gi_545778205_gb_U000_52

cmsearch-Rfam

Family :

cyano_tmRNA

Id:

RF01851

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:

23.4

E-value:

0.00033

From sequence:

2518183

To sequence:

2518108

Alignments:

                                                                                NC
                               <<<<<_______>>>>><<<<<<<_________~~~~~~>>>>>>>,, CS
               RF01851      62 AGcGGUUCGAUUCCgCUCAgCuCCAUUccuccu*[ 4]*GGgGcUGcA 107    
                               AGCGGUUCGAU CCGCU:AGCUCCA      +U      GGGGCU:+A
  gi_545778205_gb_U000 2518183 AGCGGUUCGAUCCCGCUUAGCUCCACCAAAUUU*[34]*GGGGCUAUA 2518108
                               *************************97666555...5..********* PP

RNAfold
>gi_545778205_gb_U000_52
GACAAAAAACCCCCGCUUUGCAGCGAGGGUUGGAAAUUUGGUGGAGCUAA
GCGGGAUCGAACCGCUGACCUCUUGCAUGCCAUGCAAGCGCUCUCCCAGC
UGAGCUAUAGCCCCACGAUGCGUUUACGUACCAAGUUUGCUGGGUGCAAA
AUUUGGUGGAGCUAAGCGGGAUCGAACCGCUGACCUCUUGCAUGCCAUGC
AAGCGCUCUCCCAGCUGAGCUAUAGCCCCGUCACGUAAAGCUUGUCGAGU
UGACGGGCGGCAUCAUAUGAAUUCCGCCCGAAUGUGU
(((((.........(((((((.(((.((((((.....((((.(((((..(((((.......))))).....((((((((.((((((((.((((........))))..((((.((((.(...((((..(((((.((....)).))))).)))).).)))).))))(((((.......))))).....)))))))).)))))))).))))).))))........)))))))))...)))))))))))).......(((((((..((....))...)))))))....... (-107.90)

Length sequence

: 287

Length match:

74