# STOCKHOLM 1.0
#=GF ID HepE_CRE
#=GF AC RF00550
#=GF DE Hepatitis E virus cis-reactive element
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 45.0
#=GF NC 38.5
#=GF TC 80.5
#=GF SE PMID:15890906
#=GF SS Published; PMID:15890906
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.16 -Z 2958934 CM SEQDB
#=GF DR GO; 0019080; viral gene expression;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 15890906
#=GF RT The open reading frame 3 gene of hepatitis E virus contains a cis-reactive
#=GF RT element and encodes a protein required for infection of macaques.
#=GF RA Graff J, Nguyen H, Yu C, Elkins WR, St Claire M, Purcell RH, Emerson SU
#=GF RL J Virol 2005;79:6680-6689.
#=GF CC This family represents a cis-reactive element from Hepatitis E virus which
#=GF CC is thought to be essential for "some step in gene expression" [1].
#=GF WK Hepatitis_E_virus_cis-reactive_element
#=GF SQ 46

AB097811.1/5093-5243 GAAACAGUCAAACCUGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB161719.1/5068-5218 GAGACAGUUAAACCUGUUUUAGACCUCACCAAUUCUAUUAUACAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUUUUCUGUUUUUGUUCCUCGUGCUUCUGCCUAUGCUGCCCGC
M80581.1/5023-5172   GAGUCAGUGAAGCCAGUGCUUGACCUGACAAAUUCAAUUCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AY575859.1/5097-5243 GAGACUAUUAAACCUGUGCUUGACCUUACAAACUCUAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB091394.1/5063-5209 GAGACUAUUAAACCUGUGCUUGAUCUAACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-UUUGUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGCUGUUCCUCGUGCUUUUGCCUAUGUUGCCCGC
X98292.1/5052-5201   GAGUCAGUAAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUCUGUUGUUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AB080578.1/431-577   GAGACUGUCAAACCUGUACUUGACCUCACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAA--CACCAUGCGCCCUAGGGCUGUUCUGUUGCUGUUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AF065061.1/40-189    GAGUCGGUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGUUGCCCGC
AB099347.1/5093-5243 GAAACAGUCAAACCCGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB089824.1/5099-5245 GAAACCAUUAAACCUGUGCUUGACCUUACGAAUUCUAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGCUGUUGUUCCUCAUGCUUCUGCCUAUGCUGCCCGC
AP003430.1/5082-5228 GAGUCAAUUAAACCUGUGCUUGACCUUACAAAUUCUAUUAUACAGCGGGUGGAAUGAAUAACAUGU-CUUGUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
M73218.1/5053-5202   GAGUCAGUAAAACCAGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AJ272108.1/5093-5243 GAGACAAUUAAGCCUGUCCUUGACCUUACUAGCUCCAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCCGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGUUGCCCGC
AB108537.1/5074-5224 GAAACAGUCAAACCGGUCCUAGACUUAACUAACUCUAUCAUACAUCGGAUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUUUGUUUCUGCUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AY594199.1/5101-5251 GAGACAAUUAAGCCUGUUCUUGACCUUACUAGCUCCAUCAUAUAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGCGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCCUCGUGUUUUUGCCUAUGCUGCCCGC
AF455784.1/5066-5212 GAGACUGUUAAACCGGUACUGGAUCUUACGAACUCCAUUAUACAGAGGCUAGAAUGAAUAACAUGU-CUUGUGCAUCGCCCAUGG-GAU--CGCCAUGUGCCCUCGGGCUGUUUUGCUGUUGUUCCUCGUGCUUUUGCCUAUGCUGCCCGC
AF459438.1/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AB074920.3/5083-5229 GAGACCAUUAAACCUGUGCUUGACCUUACGAAUUCCAUCAUACAGCGGGAGGAAUGAAUAACAUGU-CUUUUGCACCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AF010422.1/22-171    GAGUCAGUAAAGCCAGUGCUCGAUCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
U22532.1/1-90        -----------------------------------------------------AUGGAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCUAGACCAUGGGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUG-------C
AY204877.1/5012-5161 GAGUCUAUAAAACCAGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGCUCCUCAUGUUUCUGCCUAUGUUGCCCGC
AY245779.1/1-105     ----------------------------------------------GGGUGGAAUGAAUAACAUGUUCUUUUGCUCCUUGCAUGGCAAUGCCACCAUGCGCCCUCGGGCUCUUUUGUUUUUGCUCCUCCUGUUUUUGCUUAUGCUGCCCGC
M94177.1/5053-5202   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUCUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF051352.1/30-179    GAGUCUAUAAAGCCUGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AB073912.1/5081-5227 GAGACUAUCAAACCUGUGCUUGACCUUACAAAUUCUAUCAUACAGCGGGUAGAAUGAAUAACAUGU-CUUGUGCAUUGCCCAUGG-GAU--CGCCAUGUGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUUUGCCUAUGCUGCCCGC
AB075971.1/25-175    GAAACAAUCAAACCUGUUCUUGACCUUACUAGUUCCAUUAUAUAUCGGAUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AF010418.1/22-171    GAGUCGGUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUCUGCCUAUGUUGCCCGC
D11093.1/5053-5202   GAGUCGGUGAAGCCAGUGCUCGACUUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUGGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUCGUGCCCGC
M74506.1/5023-5172   GAGUCUGUUAAGCCUAUACUUGACCUUACACACUCAAUUAUGCACCGGUCUGAAUGAAUAACAUGU-GGUUUGCUGCGCCCAUGGGUUCGCCACCAUGCGCCCUAGGCCUCUUUUGCUGUUGUUCCUCUUGUUUCUGCCUAUGUUGCCCGC
X99441.1/5053-5202   GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AB080576.1/431-581   GAAACAGUCAAACCCGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAGUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGUUGCCCGC
AF060669.1/5106-5252 GARAAUAUUAAACCUGUGCUUGACCUUACAAAUUCCAUCAUACAACGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUUUGCCUAUGCUGCCCGC
AF051830.1/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUUUGGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCACGGGUUCGCGAUCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF001276.1/35-184    GAGUCGAUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AY115488.1/5097-5243 GAGACUAUUAAACCUGUGCUUGACUUAACAAACUCUAUCAUACAACGGGUGGAAUGAAUAACAUGU-CUUGUGCUUCACCCAUGG-GAC--CACCAUGCGCCCUAGGGCUAUUUUGUUGUUGUUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AF010421.1/22-171    GAGUCUAUAAAGCCAGUGCUUGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGUGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCUUCAUGUUUCUGCCUAUGUUGCCCGC
AB074915.3/5077-5227 GAAACUGUUAAACCUGUUUUGGAUCUCACCAAUUCCAUUAUACAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGUUUUUGCCUAUGCUGCCCGC
L25547.1/5052-5201   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGAGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUCCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF051351.1/28-177    GAGUCUAUAAAGCCUGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUAGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
D11092.1/5053-5202   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF185822.1/5002-5151 GAGUCAGUAAAACCAGUGCUUGACCUGACAAAUUCAAUUCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AF060668.1/5041-5187 GAGACUAUUAAACCUGUACUUGAUCUCACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF058684.1/39-188    GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUUUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
D10330.1/5053-5202   GAGUCAGUAAAACCGGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGACCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AF076239.3/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGGGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCUCGC
AB074918.2/5099-5245 GAGACCAUUAAACCUGUGCUUGACCUUACGAAUUCCAUCAUACAGCGGGAAGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCGUGCUUUUGCCUAUGCUGCCCGC
#=GC SS_cons         ::<<<<<<-<<<<____>>>>->->>>>>::::::::::::::::<<<<<<<-<<<---<<<<<<-.-----<<-<<<---<<<<<<<-<<<______>>>---->>>>>>>-->>>---->>---->>>>>>------>>>->>>>>>>:
#=GC RF              GAGucagUugagcCuGUgcucGAccugaCaAAuUCaAUcaUauauCGGgugGAaUgAAUAaCAuGU.CUUUUgCugcgccCAugGgccugCgACCAUGcGccCUcggcCuaUUuugcUguUGcUCcUCaUGuUUcUGCCuAuGCugcCCGC
//
