gi_545778205_gb_U000_196

cmsearch-Rfam

Family :

rne5

Id:

RF00040

Type:

Cis-reg;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family represents a conserved element found in the 5' UTR of RNase E mRNA. RNase
E is a key regulatory enzyme in the pathway of mRNA degradation in E. coli
that is able to auto-regulate the degradation of its own mRNA in response to changes
in RNase E activity. This rne 5' UTR element acts as a sensor of cellular
RNase E concentration enabling tight regulation of RNase E concentration and synthesis.

Score:

248.8

E-value:

1.1e-77

From sequence:

1144728

To sequence:

1144392

Alignments:

                                                                                       v                         NC
                               ::<<<<<<-----..<<<<<____>>>>>----...>>>>>>,,,,,,,,,<<<<<<<<---<<<<---<<<--<<____> CS
               RF00040       1 cugcccgCguuGA..cgcccUAAAgggcgAAau...GcgggcUuauaaAuUuugccUGAUugcgcaAAcAcGCaGCAAUGG 76     
                                U::CCG:GU  A  C::::UAAA::::GAAAU   :CGG::U+A   AUU:UGCC GA +G::CA  CACGCAGCAAUGG
  gi_545778205_gb_U000 1144728 GUUUCCGUGUCCAucCUUGUUAAAACAAGAAAUuuuACGGAAUAACCCAUUUUGCCCGACCGAUCAUCCACGCAGCAAUGG 1144648
                               *************88888889**988888888779********************************************** PP

                                                    v                               v                  v         NC
                               >------>>>-->>>>--->>>>>>>>-----(((((((((((------.-(((((((,,,,,<<<<<----<<<<<____ CS
               RF00040      77 CGUAAGACgUaaugcgAAAUCAggcaaUUAGCGgGCugCGGguUgcaGu.uuggCcGGaauaugGgaccauacCgggUuga 156    
                               CGUAAGACGUA+UG::   UC GGCA:UUAGC:GGCUGCGGGUUGCAGU  U: CCGG+A AU:G:A: AU+ C:GG  GA
  gi_545778205_gb_U000 1144647 CGUAAGACGUAUUGAUCUUUCAGGCAGUUAGCGGGCUGCGGGUUGCAGUcCUUACCGGUAGAUGGAAAUAUUUCUGG-AGA 1144568
                               *************************************************99**************************.*** PP

                                          v                                                                      NC
                               _______>>>>>---->>>>>,,,,,,,,<<<-<<<<-<<<<_____>>>>->>>>>>>,<<<<<--------<<<<<--- CS
               RF00040     157 auuAaAUcccGgaauugucCcuuuAuaAagGcGCUGuaUUUcaauaugAAAuaCAGgCcuaCCGAaAcuauGCGcCuCUAU 237    
                                U+A+A CC:G   U :U:C:UU AUAA :GCGC GU+UUUC   AUGAAA AC GGC: ACCGA ACU UGCGCCUCU U
  gi_545778205_gb_U000 1144567 GUAAUACCCAGU-CUGUUUCUUUGAUAAUUGCGCUGUUUUUCCGCAUGAAAAACGGGCA-ACCGACACUCUGCGCCUCUUU 1144489
                               ***********9.578*******************************************.********************* PP

                                                                                                v                NC
                               ---..--<<-<<<<<____>>>>>->>---------------->>>>>-->>>>>,,,,,,)))))))-----------)) CS
               RF00040     238 aca..aaCGACaaCCGuGAGGuuGaCGgCuUuGuAaAAguCAcGaGgCCAUCGGuUUAAcUCCgGccaGaggUuauUuUgc 316    
                               + +  +ACGA:AACCGUGAGGUU:+CG+C     A  AG+CACGAGGCCAUCGGUU A   CCGG :AG  GUUA+UUUGC
  gi_545778205_gb_U000 1144488 GAGcuGACGAUAACCGUGAGGUUGGCGACGCG--ACUAGACACGAGGCCAUCGGUUCACACCCGGAAAGGCGUUACUUUGC 1144410
                               99999***********************9876..999*********************666******************** PP

                                                  NC
                               )))))))))::::::::: CS
               RF00040     317 CCGcaGCuCUaUcgaUaA 334    
                               CCGCAGCU:  UCG+ AA
  gi_545778205_gb_U000 1144409 CCGCAGCUUAGUCGUCAA 1144392
                               ****************** PP

RNAfold
>gi_545778205_gb_U000_196
UGACGACUAAGCUGCGGGCAAAGUAACGCCUUUCCGGGUGUGAACCGAUG
GCCUCGUGUCUAGUCGCGUCGCCAACCUCACGGUUAUCGUCAGCUCAAAG
AGGCGCAGAGUGUCGGUUGCCCGUUUUUCAUGCGGAAAAACAGCGCAAUU
AUCAAAGAAACAGACUGGGUAUUACUCUCCAGAAAUAUUUCCAUCUACCG
GUAAGGACUGCAACCCGCAGCCCGCUAACUGCCUGAAAGAUCAAUACGUC
UUACGCCAUUGCUGCGUGGAUGAUCGGUCGGGCAAAAUGGGUUAUUCCGU
AAAAUUUCUUGUUUUAACAAGGAUGGACACGGAAAC
..........((((((((...(((....((((.((((..(((.(((((((..(((((.(((....(((.((..((((....))))..)).).))....))).))).))..)))))))((((.(((((((.....))))))).).))).........((((....(((((........))))).....)))))))...)))).)))))))....))))))))((.(....(((((((..(((((.....(((.((((.......))))))))))))..)))))))....)))...((((((.....(((((((....))))))).....)))))).. (-104.70)

Length sequence

: 336

Length match:

335