spf

cmscan-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:

110.4

E-value:

3.3e-24

From sequence:

1

To sequence:

109

Alignments:

                                                                    ??                                               NC
              ~~~~~~<<-<<<<<-<<<<<<<<<<<<___>>>>>>---->>>>>>>>>>>->>>>,,,,,,,,,,<<<<<<_....>>>>>><<<<<<<<<<____>>>>> CS
  RF00021   1 <[10]*GuAggguaCagaGGuaaGaugUUCuauCuuUCAGaCCuuuuaccucaCgcuAuuggAuuaGgCugau....ucaGcCGCCcCaGccaaUuuuggCu 102
                    GUAG:GUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUAC:UCACG +AU GGAUU+GGCU:A+    U:AGCCGCCCCAG:CA U +UG:CU
      spf   1 <[ 0]*GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAuauuUUAGCCGCCCCAGUCAGUAAUGACU 96 
              ......******************************************************************88999************************* PP

                            NC
              >>>>>:::::::: CS
  RF00021 103 GgGGCuUUUUUUu 115
              GGGGC+UUUUUU+
      spf  97 GGGGCGUUUUUUA 109
              ************* PP

RNAfold
>spf
UAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUA
AUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGC
GUUUUUUA
..(((((.((((((((((((...))))))....)))))))))))...............(((((((...)))))))((((((((((....))))))))))........ (-38.30)

Length sequence

: 108

Length match:

108