ssrA

cmscan-Rfam

Family :

tmRNA

Id:

RF00023

Type:

Gene;

Taxonomy:

Eukaryota; Bacteria; Viruses;

Ontology:

GO:0006401 RNA catabolic process

Description:

Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual tRNA and
mRNA-like properties. Its role is to liberate the mRNA from a stalled ribosome. To accomplish
this part of the tmRNA is used as a reading frame that ends in a
translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and
translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein
enabling recognition by a protease. Recently a number of permuted tmRNA genes have been found
encoded in two parts. tmRNAs have been identified in eubacteria and some chloroplasts but are
absent from archaeal and eukaryote nuclear genomes.

Score:

221.6

E-value:

9.2e-66

From sequence:

106

To sequence:

466

Alignments:

                                               v                                                                     NC
              [[[[[[[,..,,,,,,,,((((((((((((---(((((((((((((.(((((,,,,,<<<<<<<.______________>>>>>>>,,,,,,,,,,,,,,,, CS
  RF00023   1 GGGGcUGA..auGGuUUCGACgggggugauaAaaacuccuugaaug.CAuGcCGAGgggcgguu.acCUCGUAAAuaaAaaccgccaAAAAAAUAAaUGCaA 98 
              GGGGCUGA  +UGG+UUCGACGGG::U:::+A  A::CC:  :::: CAUGCCGAGG:GCGG:U +CCUCGUAAA   AA:CCGC:  AAAAAUA ++GCAA
     ssrA 106 GGGGCUGAuuCUGGAUUCGACGGGAUUUGCGA--AACCCA--AGGUgCAUGCCGAGGGGCGGUUgGCCUCGUAAA---AAGCCGCA--AAAAAUAGUCGCAA 198
              ******************************99..999998..66666**********8*******9*********...8*******..999*********** PP

                                       v                 v                                                           NC
              ,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<.____....>>>>>>>>>..<<<<<<.<<<<.<<<<__________>>>>->>>>.....>>>>>>,,,... CS
  RF00023  99 AcaAcAAuaacuAcuuguCgcucucgccgc.uUAA....gcggcgaga..ccuccc.uccc.ccguuuGCCcguugacgggggga.....gggaggUcA... 183
              AC+AC+A AACU     +CGCU:U: :C:: UUAA    ::G:+:A:A  CCUC:C :CC: :C:U+ GC+C+U  A:G:+:GG:     G:GAGGUCA   
     ssrA 199 ACGACGAAAACU-----ACGCUUUA-GCAGcUUAAuaacCUGCUUAGAgcCCUCUCuCCCUaGCCUCCGCUCUU--AGGACGGGGaucaaGAGAGGUCAaac 292
              ***********4.....55999999.7777677778887777777766********99999******9****99..9999888888************9*** PP

                          vv      v                    v      vv                                                     NC
              ,,,,,,,,,,,.<<<<<<<<<_....._______..._.._>>>>>>>>>,,,.,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>> CS
  RF00023 184 uaAaacGGGaU.ccccgcaacg.....cgguugc...g..gguugcggggaAa.uuaaaagaacuggccucuggauagccUGuccgUcggcgauccagaggc 273
              ++AAA+G+GAU   :CG:::       C+G+++       +G:::CG:++AAA UUAA+ +++CU G::U::::::+GC:UGUCCGUC:GC ::::::A::C
     ssrA 293 CCAAAAGAGAUc--GCGUGG--aagccCUGCCU-ggg-guUGAAGCGUUAAAAcUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGC 388
              999999999963..466666..65766333333.465.47789*******9999899999999999*********9***************99********* PP

                                                       v                                           NC
              ,,,,,,.,,,,,.,,,,,,,)))))--.-)))))))))))))-)))))))))))),<<<<<_______>>>>>]]]]]]]:::: CS
  RF00023 274 gAAaac.Agaca.aGACUAAgCaUGUA.GaaaucaaggggggaagcacuuucGGACGgGGGUUCGAuUCCCcCCAgCUCCACCa 354
              GAA    A+A A  GACUAAGCAUGUA  ::::  :GG::G+ :::A::UUCGGACG:GGGUUC+A UCCC:CCAGCUCCA   
     ssrA 389 GAAU-GuAAAGAcUGACUAAGCAUGUAgUACCG--AGGAUGU-AGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCA--C 466
              ***9.56777777***9**********777777..8999999.**************************************..9 PP

RNAfold
>ssrA
GGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGA
GGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAA
AACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGC
CUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGC
GUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUU
GUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUA
AGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCG
CCAGCUCCAC
((((((((((((.......))))))........(((..(((....)))..)))((((((............))))))........((((....))))....(((((((((((((((.........)))).))))))(((((((((((..(((........)))..)))))....))))))..................((((...((((((....))))))...)))).....((((.((((((..((((((((((.(((........))).))))))))))....)).....)))).))))...))))).(((((.((......)))))))..(((((.......)))))))))))... (-116.90)

Length sequence

: 360

Length match:

359