gi_545778205_gb_U000_226

cmsearch-Rfam

Family :

ryfA

Id:

RF00126

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

This family consists of a number of bacterial RNA genes of 305 bases in length. The
ryfA RNA gene is present in E. coli, Shigella flexneri and Salmonella species where it
is found between the ydaN and dbpA genes. The function of this RNA is unknown.

Score:

313.9

E-value:

1.5e-88

From sequence:

2653855

To sequence:

2654158

Alignments:

                                                                                                                 NC
                               ::::::((((((,<<<<_______>>>><<____>>,,,,)))))),,,,,,,,,,,(((,,,,,,,<<<<<<<______> CS
               RF00126       1 guGGcCcuuucCGCcGcCUugCAAgCgGGCauuGGCUUuaGgaaagGAuaUuCaaUggCCGUAAauGCAgGcaCacCacaG 81     
                               G+GGCCCUUUCCGCCG:CU+GCAA:CGGGC++UGGCUUUAGGAAAGGAU+UUC+ UG:CCGUAAAUGCA:G::  +CACA 
  gi_545778205_gb_U000 2653855 GCGGCCCUUUCCGCCGUCUCGCAAACGGGCGCUGGCUUUAGGAAAGGAUGUUCCGUGGCCGUAAAUGCAGGUGUUUCACAG 2653935
                               ********************************************************************************* PP

                                                                                                                 NC
                               >>>>>>,,<<<<<<<<<-<<<<<____>>>>>->>>>>>>>><<<<<<<______>>>>>>><<<<<<<---<<<<<<<<_ CS
               RF00126      82 ugCcUGcuaUCaCGgCAauauCgCCaGcGgugCUGcCGuGAuGCGGUCuucGCAugGACCGCACaAugAAGauACGauaCU 162    
                               ::C:UGCUAUC:CG:CAAUAUC:CCAG:GGUGCUG:CG:GAUGCGGUCUUCGCAUGGACCGCACAAU:AAGAUACG:U:CU
  gi_545778205_gb_U000 2653936 CGCUUGCUAUCGCGGCAAUAUCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCU 2654016
                               ********************************************************************************* PP

                                                                                                                 NC
                               ___>>>>>>>>->>>>>>>,,,,)))((-(((((,,,,,,,,,,,,......,,<<<<___>>>>,,,,,,,,,,,,,,<< CS
               RF00126     163 UUUGuauCGUaCUcaUuGUuUcUGGcgCGcUGuuaacuuauGuAAA......caggagUuucuccggcAAcuauaUuccgG 237    
                               UUUG:A:CGUACU:AUUGUUUCUGG:GCGCUGUUAAC+ A GUAAA      C GGAGU+UCUCCGGC AC+AU+U+C+GG
  gi_545778205_gb_U000 2654017 UUUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCGAGGUAAAuaauaaCCGGAGUCUCUCCGGCGACAAUUUACUGG 2654097
                               ********************************************************************************* PP

                                                                                              NC
                               <________>>>,,,,,)))))...)),,,,,,<<<<<<<<<<<____>>>>>>>>>->>:: CS
               RF00126     238 UaauuAuCAACcuucagagCAg...GuAAGcCaggagGCCGCCCUuUgGGGCGGCcuuccUU 296    
                               U+ UUA+CAACCUUCAGAGCAG   GUAAGCC+::A:GCCGCCCUUU GGGCGGC:U+::UU
  gi_545778205_gb_U000 2654098 UGGUUAACAACCUUCAGAGCAGcaaGUAAGCCCGAAUGCCGCCCUUU-GGGCGGCAUAUUUU 2654158
                               ********************************************998.************** PP

RNAfold
>gi_545778205_gb_U000_226
CGGCCCUUUCCGCCGUCUCGCAAACGGGCGCUGGCUUUAGGAAAGGAUGU
UCCGUGGCCGUAAAUGCAGGUGUUUCACAGCGCUUGCUAUCGCGGCAAUA
UCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAA
GAUACGGUGCUUUUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCG
AGGUAAAUAAUAACCGGAGUCUCUCCGGCGACAAUUUACUGGUGGUUAAC
AACCUUCAGAGCAGCAAGUAAGCCCGAAUGCCGCCCUUUGGGCGGCAUAU
UUU
((((.......)))).........(((((((((((..((((((......))))...(((((....(((((((((....)))))))))....)))))..))..))))))..((((((.....((((((((......))))))))((((((.(.((((((((....)))))))))))))))..(((((.(.(.(((((((((.(((((((.....((((((...)))))).....)))))))..))))))))).)).))))))))))).....))))).(((((((((...)))))))))..... (-127.60)

Length sequence

: 303

Length match:

302