gi_545778205_gb_U000_354

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:

26.5

E-value:

1.7e-05

From sequence:

2518231

To sequence:

2518156

Alignments:

                                                vvv                            vvv                              NC
                               [[[[[[[,.,,,,,,,,((((((((((((---~~~~~~~)))))))))))),<<<<<_______>>>>>]]]]]]]:::: CS
               RF00023       1 GGGGcUGA.auGGuUUCGACgggggugauaAa*[282]*agcacuuucGGACGgGGGUUCGAuUCCCcCCAgCUCCACCa 354    
                               GGGGCU +                                        GG C:G GGUUCGAU CC C: AGCUCCACCA
  gi_545778205_gb_U000 2518231 GGGGCUAUa----------------------G*[ 34]*---------GGUCAGCGGUUCGAUCCCGCUUAGCUCCACCA 2518156
                               ******977......................0....5...........333***************************** PP

>>

RNAfold
>gi_545778205_gb_U000_354
CUUUGCAGCGAGGGUUGGAAAUUUGGUGGAGCUAAGCGGGAUCGAACCGC
UGACCUCUUGCAUGCCAUGCAAGCGCUCUCCCAGCUGAGCUAUAGCCCCA
CGAUGCGUUUACGUACCAAGUUUGCUGGGUGCAAAAUUUGGUGGAGCUAA
GCGGGAUCGAACCGCUGACCUCUUGCAUGCCAUGCAAGCGCUCUCCCAGC
UGAGCUAUAGCCCCGUCACGUAAAGCUUGUCGAGUUGACGGGCGGCAUCA
UAUGAAUUCCGCCCGAAUGUGUCAACGGCAAAUUGCAACGUGUAGUUUCA
AUCGCUGAAAAAUCAGGCAAAUGAACAAUUUUGGAAAACCGCUCGCAUUC
AGU
.......(((((((((..(((.(((.(((.(((((((((.......))))).....((((((((.((((((((.((((........))))..((((.((((.(...((((..(((((.((....)).))))).)))).).)))).))))(((((.......))))).....)))))))).)))))))).((((........))))..)))).))).(((((...(((((((..((((((((((((..((....))...))))))......)))))))))))...)).)))))....((((....((((....)))).....))))))).)))....)))).)))))....... (-119.60)

Length sequence

: 353

Length match:

74