Description and display conventions
NumtS (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear
genomic sequences. The most credited hypothesis concerning their generation suggests that in presence
of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach
the nucleus and insert into chromosomes during break repair; although NumtS can also derive from
duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing
and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group
chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus
NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access
the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the
group has designed the Mouse NumtS tracks described below.
The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs)
obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the
mouse genome.
- "NumtS (Nuclear mitochondrial Sequences)" Track
The "NumtS
mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear
genome. The shading of the items reflect the similarity returned by BlastN, and the direction of
the arrows is concordant with the strand of the alignment. For every item, a link pointing to the
mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts.
- "NumtS assembled" Track
The "NumtS assembled" track shows items obtained by
assembling HSPs annotated in the "NumtS" track fulfilling the following conditions:
- The orientation of their alignments must be concordant.
- The distance between them must be less than 2 kb, on the mitochondrial genome as
well as on the nuclear genome.
Exceptions for the second condition arise when a long repetitive element is present between
two HSPs.
- "NumtS on mitochondrion" Track
The "NumtS on mitochondrion" track shows the mapping
of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned
by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every
item, a link pointing to the nuclear mapping is provided.
- "Mouse NumtS on mitochondrion SNP" Track
The "Mouse NumtS SNP" shows the mapping of
the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison
with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear
mapping is provided.
Methods
NumtS mappings were obtained by running Blast2seq (program: BlastN) between
each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC:
NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with
spreadsheet interpolation and manual inspection. BED format is used for the first three annotation
tracks, while for the last one the SAM/BAM format is preferred.
Credits
These data were provided by Francesco Maria Calabrese, Domenico Simone and
Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto
Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out
by Francesco Maria Calabrese, Domenico Simone and Luana Raddi.
References
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human
NumtS.
BMC Genomics. 2008 Jun 3;9:267.
PMID: 18522722; PMC: PMC2447851
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.
The reference human nuclear mitochondrial sequences compilation validated and implemented on the
UCSC genome browser.
BMC Genomics. 2011 Oct 20;12:517.
PMID: 22013967; PMC: PMC3228558
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