# STOCKHOLM 1.0
#=GF ID ROSE
#=GF AC RF00435
#=GF DE Repression of heat shock gene expression (ROSE) element
#=GF AU Bateman A; 0000-0002-6982-4660
#=GF GA 45.0
#=GF NC 44.9
#=GF TC 45.2
#=GF SE PMID:11726689
#=GF SS Published; PMID:11726689; Griffiths-Jones S
#=GF TP Cis-reg; thermoregulator;
#=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; 0002168; RNA_thermometer;
#=GF DR GO; 0009266; response to temperature stimulus;
#=GF DR GO; 0006417; regulation of translation;
#=GF RN [1]
#=GF RM 11726689
#=GF RT A mRNA-based thermosensor controls expression of rhizobial heat shock
#=GF RT genes.
#=GF RA Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F
#=GF RL Nucleic Acids Res 2001;29:4800-4807.
#=GF RN [2]
#=GF RM 15466035
#=GF RT Replicon-specific regulation of small heat shock genes in Agrobacterium
#=GF RT tumefaciens.
#=GF RA Balsiger S, Ragaz C, Baron C, Narberhaus F
#=GF RL J Bacteriol 2004;186:6824-6829.
#=GF CC This family represents a 5' UTR cis-regulatory element found in heat shock
#=GF CC mRNAs and is known as the ROSE (repression of heat shock gene expression)
#=GF CC element. The ROSE element is a negative regulator of heat shock gene
#=GF CC expression. The secondary structure is thought to be regulated by
#=GF CC temperature. This regulation blocks access to the ribosome binding site
#=GF CC under normal conditions. During heat shock however, the structure changes
#=GF CC freeing the ribosome binding site and allowing expression to occur [1,2].
#=GF WK Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ 13

CP000009.1/1450710-1450627 ---------------------CCGGCCGCC--AAA--GGGGUCGGCA----------AACAGAACU----AUC----AGUUUUGAU----CUUGUG-UCCAUGUUGCUCAAAGGAGGAUAUGGCUAUGAGAG
AY316747.1/256783-256687   ---------------------CCGACCGCCA-AAA-UGGCGUCAGCCUG---GUCAGGGAGCGCCGAG--CUU--CUUGGCGCUCC----CUCAUA-UCUAUGUUGCUCUACGGACGAUGUAGCUAUGAGAA
BA000012.4/1943819-1943723 ---------------------UCGGUCGCC-GCAUAAGGGGCCGAUGU----GUCAGGGAGCGCCAUG--CUU--CUUGGCGUUCC----CUCGUA-UCUAUGUUGCUCCAAGGAGGAUGUAGUUAUGAGAA
AY316747.1/197909-198003   ---------------------GCCGAUGCC--AAUU-GGGUCGGCAUG----GUCAGGGAGCGCCACG--CUU--CUUGGCGCUUC----CUCGUA-UCUAUGUUGCUCUACGGAGGAUGUAGCUAUGAGAA
AP003017.1/94542-94451     ---------------------UCGGG-GC---UUCG--G-CCCGACA------GAUUGGGCGUCGCAG-AGACG-CUGCGACGCUG----CUUGUAACCCAUGUUGCUUUACGGAGGAUAUGGCUAUGAGAA
AL591985.1/872145-872052   ---------------------AGAGCCGCCU-GUA-AGGGGCUCGCA----------GUCGAGGAG--CUCCGUU--CUCUUCGGCGCUCCUCAUCGUCCAUGUUGCUC-AAGGAGGAUAUGGCUAUGAGAA
U55047.1/3106-3215         CGCCGC-GACAAGCGGU----CCGGGCGCC--CUAG-GGGCCCGGCG------GAGACGGGCGCCGGA--GGUG-UCCGACGCCUG----CUCGUA-CCCAUCUUGCUCCUUGGAGGAUUUGGCUAUGAGGA
U55047.1/5180-5291         UGCCGC-GACAAGCGGU----CCGGGCGCCC-UUCGGGGGCCCGGCG------GAGACGGGCGCCGGA--GGUG-UCCGACGCCUG----CUCGUA-CCCAUCUUGCUCAGUGGAGGAUUUGGCUAUGAGGA
AJ003064.1/2430-2312       CGCCGCCGCAGGGCGGCUCU-CCGGGCGCC--UGAC-GGGCUCGGCGAAUCCAGAGACGGGCACCGG--UCGUGU-CCGGUGCC-G----CUCGUA-ACCAUUUUGCUCCGUGGAGGAUCUGGCUAUGCGCA
AJ010144.1/622-738         GCCGCC-GA-GAGGUGGCGUCCCCGACGCC--UCAU-GGGUCGGGAACGAC-UGAGACGGGCACCGG--UCGUGU-CCGGUGCC-G----CUCGUA-UCCAUUUUGCUCCUUGGAGGAUUUGGCUAUGCGCA
AJ003064.1/2697-2806       GCCACGCGGGAGCGUGGCG--CCGGAUGCC--UCUC-GGGUCCGG--------CAGACG-CCAUCGGG-CAGAA-UCCGAUGU-UG----CUCCUA-UCCAUAUUGCUCAGAGGAGGAUGUGGUUAUGAGAA
AE007872.2/51225-51317     ---------------------CCAGCCGCUG-ACGACGGGGCUGGACU----UGCUGGGAGCGCCG---CCUUU---CGGCGCUUC------CGUA-CCCAUGUUGCUUCAAGGAGGAUAUGGCUAUGGCAA
AE007872.2/441983-442075   ---------------------CCAGCCGCUGAGGUCAGGGGCUGGCC----------UUGUUGGACG---CGC---CGUCUUUCAGCGCU-CCGUA-CCCAUGUUGCUUCAAGGAGGAUAUGGCUAUGGCAA
#=GC SS_cons               .....................<<<<<<-<<..____.>>>>>>>>::......::::<<<<<<<<<<_..____._>>>>>>>>>>....<<<<<<.-<<<<<<<-<<<____>>>>>>>>>>->>>>>>::
#=GC RF                    .....................cCgGccGCC..uuau.GGggCcGgca......gaaaggggcgccggg..cuug.cccggcgcccc....CuCgUa.uCCAugUUGCUCuaaGGAGGAuaUGGCuAuGaGAA
//
