# STOCKHOLM 1.0
#=GF ID SOX2OT_exon1
#=GF AC RF01951
#=GF DE SOX2 overlapping transcript exon 1
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 65.0
#=GF NC 62.6
#=GF TC 67.2
#=GF SE Predicted; RNAz; Eberhardt R
#=GF SS Predicted; RNAz;
#=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 29

AANN01366326.1/1470-1700     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAAAACUCCCCGUGCAC----UAGGGCUGACUGUAGCUGGGGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUCAGCUGGUCCCUCUCCUCAGGUGUAGACCACCU-----AUUAUCAUUUUACCU-GUUUUGAUUCUCUGAUGA-GC
ABRN01126490.1/7524-7752     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGAAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUAUAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCA-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GG
AC125613.2/39238-39007       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAAAACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GG
ABRO01225737.1/1212-1442     ACAGCUUUGGACAAAAGUCUACACA-GCCAGU-----GCAUCU-GAA-ACUCCCC-UUUGC----ACAGGCUGACUGUAGCUGGGAGAAGACAUUUUACUCAUUUGCUCUCUCCCUUCAUGUGGUCAGCUGGCCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUCACCUAAUUUUGAUCCUCUGAUGG-GG
ABRP01114048.1/897-1125      ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUGCAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCACUUCACCU-GUUUUGAUUCUCUGAUGA-GG
ABGA01081645.1/4683-4453     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GG
AAGV020241585.1/5541-5772    ACAGCUUUGGACAAAAGUGUA--GA-GCCAGUGCAGUGCAUUU-GAA-ACUCCCCUAGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUCUUCUUUCAUACAGUCAGCUGGUCCAUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUCACCU-GUUUUGAUACUCUGAU----G
AALT01445771.1/2327-2101     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCCUGCAC----AGGAGCUGACUGUAGCUGGG-GAAGACAGUUUACUCAUUUGCUCUCUCUUUU--CAUAGUCAGCUGGUCCCUCUCCUCAGGUGUACAUCACCU-----AUUAUCAUUUCACCU-GUUUUGGUUCUCUGAUGA-GG
AC137708.16/84396-84183      ACAGCUUUGAACAAAAGUCCA--CA-GCCAGU-----GUGUUC-CAA-G-UCCC--UGCUC----A-GGGCUGACUGUGGCAGGGG----ACACUCUCC-UGCUGGCUCUCUCUGUCCACAC--UUAGCUGGCUCCUGUCCUCAGGUGCACGGCCACA---------CCCUCGCACCCAACCUUGAUCCUCUGAUGG-GG
AAFR03036277.1/29988-29757   ACAGCUUUGGACAAAAGUCUA--GA-GUCUCU-----GCAUUG-GUA-ACUCUCCGUGCACGCACAAGGGCUGACUGGGGCUGUGGGAAGACAUUUUCCUUAUUUGCCUUCUCCUUUCUUCCAGUCAUCUUGUCCCUCUUCUCAGGUGUUGUUCACCU-----AUUAUCAUUUCACCU-GUACUGGUCCUCUGUGGG-GG
AAFC03058731.1/39912-40140   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGAAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUUAGCUGGC-CCUCUUCUCAGGUGUAGAUCACGU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GG
AAPN01099322.1/2430-2657     ACAGCUUUGGACAAAAGUCUG--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCUUACAC----AAGGGCUGACUGAGGCUGUGGGAAGACAUUUUACUCAUUUGCUUUCUUUUUUCUUAGAGUCAUCUUGU-CCUUUUCUCAGGUGUUUAUCACCU-----AUUAUCCUUUCACCU-GUAUUGGUACUCUGGUGGGAG
AAHX01016250.1/33739-33953   ACAGCUUUGAACAAAAGUCCA--CA-GCCAGU-----GUGUUC-CAA-G-UCCC--UGCAC----A-GGGCUGGCUGUGGCAGGGG----ACACUCUCC-UGCUGGCUCUCUCUGACCACACA-UUAGCUGGCUCCCAUCCUCAGGUGCACGGCCACA---------CCCUUGCACCCAACCUUGAUCCUCUGAUGG-GG
AAIY01585989.1/8148-7939     -------------AAAGUCUG--CA-GCCCGA-----GCAUUU-GAA-ACUCCCC-UUCAC----AAGGGCUGACUGUAGCUGGGGGAAGACGGUCUACUCAUCUGCUCUCUCCU----UUCAGCCAGCGGGC-UGUCUUCCCAGGUGUAGAUCACCU-----AUUCUAACUUCACCU-GUUUUGAUACCCUGAUGA-GG
AAPY01688537.1/200-425       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGACUGACUGUAGCUGUGGGAAGACAUUUUCCUCAUUUGCUCUCUCCUUGCA-GCAGUCAGCUGGUCCCUCUUCUCAGGUGUAAAUCACCU-----AUUAUAAUUUCCCCCAGUUUUGAUACUCUGAUGA-GG
AAWR02011604.1/18990-19219   ACAGCUUUGCACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUGGCCGGGGGAAGACAGUUUACUCAGUUGCUCUCUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUACCACUUCACCU-GUUUUGAUUCUCUGAUGA-GG
AADA01128044.1/22312-22542   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUCUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GG
ABRQ01540146.1/2411-2186     ACCUUUCUGGACA-AAGUCUA--CA-GUCAGU-----GCCUGU-GAA-ACUCCCCU-UUAC----AACAGCUGACUACAGCUGGGUAAAGACGUUUUUCUCCUUUGCUCUCUCUUCUCAUACAGUCAGCUGGUCAGUUUCCUCAGAUGUACAUCACCU-----GUUAUAAUUUCACCC-GUGUUGCUACUCUGUUGG-GG
AANG01283917.1/126-354       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUCACUCAUUUGCGCUCUCCUUUCAUACAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCAGUUCACCU-GUUUUGAUUCUCUGAUGA-GG
ABRR01048073.1/2456-2683     AUAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUG-GGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUCAGCUGGC-CCUCUCCUCAGGUGUAGAUCAUCU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGACGA-GG
AAKN02040493.1/80620-80846   AGAGCUUUGGACAA--GUCUA--CAGACCAGU-----GCAUUU-GAA-AUUCUCUCCGCAC----CAGGGCUGAGUGUAGCU--GGGAGGACAUUUUACUCAUCUGGGCUCUCCCUUCCCACAGUCAGCUGGUCCCUCUGCUCAGGUGUAGAUCACCU-----AUUAGAAUUUCACCAAAUUUUGAUAGUCUGCUGA-GG
ABQF01023293.1/142705-142930 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCAUGCAC----AAGAGCUGACUGUGGCUCUGGGAAGACAUUUUACUCAUUUGAUUUCUUUUUUCUUGUAGUCUUCUUGU-CCAGUUCUCAGGUGUUUACCACCU-----AUCAGAAUUUCACCU-GUAUGGGUCCUGUGCUUG-AG
AANU01300153.1/26633-26403   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-AUUCCCCUUGCAC----CAGGACUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACGGUCAGCUGGUCGCUCUUCUCAGGUGUACAUCACCU-----AUUAUAAUUUUAUCUAAUUUUGAUACUGUGAUAA-GG
AAWZ02017091.1/182975-183205 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGA-----GCAUUCAGUA-AUUCCCCAUGCAC----AAGAGCUGACUGUGUCUCUGGGAAGACAUUUUACUGGUCUGCUUUCUUAUUUCCU--AGUUUUCUAGU-UCUUCUCUCAGGUGUUUGAUACUU-----AUUUGUCUCUCACCU-GCCUG-GGGCACUGCUUG-AG
AAPE02008683.1/49518-49286   ACAGCUUUGGACAAAAGUCUA--UA-GCCCGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGG-GAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUGCAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCUAACCCAUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GG
AAGW02014129.1/117891-117663 AGAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUCU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGAGAAGACAUUUUACUCAUUUGCUCUCUCCUUUCAUACGGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCC-UU-----AGCCUAAUUUCACUA-AUUUUGAUACUCUGAUGA-GG
AAEX03017260.1/647400-647628 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUGACUCAUUUGCUCUCUCCUUUCACACAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GG
AADN03005748.1/46889-46664   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCAUGCAC----AAGAGCUGACUGUGGCUCUGGGAAGGCAUUUUACUCAUUUGCUUUCUUUUUUCUUAUAGUCUUCUUGU-CCAGUUCUCAGGUGUUUACCACCU-----AUUUGAAUUUCACCU-GGGUGGGUACUGUGUUUG-AG
AAQR03159363.1/19-244        ACAGCUUUGGACAAAAGUCUA--CA-GCCAGU-----GCAUUU-GAA-AGUCCCCCUGCAC----CGGGGCUGACUGUAGCUGGGGAAAGACAUUUCACUCAUUCGCUCUUCCCUUUCAUGCA-CCAGCUGGUCCCUCUCCUCAGGUGUAGACCACCU-----AUUAUAAUUUCACCCAAUUUUGAUACUCUGAUGA-GG
#=GC SS_cons                 :::::::::::::::::::::..::.::::::.....::::::.:::.:::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.....:::::::::::::::.::::::::::::::::::.::
#=GC RF                      ACAGCUUUGGACAAAAGUCUA..uA.GCCaGU.....GCaUUu.GaA.AcUCCCCuUGCAC....aaGGGCUGACUGuaGCUGgGGGAAGACAuUUUaCUcaUUuGCUcUCUCcuUUCauacAGUCagCUgGuccCUcUuCUCAGGUGUagauCaCCU.....AUUauaaUUUCACCu.guuUUGaUaCUCUGaUgg.GG

AANN01366326.1/1470-1700     AAAGUCCCAAGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABRN01126490.1/7524-7752     AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AC125613.2/39238-39007       AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
ABRO01225737.1/1212-1442     AAA-UCCCCGAACUAAUCAACUGAGAUAGGCCUUACUUC----CAAGGCAGCCCU
ABRP01114048.1/897-1125      AAAGUCCCAGGACUUACCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABGA01081645.1/4683-4453     AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
AAGV020241585.1/5541-5772    AAAGUCCCAGGACUUGUCAGCUGGGAUAGGCCUCAUUUA----CACGACAGCUCU
AALT01445771.1/2327-2101     AAAGUCCUAGGACUUGUCGGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AC137708.16/84396-84183      AAGGUCCCAGGACUUGUCUGCUGGGACAGGCCUCACCCC----CAAG--AGCUCU
AAFR03036277.1/29988-29757   AAAGUCCUGGGACUUGUCAGCUGGUCUAGGCCUCAU--A----AAAGACAGCUCU
AAFC03058731.1/39912-40140   CAAGUCCCAGGACUUAUCAGCAGGGAUAGGCCUCAUUGC----CAAGACAGCUCU
AAPN01099322.1/2430-2657     AAAGUCCCAGGAAUUGUCCGCCGGUAUAGGCCUCAUUA------AAUGCAGCACU
AAHX01016250.1/33739-33953   AAGGUCCCAGGACUUGCCAGCUGGGACAGGCCUCACCCC----CAAG--CGCUCU
AAIY01585989.1/8148-7939     AAAGUCCCAGGACUUGUCAGCUGGGAUAGGCCCCAU-GA----CAGGGCCGCUCG
AAPY01688537.1/200-425       AGCGUCCCAGGACUUCUCAGCUGGGGUAGGCCUCA--------CAGGACAGCUGU
AAWR02011604.1/18990-19219   AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUCA----CAAGACACCUCU
AADA01128044.1/22312-22542   AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
ABRQ01540146.1/2411-2186     AAAGCCCCAGGGCUUAUCAACUGGUACAGGCCUCAUUC-----CUAGACAUCUC-
AANG01283917.1/126-354       AAAAUCCCGGGACUUAUCAGCCGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABRR01048073.1/2456-2683     AAGGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AAKN02040493.1/80620-80846   AAAGUCCCAGGAUUUAGCAGCUGGGAUAGGCCUCACUCA-----AAGACAGCUCU
ABQF01023293.1/142705-142930 AAAGUCCCAGGACCUGUCAGCUG-CAUAGGCCUCAU--A----AAAGACAGCUCU
AANU01300153.1/26633-26403   AAAGUCCCAGGACUUAUCAGCUGGGACAGGCCUCUCUUA----CAAGACAGCUCU
AAWZ02017091.1/182975-183205 AAUAUUCUGCACCAUGUCAGCUGAUGUAGGUCUCAUAAAGAGUAAAGACAGCUCU
AAPE02008683.1/49518-49286   AAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AAGW02014129.1/117891-117663 AAAGUCCCAGGACUUAUCAGCUGGGACAGGCCCCACUUU----CGAGACAGCUCU
AAEX03017260.1/647400-647628 AAAAUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AADN03005748.1/46889-46664   AAAGUCCCAGGACUUGACAGCCG-UAUAGGCCUCAU--A----GAAGGCAGCUCU
AAQR03159363.1/19-244        AAAGUCCCAGGACUUCCCAGCUGGGAUAGGCCUCA--------CAAGACAGCUGU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::....::::::::::::
#=GC RF                      AAaGUCCCaGGaCUUguCaGCUGGgauAGGCCUCAuuua....cAaGaCAGCUCU
//
