RyiA_SraJ,

cmscan-Rfam

Family :

GlmZ_SraJ

Id:

RF00083

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This RNA was discovered in E. coli during a large scale screen [1]. The sraJ gene
was expressed in early logarithmic phase, but its level decreased with cell growth [1]. Specific
cleavage products of this RNA were found [1]. The function of this RNA is unknown.

Score:

204.4

E-value:

5.8e-54

From sequence:

6

To sequence:

211

Alignments:

                                                                                                                     NC
                 <<---<<<<<<<<<<-----<<<<<---<<______>>-->>>>>----->>>>>>>->>>-->>,,,,,,,,,(((((((,,,<<<<--------<<< CS
     RF00083   1 GuAGAUGCUCaUcCCAuuUcuUaUGuUuGCcUuauuGCuUCAuAaACuCaGGgAuGAuGCAGAgCCGaUUuUAcGGuGCcUAUuGuCCAucUaAcaGaU 99 
                 GUAGAUGCUCAU:CCAU+UCUUAUGUU+GCCUUA+UGC+UCAUAAACUC GG:AUGA+GCAGAGCCG+U  UACGGUGC:UAU+GUCCA CU+ACAGAU
  RyiA_SraJ,   6 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUAGUGCCUCAUAAACUCCGGAAUGACGCAGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAU 101
                 *********************************************************************..******************.********* PP

                                                                                                                     NC
                 <______________>>>>-..------>>>>,,,<<_____>>,))))))),,,,,,,,,<<<_____>>>,,,,,,,,,,,,<<<<<<<<<<<____ CS
     RF00083 100 GUcgaauuuauuccuCAuCA..CAuacuGGaCAuAaCGUUGAGuGAgGCaCCgauuuUGUUGUCuuacAGACCUGAaaauUUUagaCGCcuGCccuuua 196
                 GUCG   UUAU+CCUCAUCA  CA+++UGGACA+AACGUUGAGUGA:GCACC A  UUGUUGUC+UACAGACCUG     UUU+:ACGCCUGC:C+ UA
  RyiA_SraJ, 102 GUCGC--UUAUGCCUCAUCAgaCACCAUGGACACAACGUUGAGUGAAGCACCCA-CUUGUUGUCAUACAGACCUG-----UUUUAACGCCUGCUCCGUA 192
                 *****..99*******************************************55.566*****************.....***************9999 PP

                                      NC
                 ....>>>>>>>>>>>::::: CS
     RF00083 197 ....ggGCagGCGucUUUUU 212
                     G:GCAGGCGU: UUUU
  RyiA_SraJ, 193 auaaGAGCAGGCGUU-UUUU 211
                 9999**********8.678* PP

RNAfold
>RyiA_SraJ,
aacgaguagaugcucauuccaucucuuauguucgccuuagugccucauaa
acuccggaaugacgcagagccguuuacggugcuuaucguccacugacaga
ugucgcuuaugccucaucagacaccauggacacaacguugagugaagcac
ccacuuguugucauacagaccuguuuuaacgccugcuccguaauaagagc
aggcguuuuuu
((((.((...((((((((((.....(((((..(((....)))...))))).....))))))).)))..))))))...(((((((..((((((.((.(.((((..((....))..)))).).))...)))))..........)..)))))))........(((.....))).......(((((((((((........))))))))))).... (-63.30)

Length sequence

: 211

Length match:

204