tp1,

cmscan-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:

307.0

E-value:

2.5e-87

From sequence:

1

To sequence:

303

Alignments:

                                                                                                                     NC
              ::::::((((((,<<<<_______>>>><<____>>,,,,)))))),,,,,,,,,,,(((,,,,,,,<<<<<<<______>>>>>>>,,<<<<<<<<<-<<< CS
  RF00126   1 guGGcCcuuucCGCcGcCUugCAAgCgGGCauuGGCUUuaGgaaagGAuaUuCaaUggCCGUAAauGCAgGcaCacCacaGugCcUGcuaUCaCGgCAauau 102
              G+GGCCCUUUCCGCCG:CU+GCAA:CGGGC++UGGCUUUAGGAAAGGAU+UUC+ UG:CCGUAAAUGCA:G::  +CACA ::C:UGCUAUC:CG:CAAUAU
     tp1,   1 GCGGCCCUUUCCGCCGUCUCGCAAACGGGCGCUGGCUUUAGGAAAGGAUGUUCCGUGGCCGUAAAUGCAGGUGUUUCACAGCGCUUGCUAUCGCGGCAAUAU 102
              ****************************************************************************************************** PP

                                                                                                                     NC
              <<____>>>>>->>>>>>>>><<<<<<<______>>>>>>><<<<<<<---<<<<<<<<____>>>>>>>>->>>>>>>,,,,)))((-(((((,,,,,,,, CS
  RF00126 103 CgCCaGcGgugCUGcCGuGAuGCGGUCuucGCAugGACCGCACaAugAAGauACGauaCUUUUGuauCGUaCUcaUuGUuUcUGGcgCGcUGuuaacuuauG 204
              C:CCAG:GGUGCUG:CG:GAUGCGGUCUUCGCAUGGACCGCACAAU:AAGAUACG:U:CUUUUG:A:CGUACU:AUUGUUUCUGG:GCGCUGUUAAC+ A G
     tp1, 103 CGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCUUUUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCGAGG 204
              ****************************************************************************************************** PP

                                                                                                                    NC
              ,,,,......,,<<<<___>>>>,,,,,,,,,,,,,,<<<________>>>,,,,,)))))...)),,,,,,<<<<<<<<<<<____>>>>>>>>>->>:: CS
  RF00126 205 uAAA......caggagUuucuccggcAAcuauaUuccgGUaauuAuCAACcuucagagCAg...GuAAGcCaggagGCCGCCCUuUgGGGCGGCcuuccUU 296
              UAAA      C GGAGU+UCUCCGGC AC+AU+U+C+GGU+ UUA+CAACCUUCAGAGCAG   GUAAGCC+::A:GCCGCCCUUU GGGCGGC:U+:: U
     tp1, 205 UAAAuaauaaCCGGAGUCUCUCCGGCGACAAUUUACUGGUGGUUAACAACCUUCAGAGCAGcaaGUAAGCCCGAAUGCCGCCCUUU-GGGCGGCAUAUU-U 303
              ***********************************************************************************998.*********987.8 PP

RNAfold
>tp1,
cggcccuuuccgccgucucgcaaacgggcgcuggcuuuaggaaaggaugu
uccguggccguaaaugcagguguuucacagcgcuugcuaucgcggcaaua
ucgccaguggugcugucgugaugcggucuucgcauggaccgcacaaugaa
gauacggugcuuuuguaucguacuuauuguuucuggugcgcuguuaaccg
agguaaauaauaaccggagucucuccggcgacaauuuacuggugguuaac
aaccuucagagcagcaaguaagcccgaaugccgcccuuugggcggcauau
uu
((((.......)))).........(((((((((((..((((((......))))...(((((....(((((((((....)))))))))....)))))..))..))))))..((((((.....((((((((......))))))))((((((.(.((((((((....)))))))))))))))..(((((.(.(.(((((((((.(((((((.....((((((...)))))).....)))))))..))))))))).)).))))))))))).....))))).(((((((((...))))))))).... (-127.60)

Length sequence

: 302

Length match:

301