M. Alm Rosenblad, C. Zwieb, T. Samuelsson (ref. Rosenblad,MA , Zwieb,C , Samuelsson,T )
"Identification and comparative analysis of
components from the signal recognition
particle in the lower eukaryotes".
BMC Genomics 2004 5:5
Acknowledgements T.cruzi : The source is the TIGR-SBRI-KI T. cruzi sequencing consortium (TSK-TSC). Chlamydomonas : These sequence data were produced by the US Department of Energy Joint Genome Institute, http://www.jgi.doe.gov/ and are provided for use in this publication/correspondence only. Giardia : Giardia lamblia Genome Project, Marine Biological Laboratory at Woods Hole, funded by the NIAID/NIH under cooperative agreement AI 043273.
Eimeria, Theileria, Leishmania : These sequence data were produced by the resp. Sequencing Group at the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/.
Candida albicans : Sequence data was obtained from the Stanford Genome Technology Center website at http://www-sequence.stanford.edu/group/candida. Sequencing of Candida albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund.
Table 1 update
SRP RNA sequences:
Predicted SRP RNAs (postscript, pdf)
Chlamydomonas reinhardtii :
The two found sequences, one of which is equal to X71484, may be folded according to the consensus structure, but the 5' end differs (GCGCC, GCC). Above is a folding where the first and last nucleotides (TTT) have been removed.
Plasmodium falciparum :
The found SRPRNA overlaps with the last exon of a putative RNAhelicase protein in the annotation. The last exon of this predicted protein is, however, not supported by homology to other proteins (not even in P.yoelii) and is therefore probably not correct.
The found Plasmodium SRPRNAs may be divided into three groups. Primary sequence alignments with additional sequences were made with clustalw. P.chabaudi is cut in the 5' end because contig ended there.
Additional SRP21 secondary structure predictions
SAMT02 (+ SRP9/14, with Birse et al. SS in alignment)
SSpro and SSpro8 (SRP21 from the same species as in manuscript)
Update of Table 1 with new candidates (these are not confirmed):
Organism SRPRNA SRP9/21 SRP14 SRP19 SRP54 SRP68 SRP72
-------- ------ ------- ---------------- -------- ----- ----- -----
Giardia lamblia p [e] ? ? EAA38699 + + +
Entamoeba histolytica + [f] ? ? + 81.m00151[d] + +
C. reinhardtii + + + 818 [a] + + +
Neurospora crassa + + +[XP_331181.1] + + + +
Aspergillus nidulans + EAA65246 EAA60923 [b] EAA65148 + + +
Candida + + + [c] + + + +
'+' = found according to paper; '?' = not yet found;
Accession given for new candidates found by blast searches (not confirmed in any other way!).
[a] scaffold_818 (from chlre1.fasta) join(30398..30415,30504..30579,30659..30729,301538..301634,302501..302691).
BLAST hits and Genscan prediction.
[b] Start of sequence does not match well to other SRP14 and structure prediction.
[c] Found in scrap file (by Blackwell, van Nues, Brown) not included in genome assembly.
[d] E.histolytica TIGR DB, temporary identifier. Pos 4026-5488 on assembly Scaffold 00081.
[e] S-domain identified
[f] SRP RNA identified in 5 Entamoeba species (unpublished)
Updated: 2004-Oct-20, MAR