gi_545778205_gb_U000_61

cmsearch-Rfam

Family :

GadY

Id:

RF00122

Type:

Gene; sRNA;

Taxonomy:

Bacteria;

Ontology:

GO:0003729 mRNA binding

Description:

This family represents a GadY RNA (previous named IS183 in [1]). GadY can form base pairs
with the 3' UTR of its target mRNA gadX, this pairing is thought to confer
increased stability to the transcript, allowing accumulation of gadX (a transcriptional regulator of the acid
response) and therefore increased expression of downstream acid resistance genes [2].

Score:

150.0

E-value:

1.4e-33

From sequence:

3664861

To sequence:

3664974

Alignments:

                                                                                                                 NC
                               :::<<<<--<<<<<------<<<<<<____>>->>>>>>>>>---->>>>,,,,<<<<<<<_______>>>>>>>,,,,,, CS
               RF00122       1 CUUaCuGAGagCaCAAAGUUuCCCGuGCCAaCAGGGaGuGuuAUAACgGuUUAUuaGuCuGGAGACGGCaGaCuaUCCUCU 81     
                               CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCU
  gi_545778205_gb_U000 3664861 CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCU 3664941
                               ********************************************************************************* PP

                                                                 NC
                               ,<<<<<<_______>>>>>>::::::::::::: CS
               RF00122      82 UcCcGGuCCCCUAUgCCgGgUUUUUUUUAUGUC 114    
                               UCCCGGUCCCCUAUGCCGGGUUUUUUUUAUGUC
  gi_545778205_gb_U000 3664942 UCCCGGUCCCCUAUGCCGGGUUUUUUUUAUGUC 3664974
                               ********************************* PP

RNAfold
>gi_545778205_gb_U000_61
UUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUU
UAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCGGG
UUUUUUUUAUGUC
..((((..(((((......((((((....)).)))))))))....))))....(((((((.......))))))).......((((((.......))))))............. (-29.50)

Length sequence

: 113

Length match:

112