The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand

Capone, Giovanni; Novello, Giuseppe; Fasano, Candida; Trost, Brett; Bickis, Mik; Kusalik, Anthony; Kanduc, Darja

doi:10.1186/1471-2105-11-383

Table 1 The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand

From: The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand

Organisms hosting the ATGTGGCATATGTGC oligodeoxynucleotide coding for MWHMC pentapeptide:
Taxonomic ID	Organism	Location of the oligodeoxynucleotide:
		DNA minus strand	Intron	Pseudogene	Frameshift	UTRs
293826	Alkaliphilus metalliredigens (1)	+
491915	Anoxybacillus flavithermus (1)	+
290318	Chlorobium phaeovibrioides (1)				+
7719	Ciona intestinalis (1)					+
37769	Cryptococcus bacillisporus (1)	+
7955	Danio rerio (1)				+
352472	Dictyostelium discoideum (1)	+
7220	Drosophila erecta (1)	+
7227	Drosophila melanogaster (1)	+
7238	Drosophila sechellia (1)	+
7240	Drosophila simulans (1)	+
7245	Drosophila yakuba (2)	+			+
9595	Gorilla gorilla gorilla (1)	+
9606	Homo sapiens (4)	+++		+
9544	Macaca mulatta (1)	+
10090	Mus musculus (2)	++
39947	Oryza sativa Japonica (3)	++	+
1308	Streptococcus thermophilus (2)	+			+
9823	Sus scrofa (1)	+
377629	Teredinibacter turnerae (1)	+
296543	Thalassiosira pseudonana (1)	+
Organisms hosting the TGGTTTCAGTGCATG oligodeoxynucleotide coding for WFQCM pentapeptide:
Taxonomic ID	Organism	Location of the oligodeoxynucleotide:
		DNA minus strand	Intron	Pseudogene	Frameshift	UTRs
315750	Bacillus pumilus (1)					+
3708	Brassica napus (1)	+
485918	Chitinophaga pineni (1)	+
8330	Cynops pyrrhogaster (1)	+
7955	Danio rerio (3)	++				+
9685	Felis catus (1)	+
69293	Gasterosteus aculeatus (1)	+
233412	Haemophilus ducreyi (1)				+
9606	Homo sapiens (7)	+++++++
284590	Kluyveromyces lactis (2)	+			+
9544	Macaca mulatta (1)	+
269797	Methanosarcina barkeri (1)	+
10090	Mus musculus (5)	+++++
7955	Nicotiana plumbaginifolia (1)	+
9598	Pan troglodytes (1)	+
500485	Penicillium chrysogenum (2)	+				+
3988	Ricinus communis (1)				+
29760	Vitis vinifera (2)	+				+
8364	Xenopus tropicalis (1)	+

The never-expressed MWHMC and WFQCM pentapeptides are reported as examples. Pentapeptide sequences were retrotranslated into the most likely pentadecameric oligodeoxynucleotide coding sequences. Then, each pentadecameric oligodeoxynucleotide sequence was used as a probe to scan the entire NCBI nucleotide collection for exact pentadecameric matches using BLAST (blastn) program with no gaps allowed. The organism hosting the oligodeoxynucleotide sequence(s) is identified by its taxonomic identification number and latin name. Plus sign(s) indicate the oligodeoxynucleotide location(s) in the DNA. Abbreviation: UTRs, untranslated regions. Total number of oligodeoxynucleotide sequence occurrences is in parentheses. See also Additional file 1, Table S1.

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ISSN: 1471-2105

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