gi_545778205_gb_U000_356

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:

18.3

E-value:

0.0055

From sequence:

925971

To sequence:

925884

Alignments:

                                                     vvvvv    vvvvvvvvvvv v                   v vvvvvvvvvvv  vvvv NC
                              [[[[[[[,.,,,,,,,,((((((((((((---(((((((((((((((((~~~~~~~))))--.-)))))))))))))-))))) CS
               RF00023      1 GGGGcUGA.auGGuUUCGACgggggugauaAaaacuccuugaaugCAuG*[244]*CaUGUA.Gaaaucaaggggggaagcac 318   
                              GG G: G+       UC           :+A      + + + :GCA:         :UGUA   :           A:    
  gi_545778205_gb_U000 925971 GGUGAGGUg------UC-----------CGA-GUGGCUGAAGGAGCACG*[  9]*UGUGUAu--A------CGGC-AACGUA 925914
                              ******987......44...........222.22222222344556655....7..4555531..2......2222.122222 PP

                              v                                    NC
                              ))))))),<<<<<_______>>>>>]]]]]]]:::: CS
               RF00023    319 uuucGGACGgGGGUUCGAuUCCCcCCAgCUCCACCa 354   
                              U      CGGGGGUUCGA UCCCCCC :C CC CCA
  gi_545778205_gb_U000 925913 U------CGGGGGUUCGAAUCCCCCCCUCACCGCCA 925884
                              2......***************************** PP

RNAfold
>gi_545778205_gb_U000_356
AGUUCACUGCCGUACAGGCAGCUUAGAAAUUCACAGGUAACAUACUCCAC
CCGCCCACCAUGUUCACUGCCGUACAGACAGAUAAAAUGCGAAAAAAAAG
CUCGCACUUUCGUACGAGCUCUUCUUUAAAUAUGGCGGUGAGGGGGGGAU
UCGAACCCCCGAUACGUUGCCGUAUACACACUUUCCAGGCGUGCUCCUUC
AGCCACUCGGACACCUCACCAAAUUGUUUUGCUACCAAACCUCAUGGGUG
GCAACGGGGCGCUACUAUAGGGAGUUGGAGUAAAACGGUCAAGAAGAAUU
UUAAUGAUAAUUAUUGUUUGCUCAUACUGUAAACAAGUUGUGCAGUAUAU
CUA
......(((((.....)))))..((((.((((((((......(((((((....(((......((((((((((((.....(((................((((((.((....)).))))))..))).....))))))))))))(((((........))))).(((((....)))))...........((..(((((((....((((((((((........((((....))))..........)).))))))))...)))))))..))...)))...))))))).....((((..((.....))..)))).....((((((((.......)))))))).))))).)))...)))) (-98.30)

Length sequence

: 353

Length match:

86