Transcript_101

cmscan-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:

271.6

E-value:

7.2e-74

From sequence:

1

To sequence:

299

Alignments:

                                                                           v        v                       v    v   NC
                     (((<<<<<<<<____>>>>>>>>,,,,<<<_________>>>)))-((((((((((-((((((((((((((((----((((((((-(((((-((( CS
         RF00017   1 gCcGGGcgcgguGgCgcgcgCCUGUAAuccaagcUaCUgggagGcuggggggggggggucgcgugcggccggGAguucugggccggcagcguccc 95 
                     GCCGGGCGCGGUGGCGCGCGCCUGUAAUCCAAGCUAC GGGAGGCU::G:::GG GG::CGC: G:G::C:GGAG UCUG:GC:  C GCG  C:
  Transcript_101   1 GCCGGGCGCGGUGGCGCGCGCCUGUAAUCCAAGCUACCGGGAGGCUGAGGCCGGCGGAUCGCUUGAGCUCAGGAGCUCUGUGCUG-CCGCGGACU 94 
                     *************************************************************************************.********* PP

                                              vv                v                  v                                 NC
                     ((((---((((((((((-(((((((((((((((<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>><<___>><<<<<<<---<<<<< CS
         RF00017  96 augccGAccgggcGuCcgcgcuaggcucggcGUcgacauggggcccccggcGGAGgccgggggccccaggucgccuAAggaGgggcGaAccggcc 190
                     AUGCCGA:C:GG:GUCCGC:CUA:G  CGG::UCGA:AUGG:G :CC:G :GGAG: C:GG: C:CCAG:UCGCCUAAGGAGGGG:GAAC:::CC
  Transcript_101  95 AUGCCGAUCGGGUGUCCGCACUAAGCUCGGUAUCGAUAUGGUGCUCCUGGGGGAGCUCGGGACCACCAGGUCGCCUAAGGAGGGGUGAACCGGCC 189
                     *********************************************************************************************** PP

                                                          vv                           v   v                     v   NC
                     ----<<<____>>>---->>>>>->>>>>>>))))))))))-)))))))---))))))))))))))))))))-)))))))))))))))))--))) CS
         RF00017 191 cAGGgcgGAAAcgcAGCAggcagAAgcccCcGCgccgagccGuagcggGAUagCgcccgggaaugggcgcugCcggcccagCccggccgauAacg 285
                     CAGG:CGGAAACG:AGCAGG:::AA:CCCCCG::CCG  C:GUAG:GGGAU GC:CC:G:GAAU:G CGC G  :GC:CAGCC:G::C:A+A :G
  Transcript_101 190 CAGGUCGGAAACGGAGCAGGUCAAAGCCCCCGUGCCGCUCAGUAGUGGGAUCGCGCCUGUGAAUAGACGCUG-UAGCGCAGCCUGAGCAACACAG 283
                     ************************************************************************.********************** PP

                          v           NC
                     )))))))))))))):: CS
         RF00017 286 cgacacccccccccUU 301
                     CG::A CC:::C::UU
  Transcript_101 284 CGGGACCCGGUCUUUU 299
                     **************** PP

RNAfold
>Transcript_101
GCCGGGCGCGGUGGCGCGCGCCUGUAAUCCAAGCUACCGGGAGGCUGAGG
CCGGCGGAUCGCUUGAGCUCAGGAGCUCUGUGCUGCCGCGGACUAUGCCG
AUCGGGUGUCCGCACUAAGCUCGGUAUCGAUAUGGUGCUCCUGGGGGAGC
UCGGGACCACCAGGUCGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAA
CGGAGCAGGUCAAAGCCCCCGUGCCGCUCAGUAGUGGGAUCGCGCCUGUG
AAUAGACGCUGUAGCGCAGCCUGAGCAACACAGCGGGACCCGGUCUUUUG
(((...(.(((((((.................))))))).).))).((((((((.(..(((((((.(((((((....(((((((((.(((..((((......(((((((((.(((((....((((((((((.(((((.(((((((....))))))).))))).))))........(((((.....((((....(((....)))....))))...))))).)))))).....)))))))...)))))))...)))).))).))))))))))))))))..)).)))))..)))))))))... (-142.53)

Length sequence

: 300

Length match:

297