chr2_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:

20.3

E-value:

0.0062

From sequence:

250534

To sequence:

250440

Alignments:

                     v                                                                                         v  NC
                 :::((((((,,,,,~~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))))) CS
  RF00223      1 cgCcgGCcaAGACa*[154]**[15]*GAcUgCcUGcaacguugugcguuucUgcUGcCCaacUgGCuGGCAAGAUGAAGCUCUCCcUGGugGCcg 252   
                 CGC: G::A GAC                 UG  U C+A G+UG GC    C  CUG+CC ACU G UGGC   A GA GCUC C C G U::C :
     chr2 250534 CGCUGGUGAUGACG*[  2]**[ 2]*---UGAGUACGAUGCUGGGCAGCGCCUCUGACCCACUCGUUGGCGUCACGACGCUCACACGGCUCACAG 250451
                 **************....9.....8.....566677788888888899999999****************************************** PP

                             NC
                 ::::::::::: CS
  RF00223    253 CGaUGCUGCUG 263   
                 CG  GCUG   
     chr2 250450 CGUAGCUGAAC 250440
                 *********** PP

>>

RNAfold
>chr2_5
GCCUCAAGCGCGCCACCGCUGUCUCUAUCGCUGCCUUCGCUGGAGCAGUU
UGUGUCCGUAGCACUGGUGGACGAAAACGCCCCGUUCAGCUACGCUGUGA
GCCGUGUGAGCGUCGUGACGCCAACGAGUGGGUCAGAGGCGCUGCCCAGC
AUCGUACUCAGCUCCGUCAUCACCAGCGAUACGGCGACGGCGGCCACCAG
CGUUGCUGCUGCGUCUGACGCGAGCACGAAGGACGAAGAGGCUGAAGGUC
GCCGCUGCGCAA
((....((((.((.(((...((((((.(((...((((((((((.(((((.......((((((..(((.((.((....)))))))....))))))((.(((.((((((..((((....))))..)))..))).))).))..))))))))))..........(((((((((..((((((.....(((((((..((...))..))))))))))).)).))))).))))..))))).)))))))))....))).))))))..)).. (-104.00)

Length sequence

: 262

Length match:

93