chr11_5

cmsearch-Rfam

Family :

IRES_Bip

Id:

RF00223

Type:

Cis-reg; IRES;

Taxonomy:

Eukaryota;

Ontology:

GO:0043022 ribosome binding

Description:

This family represents the bip internal ribosome entry site (IRES). BiP protein expression has been found
to be significantly enhanced by the heat shock response due to IRES-dependent translation. It is
thought that this translational mechanism is essential for the survival of cells under stress [1].

Score:

22.6

E-value:

0.0012

From sequence:

509279

To sequence:

509373

Alignments:

                     v                                                                                         v  NC
                 :::((((((,,,,,~~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))))) CS
  RF00223      1 cgCcgGCcaAGACa*[154]**[15]*GAcUgCcUGcaacguugugcguuucUgcUGcCCaacUgGCuGGCAAGAUGAAGCUCUCCcUGGugGCcg 252   
                 C+CC GCC: G  +                           U+GU C  U C G+ GCCC ACUGGC G  AA  UG A   C  C UGG:GGC G
    chr11 509279 CACCGGCCGUGUGU*[ 10]**[ 8]*--------------UCGUCCACUGCCGUAGCCCGACUGGCAGAAAACGUGGA---CAGCUUGGCGGCAG 509362
                 ***********988....9.....6................5566777788899***************9999999876...88899********* PP

                             NC
                 ::::::::::: CS
  RF00223    253 CGaUGCUGCUG 263   
                   +UGCUGCUG
    chr11 509363 UAGUGCUGCUG 509373
                 *********** PP

>>

RNAfold
>chr11_5
GCAGGACGGUUUCGAUUCGGAGGAUGACGAUGACGCAUCUGUCGAGAGCA
GCGAUAGCCACUUCAGAUCCGGUGGACGUCUUCCACCGGCCGUGUGUGUG
GUGAACGUUCCUCUCUCGUCCACUGCCGUAGCCCGACUGGCAGAAAACGU
GGACAGCUUGGCGGCAGUAGUGCUGCUGGAAUCGCAGUGCAGUGUGCGCG
AGUUGGUCUCCGCCUCUGCCGCCGGUAGACACAACAGCAGCAGUGUCAGC
ACAGGGACAAAC
....(((((...((..(((........)))...))...)))))(((((.((((...(((((..((.((((((((((.....))))))))..)).)).)))))...)))).)))))..((((.(((.......(((..(((((((....(((((((((((((((.((.(.(((((((.......)))))))).))))).)))))))...))))).))))))).)))..(((((..........)))))....))))))).... (-98.40)

Length sequence

: 262

Length match:

93