chr36_3

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:

20.5

E-value:

0.0052

From sequence:

1994043

To sequence:

1993928

Alignments:

                       v  v                                                                                 v  v NC
                  :::((((((,,,,,~~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))) CS
  RF00223       1 cgCcgGCcaAGACa*[154]**[15]*GAcUgCcUGcaacguugugcguuucUgcUGcCCaacUgGCuGGCAAGAUGAAGCUCUCCcUGGugGC 250    
                  + CC:  C AGAC                  G CUGCA C U G  C U    GC G C  AC   CU GCAA AUGAAGC   C+ UG  G  
    chr36 1994043 UUCCCUUCAAGACG*[ 11]**[16]*----GACUGCACCUUGGCACUUACGAGCAG-CGUACACUCUUGCAACAUGAAGCAUGCUAUGAAGGU 1993941
                  **************....*.....9......56677777777777777777777766.46677888999************************* PP

                                NC
                  ))::::::::::: CS
  RF00223     251 cgCGaUGCUGCUG 263    
                  :GCGAUGC GCUG
    chr36 1993940 GGCGAUGCAGCUG 1993928
                  ************* PP

>>

RNAfold
>chr36_3
UCCACCCACCCCACGGCGCCUCCGACAUUCCGUGGGAGUAGAGGUGAUCG
UUGAUGGUGACCACGCCGCUCUCCAGCUGCAUCGCCACCUUCAUAGCAUG
CUUCAUGUUGCAAGAGUGUACGCUGCUCGUAAGUGCCAAGGUGCAGUCGU
UCGCCAUCUGGAUACCCUCUUCCUCCGUCUUGAAGGGAACGACGGGGAGA
AUCGGUCCGAAGGUCUCCUCCUUCAUAAUACGCAUCGUUGGCGUGCAGCC
GCUGAGGACCGUG
.......(((((((((.............))))))).))(((((..(((...((((((((..(((..........((((((((..((((((..(((((((...))))))).))).)))..((((.......))))....)))))))))))))))))))..)))..)))))(((((((((((......)).))))))).))..(((((((((((......)))))..........(((.((((.....)))).))))))))).. (-88.00)

Length sequence

: 263

Length match:

114