gi_545778205_gb_U000_355

cmsearch-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:

231.6

E-value:

3.3e-68

From sequence:

2755593

To sequence:

2755955

Alignments:

                                                                v                                                NC
                               [[[[[[[,..,,,,,,,,((((((((((((---(((((((((((((.(((((,,,,,<<<<<<<.______________>> CS
               RF00023       1 GGGGcUGA..auGGuUUCGACgggggugauaAaaacuccuugaaug.CAuGcCGAGgggcgguu.acCUCGUAAAuaaAaa 77     
                               GGGGCUGA  +UGG+UUCGACGGG::U:::+A  A::CC:  :::: CAUGCCGAGG:GCGG:U +CCUCGUAAA   AA:
  gi_545778205_gb_U000 2755593 GGGGCUGAuuCUGGAUUCGACGGGAUUUGCGA--AACCCA--AGGUgCAUGCCGAGGGGCGGUUgGCCUCGUAAA---AAG 2755666
                               ******************************99..999998..66666**********8*******9*********...8** PP

                                                                             v                 v                 NC
                               >>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<.____....>>>>>>>>>..<<<<<<.<<< CS
               RF00023      78 ccgccaAAAAAAUAAaUGCaAAcaAcAAuaacuAcuuguCgcucucgccgc.uUAA....gcggcgaga..ccuccc.ucc 150    
                               CCGC:  AAAAAUA ++GCAAAC+AC+A AACU     +CGCU:U: :C:: UUAA    ::G:+:A:A  CCUC:C :CC
  gi_545778205_gb_U000 2755667 CCGCA--AAAAAUAGUCGCAAACGACGAAAACU-----ACGCUUUA-GCAGcUUAAuaacCUGCUUAGAgcCCUCUCuCCC 2755739
                               *****..999**********************4.....55999999.7777677778887777777766********9999 PP

                                                                                     vv      v                   NC
                               <.<<<<__________>>>>->>>>.....>>>>>>,,,...,,,,,,,,,,,.<<<<<<<<<_....._______..._. CS
               RF00023     151 c.ccguuuGCCcguugacgggggga.....gggaggUcA...uaAaacGGGaU.ccccgcaacg.....cgguugc...g. 212    
                               : :C:U+ GC+C+U  A:G:+:GG:     G:GAGGUCA   ++AAA+G+GAU   :CG:::       C+G+++      
  gi_545778205_gb_U000 2755740 UaGCCUCCGCUCUU--AGGACGGGGaucaaGAGAGGUCAaacCCAAAAGAGAUc--GCGUGG--aagccCUGCCU-ggg-g 2755812
                               9******9****99..9999888888************9***999999999963..466666..65766333333.465.4 PP

                                 v      vv                                                                       NC
                               ._>>>>>>>>>,,,.,,,,,,,,,,,,<<<<<<<<<<-<<<________>>>->>>>>>>>>>,,,,,,.,,,,,.,,,,, CS
               RF00023     213 .gguugcggggaAa.uuaaaagaacuggccucuggauagccUGuccgUcggcgauccagaggcgAAaac.Agaca.aGACU 289    
                                +G:::CG:++AAA UUAA+ +++CU G::U::::::+GC:UGUCCGUC:GC ::::::A::CGAA    A+A A  GACU
  gi_545778205_gb_U000 2755813 uUGAAGCGUUAAAAcUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAU-GuAAAGAcUGACU 2755892
                               7789*******9999899999999999*********9***************99************9.56777777***9* PP

                                                      v                                           NC
                               ,,)))))--.-)))))))))))))-)))))))))))),<<<<<_______>>>>>]]]]]]]:::: CS
               RF00023     290 AAgCaUGUA.GaaaucaaggggggaagcacuuucGGACGgGGGUUCGAuUCCCcCCAgCUCCACCa 354    
                               AAGCAUGUA  ::::  :GG::G+ :::A::UUCGGACG:GGGUUC+A UCCC:CCAGCUCCACCA
  gi_545778205_gb_U000 2755893 AAGCAUGUAgUACCG--AGGAUGU-AGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA 2755955
                               *********777777..8999999.***************************************** PP

>>

RNAfold
>gi_545778205_gb_U000_355
GGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGA
GGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAA
AACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGC
CUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGC
GUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUU
GUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUA
AGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCG
CCAGCUCCACCA
((((((((((((.......))))))........(((..(((....)))..)))((((((............))))))........((((....))))....(((((((((((((((.........)))).))))))(((((((((((..(((........)))..)))))....))))))..................((((...((((((....))))))...)))).....((((.((((((..((((((((((.(((........))).))))))))))....)).....)))).))))...))))).(((((.((......)))))))..(((((.......)))))))))))..... (-116.90)

Length sequence

: 362

Length match:

361