sapiens SOX2 overlapping transcript (SOX2-OT), transcript variant 4, long non-coding RNA

000001 AAAAATGTTG AATATCAACA ATGGGTTTCA GTGCTGTATT GTTGAGTTTT GTATGAACTA ATCTAGCTTC TCTAAAAAAA 000080
000081 AAAAAAAAAA AAAAAAAAAG AAAGAAAAGA AAGAAAGAAA AGAAAGAAAG AAAGAAAAAA AAAGAAAAGA AAAAAAAGAG 000160
000161 AACCACAGCT TTGGACAAAA GTCTATAGCC AGTGCATTTG AAAACTCCCC TTGCACCAGG GCTGACTGTA GCTGGGGGAA 000240
000241 GACATTTTAC TCATTTGCTC TTTCCTTTCA TACAGTCAGC TGGTCCCTCT TCTCAGGTGT AGATCACCTA TTATAATTTT 000320
000321 ACCTAATTTT GATACTCTGA TAAGGAAAGT CCCAGGACTT ATCAGCTGGG ATAGGCCTCA CTTACAAGAC AGCTCTGTTC 000400
000401 AGTATTTGGA AGAAAGCCTG ACAGGTTTCT TCGGAAAAGT GGCCATCCAT GGAATGAATG AAATGTTCTC TTTCTATTCC 000480
000481 AGGGATTGCA GTGGCAAAGC TAGGCTAGGT CTTGGAGGCT GGTGTAAGGC GATGTGGGTG AAGGCAGGAG GCTGATGGAA 000560
000561 AGACTGGGGG GAAGAAAAGC CGAAATGGAT TCACGGTGCC TTGGATGAAG GACGAGAGGG GAACTGCAAG CTCCTTCAAC 000640
000641 TGGTTCTGTC CGGTGAGAAG TGATCAAGCT TGGGCTGACA AGAGGCTCAG GGAGCCCTCA CGTTCTTTCG CTTTTTTACC 000720
000721 TGCCAATCAA ACTGCTACAA GACAACACCC TGATCTGGCA TGGACATCGC GGGTCCAAGC CTGTAGCCCC AAATCGGATA 000800
000801 ATCTCTGCAG CTGATAACAA GCAAAAGAGA AGCCAGGCAA CAGCCATATT AAAGAAGAAA ACAATCAACT CTGAGATCCA 000880
000881 ACTTAGAAAT AATGTTTCAT TCAAGATAAG GCTCGTGGCT TAGGAGATTG TGACCTGGCT TGCATCATTC TAAGACTTCT 000960
000961 ATCGTCTGTT TTCAAAACCC AAGGAGGACC TCCTTTTCTG TGTGATAGTT CCTCATGCTT TGCCAGCCAC TGGGTCTTTA 001040
001041 AGGAAGCTTG CCAAGAGTTC CCGGCTGGGA AGGACAGTTC GAGTTCATCA TAGACAATGA GCTGGCACCA CAGTTTAAGT 001120
001121 GACTCACCAA CCTGGTTGCC CACTTCAAAA TGTCAAGAAC CACACTATCT AATTGAAAGA ACTGTGTTTT AGCAAAGTGT 001200
001201 AATTGGATCG CCTGGCAAGA TCATCTCAAA CTATGTCTCT GACCTTGCCT TTCAGTGGCT ATTTTGAGCA CAAGAGGAGA 001280
001281 AAGGAAATGA TTCCTGAATT ATATCTTGTT TTTAAAAATT AAGATTAATT AATACTTGGT TTTATGTTCA TTCCATTGTA 001360
001361 GGAACTTAGT GATTATTACA AAACAGTCAA AATAGGTCAT AGCAAAATGA ACGTTTAAGA TTAGGTTAAA ACATTCCTCT 001440
001441 GAAATTTTAG TATTCACTTT TGAAGTGTCA ATTACTATAT TTCTGTAATT TCTCATTTTT TTCTTGGCTT AGAGTCAAGA 001520
001521 TGAAAAATGA TATTTGAATC AAAGACATTG TTTTGTTATA TAGCCACTCC TTTCTAAAAT GCAAATCCAC CCTCCCCTCA 001600
001601 CCAATGCTTT ATTCTTTGTG CGCGCACACA CACACACACA CACACACACA CACACACACA CACACAGACA TACACAGAAC 001680
001681 CAGCACCCAA ATGGTAGAGG AGGTCCTTCC AAGACTTCTA GGACCTGGAT CATGTAAGCA GTAGATGAGA AAATGAAGTA 001760
001761 AGAGATATAG AGTAATAACA ATAAAAGTCA ATGATTTCAT TTTACAAAAA AGTCATTGTG TAGTACTCAG ATATTTTTAA 001840
001841 GAGCAAGTAT TATTATGACT AAAGTATATT ATACTTCTAA ATTATTATGA TTCTCATCTA ATTTCAAGCC ACACATAGGC 001920
001921 GCCATTTGAA AGCATTTTGT GTTACAACCT ATCAACAAAA ATCAACTAAT AGTTTTATAA CGTGCATAGG TTTACCCCAT 002000
002001 GGGGAATTAA AATTTTTATC TGCAAGTATT TCTGTTGTTG TGAGACTTTA GGA