# STOCKHOLM 1.0
#=GF ID DLX6-AS1_2
#=GF AC RF01888
#=GF DE Embryonic ventral forebrain RNA 1 conserved region 2
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 150.0
#=GF NC 130.1
#=GF TC 165.4
#=GF PI Evf1_2;
#=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 44.87 -Z 2958934 CM SEQDB
#=GF DR SO; 0001463; lincRNA;
#=GF DR GO; 0045893; positive regulation of transcription, DNA-templated;
#=GF DR GO; 0030900; forebrain development;
#=GF RN [1]
#=GF RM 15183307
#=GF RT Developmental regulation of EVF-1, a novel non-coding RNA transcribed
#=GF RT upstream of the mouse Dlx6 gene.
#=GF RA Kohtz JD, Fishell G
#=GF RL Gene Expr Patterns. 2004;4:407-412.
#=GF RN [2]
#=GF RM 16705037
#=GF RT The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved
#=GF RT region and functions as a Dlx-2 transcriptional coactivator.
#=GF RA Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD
#=GF RL Genes Dev. 2006;20:1470-1484.
#=GF CC Evf-1 (Embryonic ventral forebrain-1) is a developmentally-regulated long
#=GF CC non-coding RNA. In rats, it is expressed in neurons in the subventricular
#=GF CC zone of the developing forebrain. Its expression is linked to that of the
#=GF CC Shh (sonic hedgehog) and Dlx families of genes, which are important in
#=GF CC ventral forebrain and craniofacial development [1]. An alternatively
#=GF CC spliced form of Evf-1, Evf-2, forms a stable complex with the Dlx-2
#=GF CC protein. This complex activates transcription of Dlx-5 and Dlx-6 [2].
#=GF WK DLX6-AS1
#=GF SQ 19

AAHY01051190.1/2155-2361     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUAAGGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACUUGCAAUUAUAUACAAGGAGACAUAAC-UCCUAAUUCCUUCUUCCUACCUGAAGCAGAAGAAUUUUAAUUGCUU--GGAAAAAUAUG
AAQQ01558328.1/1452-1658     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUUCAGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAGUCACUAAAACAAGAAAAAUGAAACAUGCAAUUAUAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCCAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
AAGV020161035.1/4535-4741    AAUAGUCAAACAAAUUAGCGAUGAGGCCACCAGGAGAGUAUAUUCAACCCCAAUUCAGAGAUGUCUCGGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACAUGCAAUUAUAUAUAAGGAGACAGAAC-UCUGAAGUCUUUCAUCCUUGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAAAAG
ABBA01045758.1/12184-12390   AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCUGGAUUCAAAGAUGUCUCAGUUUAUUAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUGAAACAUGCAAUUAGAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
ABDC01134893.1/2108-2314     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCCACCCUGAUUCAGACAUAUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAAUAAGAAAGAUGAAACAUGCAAUUACAUACAAGGAGACAGAAU-UCCUAAUUCUUUCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
ABRT010013038.1/1082-1288    AAUAGUCUAACAAAUUAGCAACAGGGCCACCAAGAGAGUACAGUCAACCCUGAUUCAGAGAUGUCUCUGUUUAUCAGUUUU-CUGCCAAUCAUUAAAACAAAAAAGGUGAAACAUGCAAUUAUAGACAAGGAGACAGAAC-UCCUAGUUCUUCCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGGAAAAUAAG
AAHX01028381.1/35995-35789   AAUAGUCAAACAAAUUAGUAAUGGGGCCACCAAGAGAGUACAUUCAACCCUCAUAAGAAGAUGUCUCGGUUUAUCAGUUUU-CUGUCAAUCAUUAAAGCAAGAAAGAUGAAACUUGCAAUUAUAUACAAUGAAACACAAC-UCCUAAUUCUUCUAUCCUACCUGAAGCAGAAGAGUCUUAAUUGCUU--GGAAAAAAAAU
ABVD01005901.1/2148-2354     AAUAGUCAAACAAAUUAGUGAUGGGGCCACCAGGAGAGUACCUUCAACCGUGAUUCAGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUAAAACAUGAAAUUAUAUACAAGGAGACAGAAC-UCCAAAUUCUUUCAUCCUUGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
AACN010010072.1/2951-2746    AAUAGUCAAACAAAUUAGCAAUGGAGCCACCAAGAGAGUACAUUUACCUCUGAUUCAGAGAUGUCUGAGUUUAUCAGUUUU-CUGCCAAUCAUUAAA-CAACAAAGAUGAAACAUGCAAUUAUAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUUCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
ACBE01072604.1/90-294        AAUAGUCAAACAAAUUAGCAAUGGAGCCACCAAGAGAGUACAUUCAAC-CUGAUUCAAAGAUGUCUCAAUUUAUCAGUUUU-CUGUCAAUCAUUAAA-CAACAAAAAUGAAACAUGCAAUUAUACACAAGGAGAAAUAAC-UCCUAAUUCUUUCAUUCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAG
AAWR02013862.1/6264-6465     AAUAGUCAAA-----UAGCAAUGGGGCUACCAAGAGAGUACAUUCAACCCUGGUUCAGUGAUGUCUCAGGUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUGAAACAUGCAAUUAUAUACAAGGAGAAAGAAC-UCCUAAUUCUUUCAUCUUAGCUGAAGAAGAAGAGUUUUAACUGCUU--GGAAAAAUAAG
ABRN01434825.1/4865-5066     ACUAGUCAAACAGAUUAGCAAUGGGACCACCAAGAGAGUACAUUCAACCCCAAUUCAGAGAUGUCUCAGUUUAUCUGUUUU-CUGUCAAUCAUUAA-----GAAAGAUGAAAUAUACAAUUAUGUGCAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGCUGAAGCAAAAGAAUUUUAAUUGCUU--AAAAAAAUUAG
AAIY01400228.1/2400-2606     AAUAGUCAAACAAAUUAAUGAUGGGGCCACCUCAAGAGUAGAUUCA-CCCCAAUUCAGAGAUGUCUCAGUUGAUCAGUUUU-CUGUCAAUCAGGAGAACAGGAAAAAUGAAAUAUGCAAUUAUAGUUGGGGAGGCAGUACCUCUUCAUUCUUUCAUCCCAGCUGAAGCAGAAGAGUCUUAAUUGCUU--GGAAAAAUAAG
AAFC03001286.1/40876-41081   AAUAGUCAAACAAAUUAGCAAUGGGGCCACUAAGA--GCACAUUCAACCCUGAUUCAGAGAUGUUUCAGUUUAUCUGUUCU-CUGUCAAUCAUUAAA-CAAGAAAGAUGAAAUAUACAGUUAUGUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGUUGAAGCAAAAGAAUUAUAAUUGCUUGAAAAAAAAUAAG
ABRR01115815.1/1815-2012     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAAAGUACAUUCAACACUGAUUCAGAGAUAUCUCAGCUUAUCUGUUUU-CUAUCAGUUAUGGAA-CAAGAAAGAUGAAAUAUGCAAUUAUAUACAAGGAAACAUAAC-UCCUAAUUCUUUCAUUCUAGAUGAAACAAGAG--------UUGCUU--AAAAAAAUAAG
AC122240.4/64364-64570       AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUAAGGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACUUGCAAUUAUAUACAAGGAGACAUAAC-UCCUAAUUCCUUCUUCCUACCUGAAGCAGAAGAAUUUUAAUUGCUU--GGAAAAAUAUG
AAPE02008847.1/118645-118851 AAUAGUCAAACAAAUUAGCAGUGGGGGCACCAAGAGAGCACAUCCAUCCCUGAUUCAGAGAUGUCUUCGUUUAUCAGUUUU-CUGUCAAUCAGUAAAACAAGAAAGAUGAAACAUGCAAUUAUAUACAAGGAGACAGGAC-UCCUAAUUCUUUCACCCGAGCUGAAGCAGAAGAGUUUUAAUUGCUU--UGAAAAAUGAG
AAQR03012796.1/7005-7205     AACAGUCAAACAAAUUAGCAAUGAGGCCACCAAGAGAGUACAUUCAACCCUGAUUCAGAGAUAUCUCAGUUUAUCAGUUUUUCUGUCAAUCAUUAAAAUAAGAAAGAUGAAACAUCCAAUUAUACACAAGGAGACAGAAU-UC-------UUUCAUCAUAGCCAAGACAGAAGAAUUUUAAUUGCUU--GGAAAAGUAAG
AAGW02035474.1/82077-82283   AAUAGUCAAACAAAUUAGCAAGGAGGCCACCAAGAGAGUAUAUUCAACCCUGAUUCAGAGAUGUCUUGGUUUAUCAGUUUU-CUGUCAAUCAUCAAAACAAGAAAAAUGAAACAUGCAAUUACAUACAAGGAGUCAGAAC-UCAUAAUUCUUUCAUCUCAGCUGAAGCAGAAGCAUUUUAAUUGCCU--GGAAAAAUGUG
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::
#=GC RF                      AAUAGUCAAACAAAUUAGcaAuGGGGCCACCAaGAGAGUAcAUUCAaCcCugAUucaGAGAUGUCUcaGuUUAUCaGUUUU.CUGUCAAUCAuuAAAaCAAGAAAgAUGAAAcaUGCAAUUAuAuaCAAGGAGaCAgaAC.UCcuaAUUCUUUCaUCcuaGCUGAAGCAGAAGAgUuUUAAUUGCUU..gGAAAAAUaaG

AAHY01051190.1/2155-2361     AUUUUUCUUUU
AAQQ01558328.1/1452-1658     AUUUUUGUUUU
AAGV020161035.1/4535-4741    AUUUUUGUUUU
ABBA01045758.1/12184-12390   AUUUUCGUUUU
ABDC01134893.1/2108-2314     AUUUUUGUUUU
ABRT010013038.1/1082-1288    ACUUGUGUUUU
AAHX01028381.1/35995-35789   AUUUUUCUUUC
ABVD01005901.1/2148-2354     AUUUUUGUUUU
AACN010010072.1/2951-2746    ACUUUUAUUUU
ACBE01072604.1/90-294        AUUUUUAUUUU
AAWR02013862.1/6264-6465     AUUUUUGUUUU
ABRN01434825.1/4865-5066     AUUUUUGUUUC
AAIY01400228.1/2400-2606     AUUUUUGUUUC
AAFC03001286.1/40876-41081   ACUUUUGUUUC
ABRR01115815.1/1815-2012     ACCUUUGUUUU
AC122240.4/64364-64570       AUUUUUCUUUU
AAPE02008847.1/118645-118851 AUUUUUGUUUU
AAQR03012796.1/7005-7205     ACUUUUGUUUU
AAGW02035474.1/82077-82283   AUUUUUGUUUU
#=GC SS_cons                 :::::::::::
#=GC RF                      AuUUUUgUUUu
//
