# STOCKHOLM 1.0
#=GF ID SOX2OT_exon2
#=GF AC RF01952
#=GF DE SOX2 overlapping transcript exon 2
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 45.0
#=GF NC 42.5
#=GF TC 57.7
#=GF SE Predicted; ClustalW; Eberhardt R
#=GF SS Predicted; Pfold;
#=GF TP Gene; lncRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0001463; lincRNA;
#=GF RN [1]
#=GF RM 12612584
#=GF RT Mutations in SOX2 cause anophthalmia.
#=GF RA Fantes J, Ragge NK, Lynch SA, McGill NI, Collin JR, Howard-Peebles PN,
#=GF RA Hayward C, Vivian AJ, Williamson K, van Heyningen V, FitzPatrick DR
#=GF RL Nat Genet. 2003;33:461-463.
#=GF RN [2]
#=GF RM 19767420
#=GF RT Complex architecture and regulated expression of the Sox2ot locus during
#=GF RT vertebrate development.
#=GF RA Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,
#=GF RA Mattick JS
#=GF RL RNA. 2009;15:2013-2027.
#=GF CC SOX2 overlapping transcript (SOX2OT) is a long non-coding RNA, containing
#=GF CC at least 5 exons. The SOX2 gene, an important regulator of neurogenesis,
#=GF CC lies within one of the introns of SOX2OT [1]. SOX2OT and SOX2DOT (an
#=GF CC isoform of SOXOT transcribed from a distal highly conserved element) are
#=GF CC expressed in zones of neurogenesis within the brain. It is associated with
#=GF CC central nervous system structures in zebrafish and chicken embryonic
#=GF CC brains, and is dynamically regulated during embryogenesis [2]. SOX2OT may
#=GF CC play a role in vertebrate development [2].
#=GF WK SOX2OT
#=GF SQ 14

BC041898.2/209-277         AAAGCCUGACAGGUUUCUUCGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
AALT01445771.1/1960-1892   AAAGCCUGACAGGUUUCUCUGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUCUUCCA
AAKN02040493.1/81032-81100 AAAACCUGACAGGUUUCUUCGGGAAAGUGGCCAUCCAUGGAAUGAGUGAAAUGUUCUCUUUCUGUUCCA
AAPY01688537.1/555-623     AAAGCCUGACAGGUUUCUCCGGAAACGUGACCAUCCACGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
ABRO01225737.1/1582-1650   CAAGCCUGACAGGUUUCUCCAGGAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
AAFC03058731.1/40275-40343 AAAGCCUGACAGGUUUCUCCGGGAAAGUGACCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCU
AANN01366326.1/1881-1949   AAAGCAUGACAGUUUUCUCCGGAAAAGUGGUCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUGUUCCA
AAGV020241585.1/5906-5973  AAACCCUGACAGCUUUCUCUGGAAAAGUGGCCAUC-AUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCA
AAHX01016250.1/34120-34186 CAAACCUGACAGAUUUCUCCAGAAAAGUGGCCAUCCAUGGAAUGAGUGAAAU--ACUCUUUCUAUUCCA
ABRP01114048.1/1258-1324   AAAACCAGACAGUUUUCUCCGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCCCUU-CUA-UCCA
AC137708.16/84020-83954    CAAACCUGACAGAUUUCUCCAGAACAGUGGCCAUCCAUGGGAUGAGUGAAAG--CCUCUUUCUAUUCCA
ABRQ01540146.1/2165-2098   CAAGCUUGACAGGUAUCUCCAUAAAAGUGGCCAUCCA-GGAAUGAAUGAAGUGUUCCCUUUCUGUUCCA
ABQO010031765.1/709-777    AUAGUGUGACAGGUUUCAGCGAAAAGGGGGUCCUCCUCGGAAUGAAUGAAAGGUCCUUUUCCCAUUCCA
AAPE02008683.1/49152-49084 AAAACCUGACAGGUUUCUCUGGAAAAGGGGCCUUCCGUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    aAAgCcUGACAGgUUUCUcCGGAAAaGUGGCCAUCCaUGGAAUGAAUGAAAUGUUCuCUUUCUaUUCCA
//
