# STOCKHOLM 1.0
#=GF ID HOXA11-AS1_4
#=GF AC RF02140
#=GF DE HOXA11 antisense RNA 1 conserved region 4
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 80.0
#=GF NC 68.3
#=GF TC 87.9
#=GF SE Predicted; CMfinder; Eberhardt R
#=GF SS Predicted; CMfinder;
#=GF TP Gene; lncRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 45.48 -Z 2958934 CM SEQDB
#=GF DR SO; 0001463; lincRNA;
#=GF DR GO; 0010629; negative regulation of gene expression;
#=GF RN [1]
#=GF RM 9745033
#=GF RT Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT antisense transcripts.
#=GF RA Potter SS, Branford WW
#=GF RL Mamm Genome. 1998;9:799-806.
#=GF RN [2]
#=GF RM 12050232
#=GF RT HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT uterine endometrium.
#=GF RA Chau YM, Pando S, Taylor HS
#=GF RL J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK HOXA11-AS1
#=GF SQ 20

AF071164.1/5119-5351       GUUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GAAAUAUUCUUAUUAUGUAUUUUCUCC-AAAUAAUGGCCUACCAUU
ABVD01019940.1/888-1120    AGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACGCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUCAUUUAUUGCUGAGCUGACUGUAACUGACUCAGUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCCCC-AAAUGAUGGCCCACCAUU
ABRP01099870.1/3626-3858   GGUAUUUAUAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGUGGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUGAUGGCCCACCAUU
AAPY01076971.1/894-1126    GGUAUUUACAUAUCUCAGGGCGAUUU--AGAGAAUAAACUCUA-----GGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUAAUGGUCCACCAUU
AAHY01053339.1/13083-12851 GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACGCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UUUAAUCAUGUAUUGCUCUG-GAAAA-GAACUACUCUCGUUAUGUAUUUUCUCC-AAAUAAUGACCCACCAUU
AANN01604120.1/4844-4612   GGUAUUUAUACAUCUCGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUUGCC-AAAUGGUGACCCACCAUU
AAKN02039092.1/12920-13152 GGUAUUUACAUAUCUUGAGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGCAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUUAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUAAUGACCUGCCAUU
ABRN01187570.1/5318-5551   GGUAUUUAUAUAUCUCGGGGAGAUUU--AGAGUAUAACCUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUAACUGUAACUGACACAAUAACAAAAUCUAAUCGUGUAUUGCACUG-CAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCU-AAAUGAUGGCUCACCAUU
AAIY01705046.1/1523-1291   GGUAUUUACAUAUCUCGGGGAGAUUU--AGAGUAUAAUCUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUCGCUGAGCUGACUGUAACUGACUCAAUGGCAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GGAAUAUUCU-AUUAUGUAUUUCCCCCCAAAUGAUGGCUUACCACU
ABRQ01101202.1/2639-2874   GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUUUAUUUAUUUAUUGCUGAGCUGACUGUAACCGACUCAGUCACAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GAAAUAUUCUUAUUACAUAUUUUCCCC-AAAUGAUGUUGCACCAUU
ABRO01036384.1/16802-17035 AGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCAAUUU-AUUUAUUUAUUGCUGAGCUGACCAUAACUGACUCAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAAAGAAAUAUUCUCGUUCUGUAUUUUCUCC-AAAUAAUAACCCACCAUU
AAGV020458989.1/269-494    GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAAUGUCAUCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCGGUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAU---GUAUUUUCCUC-AAAUGAUGGCGCGCCAUU
AAPN01063703.1/15252-15484 GGUAUUUACAUAUCUGGGGAAAAUUU--CGAUUAUAAAUUUUA-----AGAUCUUC-UGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGAUCGUAACUGACUCAAUAACAAA-UCUAAUCAUGUUUUGCCCUG-GAAAA-GAACUAUCCUCAUUAUGUAUUUUCGCC-AAAUUAUAGCACACUAUU
AAYZ01055296.1/1799-2024   GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGCAUAAACUCCA-----AGAUCUUG-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACGGACUCAAUAACAAA-UCUAAUCAUGUAUUACCCUG-GAAA------UAUUCU---UAUGUAUUUUCUCC-AAAGAAUGGCUCACCAUU
AAFR03047692.1/44711-44480 GGUGUGUAUAUAU-----GAAGAUUU--GCAGCCUAAAUUCCAUCCAAAGAUCUUC-AGUAUUUAAAUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACCGUAACUGACUUAAUAACAAA-UCUAAUCAUGU-UUGCUCCG-GGAAA-GAAAUAUUCUCAUUAUGUAUUUUCACC-AAAUGAUGGCUCACCAUU
AAQQ01071885.1/63-291      AUUCUUUAUAUAUGU-AGAGAGAUUUUAGAAGUAUAAACUCUA----AAGGUCUUUUGGUAUUUAAGUGUCAACAUCGAUUAAAUGUAUUUAUUGCUGAGCUGACUGUAACCGACUCAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAA-AAAAUAUUCUCAUUAUGUCUUUUCUCC-AAAUAAUGACCCACCAUU
ABQF01013713.1/13270-13498 AGUAUUUAUAUAUCCGGAGAAAGUUC---UCUAGUAAAUUCUG----GAGAUCCUC-GGUAUUUAAAUGUCAACAUCGAUUU-GUUUAUUUAUUGCUUAGCUUAUCGUAACCGACUCAAUAACAAA-UCUAAUCAUGUUAUGCAGAGAGAAA-----AUAUUCUCAUUAUGUAUUUCCCCU-ACAUUAUAGUUAACUAUU
AF327372.1/6683-6451       AGUAUUUAUACGUCCGGAGAAAGUUC---UAUAGUAAAUUCGG----GAAAUCUUC-GCUAUUUGAAUAUCAACGUCGAUUU-GUUUAUUUAUUGCUCGGCUUAUCGUACCAGACUCCGUAACAAA-UCUAAUCAUGGUGCUCGCAG-GAAAAGAAAAUAUUCUCAUUAUGUAUUUUCCCU-CCAUUAUAGUUAACUGUU
AAGW02035946.1/12410-12186 GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUG-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUGAUCUUGUAUUAUACUG-GAAA------UAUUCU---UAUGUAUUCUCUCC-AAAUAAUGGCUCACUAUU
AAGU03015373.1/12862-12630 GGUAUUUACAUAUCUUGGAGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCCGAGCUGACUGUAACUGACUCAGUAACAAA-UCUAAUCGCAUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUUCCC-AAAUGAUGGCCCACCAUU
#=GC SS_cons               ::::::::::::::::::::::::::..:::::::::::::::.....::::::::.:::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::.:::::.:::::::::::::::::::::::::::.::::::::::::::::::
#=GC RF                    gGUaUUUAcAUAUCuuGGGGAGaUUU..agAguaUAAacUCua.....AGAUCUUu.GGUAUUUAAGUGUCAaCAUCGAUUU.aUUUAUUUAUUGCUgAGCUgAcuGUAaCuGACUCaaUaACAAA.UcUAAUCaUGUauUGCaCuG.GAAAA.GAAaUAUUCUCAUUAUGUAUUUUCuCc.aaAUgAUGgcucACcAUU

AF071164.1/5119-5351       GCAUUUGAAUACCUGCUGUAAAUAU--CAAUAAUAUGAAGUAA-UUACU
ABVD01019940.1/888-1120    GCAUUUGAAUACCUGCUGUCAAUAU--CAAUAAUAUCGAGUAA-UUACU
ABRP01099870.1/3626-3858   GCAUUUGAAUGCCCACUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AAPY01076971.1/894-1126    GCAUUUGAAUACCCGCUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAHY01053339.1/13083-12851 GCAUAUGAAUGCCCACUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AANN01604120.1/4844-4612   GCAUUUGAAUACCGGUUGUAAAUAU--CAAUAAUAUCCAGUAA-UUACU
AAKN02039092.1/12920-13152 GCAUUUGAAUACUCACUGUAAAUAU--CAAUAAUAUCGAGUAA-UUAUU
ABRN01187570.1/5318-5551   GCAUUUGAAUACUCGCUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAIY01705046.1/1523-1291   GCAUUUGAAUGCCCGCAGUAAAUAU--CAAUAAUAUCAGGUAA-UUAUG
ABRQ01101202.1/2639-2874   GCUUUUGAAUACCUGUUGUAAAUAUAUCAAUAAUAUUAGGUAA-UUACU
ABRO01036384.1/16802-17035 CUAUUUGAAUACCCACUGUAAAUAU--CAAUAAUAGUGAGUAA-UUAUU
AAGV020458989.1/269-494    GCAUUU----ACCUGGUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAPN01063703.1/15252-15484 CCACUUGAAUACCAGCUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AAYZ01055296.1/1799-2024   GCAUUUGAAUGCCCGCUAUAAAUAU--CCAUCAUAUCGAGUAAAUUACU
AAFR03047692.1/44711-44480 CCAUUUGAAUACCGGCCAUAAAUAU--CAAUAAUACGCAGUAA-UUACU
AAQQ01071885.1/63-291      ------GAAUACC--CUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
ABQF01013713.1/13270-13498 GCGUUUGAAUUCAAGCUGUAAAUUC---AAGAUUAUCAAGUAA-UUACU
AF327372.1/6683-6451       ACAUUUGAAUUCGAGCUGUAAAUUC---AAUAUUAUCAAGUAA-UUACU
AAGW02035946.1/12410-12186 GCAUUUGAAUGCCCACUAUAAAUAU--CAAUAAUAUCGAAUAA-UGACU
AAGU03015373.1/12862-12630 GCAUUUGAAUACCUGCUGUAAAUAU--CAAUAAUAUUAGGUAA-UUACU
#=GC SS_cons               :::::::::::::::::::::::::..::::::::::::::::.:::::
#=GC RF                    gCaUUUGAAUaCccGcUGUAAAUaU..CAAUAaUAUcgaGUAA.UUACU
//
