chr5_3

cmsearch-Rfam

Family :

Metazoa_SRP

Id:

RF00017

Type:

Gene;

Taxonomy:

Eukaryota; Archaea;

Ontology:

GO:0006617 SRP-dependent cotranslational protein targeting to membrane, signal sequence recognitionRF00017

Description:

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational
targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and
six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a
7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. Eukaryotic and archaeal 7S
RNAs have very similar secondary structures, as represented by this family. Eight helical elements fold
into the Alu and S domains, separated by a long linker region [1,2]. The Alu
domain is thought to mediate the peptide chain elongation retardation function of the SRP [1].
The universally conserved helix which interacts with the SRP54 M domain mediates signal sequence recognition
[2,3]. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in
SRP assembly and stabilises helix 8 for SRP54 binding [1]. The Signal Recognition Particle Database
(SRPDB) [4] provides compilations of SRP components, with phylogenetic data and structural illustrations. Many sequences
below the threshold for this family are clearly closely related, but are most likely to
be SRP RNA derived pseudogenes. The human genome in particular is known to contain a
large amount of SRP RNA related sequence, including Alu repeats. While the threshold of this
family is set high so as to minimise the number of hits to such regions,
it is likely that some remain.

Score:

61.1

E-value:

2.3e-13

From sequence:

350314

To sequence:

350036

Alignments:

                         vvv    vvv                            vvvv    vv v    v    v          vvvv  v  v    vv   NC
                 (((<<<<<<<<____>>>>>>>>,,,,<<<_________>>>)))-((((((((((-((((((((((((((((----((((((((-(((((-(((( CS
  RF00017      1 gCcGGGcgcgguGgCgcgcgCCUGUAAuccaagcUaCUgggagGcuggggggggggggucgcgugcggccggGAguucugggccggcagcguccca 96    
                 GCCGG:::       G+ :::CUGUAA:C        U  G:GGCU+   :GG:  G :CG  :::G+C::GGA   :    :: G  GCG+  ::
     chr5 350314 GCCGGAGC-------GUUGCUCUGUAACCU-------UCGGGGGCUUCCUAGGUG-GAGCGGGGGUGUCGUGGACCAGCGAGGGUG--GCGCGCUG 350236
                 *****997.......34589*******999.......45999***5545544444.445555555666777778666544333333..3344679* PP

                              v      vv   v                 vv                    vv          v     vv v          NC
                 (((---((((((((((-(((((((((((((((<<<.<<<<<<<<<<<<<<<____>>>>>....>>>>>>>>>>>>><<___>><<<<<<<---<< CS
  RF00017     97 ugccGAccgggcGuCcgcgcuaggcucggcGUcga.cauggggcccccggcGGAGgccgg....gggccccaggucgccuAAggaGgggcGaAccg 187   
                 :G:+GAC::GG:G :C :GC  GGC ::G:GUCG: :: G:::  CCC:::G AG:::GG    G  :::C :::CG+: AA:  G :G::AAC::
     chr5 350235 CGUUGACGCGGUGCUC-UGCUUGGCUGUGUGUCGGuGUGGCCUGCCCCCCUGUAGAGGGGugucGU-AGGCUACCCGUUGAAG-CGAGGGAAACCG 350143
                 *************998.88****************4555555555577*********987334344.55555559**999987.7788888999** PP

                                                v v      v     vv        v            vv     v  v  vvvv      v    NC
                 <<<----<<<____>>>---->>>>>->>>>>>>))))))).)))-)))))))---)))))))))))))))..)))))-))))))))))))))))) CS
  RF00017    188 gcccAGGgcgGAAAcgcAGCAggcagAAgcccCcGCgccga.gccGuagcggGAUagCgcccgggaauggg..cgcugCcggcccagCccggccga 280   
                 G::CAGG:CGGAAACG:A CA::C:: ::C: C GC:C::  GCCG  GC:G:AU  C:CC::G:A:::    CGC+   ::    :CC::G C::
     chr5 350142 GGUCAGGCCGGAAACGGAACAGCCCA-UCCUGC-GCACGUCcGCCGUUGCAGAAUCACGCCGCGGAGCAUGacCGCA--CUUGAGCCCCACG-CGC 350052
                 *************************8.677776.99999767*******8899****************77544443..3333333344443.333 PP

                    v    vvv    vvvv   NC
                 --))))))))))))))))):: CS
  RF00017    281 uAacgcgacacccccccccUU 301   
                   :  CG: A :CC:    UU
     chr5 350051 --CGUCGCAAAACCUU---UU 350036
                 ..33333334444444...** PP

RNAfold
>chr5_3
GCGCCUCCGGAAAAGGUUUUGCGACGGCGCGUGGGGCUCAAGUGCGGUCA
UGCUCCGCGGCGUGAUUCUGCAACGGCGGACGUGCGCAGGAUGGGCUGUU
CCGUUUCCGGCCUGACCCGGUUUCCCUCGCUUCAACGGGUAGCCUACGAC
ACCCCUCUACAGGGGGGCAGGCCACACCGACACACAGCCAAGCAGAGCAC
CGCGUCAACGCAGCGCGCCACCCUCGCUGGUCCACGACACCCCCGCUCCA
CCUAGGAAGCCCCCGAAGGUUACAGAGCAACGCUCCGGCUUGCAAAGCGC
((((..(((((....((((((.(((....((.((((((....((((((((((((....)))))))..)))))...((((..(((((..((((.((((((((.((....((((((.((.((((.(((..........))).)))).......(((((....)))))))))))))..)).))...)))))).(((.(((...(((((.......))))).....)))))).)))).)).)))..))))(((.....)))))))))))...))).)))))).....)))))........)))) (-109.70)

Length sequence

: 300

Length match:

277