gi_545778205_gb_U000_263

cmsearch-Rfam

Family :

Spot_42

Id:

RF00021

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

The physiological role of Escherichia coli Spot 42 (spf) RNA has remained obscure, even though the
109-nucleotide RNA was discovered almost three decades ago. Spot 42 seems to have a regulatory
role on the galactose operon [1]. It is proposed that Spot 42 acts by an
antisense mechanism where the RNA binds to the galK translation initiator region [1]. Changes in
Spot 42 levels are implicated in affecting the adjacent DNA polymerase I levels [2]. The
Hfq protein has been shown to interact with several small regulatory RNAs in E. coli,
and the protein is required for OxyS, DsrA, RprA and Spot 42 RNA regulation [3].

Score:

122.0

E-value:

9.6e-26

From sequence:

4049889

To sequence:

4050007

Alignments:

                                                                                                                 NC
                               ::::::::<<<<-<<<<<-<<<<<<<<<<<<___>>>>>>---->>>>>>>>>>>->>>>,,,,,,,,,,<<<<<<_.... CS
               RF00021       1 aaUuaucggcGuAggguaCagaGGuaaGaugUUCuauCuuUCAGaCCuuuuaccucaCgcuAuuggAuuaGgCugau.... 77     
                               A+UUA + :CGUAG:GUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUAC:UCACG:+AU GGAUU+GGCU:A+    
  gi_545778205_gb_U000 4049889 AGUUAGUCGCGUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAuauu 4049969
                               ****************************************************************************88999 PP

                                                                      NC
                               >>>>>><<<<<<<<<<____>>>>>>>>>>:::::::: CS
               RF00021      78 ucaGcCGCCcCaGccaaUuuuggCuGgGGCuUUUUUUu 115    
                               U:AGCCGCCCCAG:CA U +UG:CUGGGGC+UUUUUU+
  gi_545778205_gb_U000 4049970 UUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA 4050007
                               ************************************** PP

RNAfold
>gi_545778205_gb_U000_263
GUUAGUCGCGUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUU
ACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAA
UGACUGGGGCGUUUUUUA
...((((((((.(((((.((((((((((((...))))))....))))))))))).)))).....)))).(((((((...)))))))((((((((((....))))))))))........ (-43.20)

Length sequence

: 118

Length match:

117