Spectral Analysis of DNA Sequence: The Exon's Location Method
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Abstract:
The system's analysis concepts based on signal processing methods are considered as very important tools in the genomic field's exploration. Spectral analysis of DNA sequences reveals genome's specific periodicities. Studying one organism's genome requires three steps. First, the DNA coding method: the DNA's string data are transformed into numerical signal. Second periodicities are detected by spectral analysis. Third, following the evolution of this periodicity along the genome allows the exon's, or protein coding region's, location. In this paper, we expose the exon's location method: including the coding and spectral analysis steps. After, we propose a two dimensional graphical representation for the spectrum. The experimental result including a variety of coding indicator's methods reveals the importance of each base's combination, from one base to four group bases, in the exon's enhancement. The contributions in percent of each of this group's indicator are finally estimated.Keywords:
Coding region
genomic DNA
To investigate the structure and sequence of SCF gene in goat, primers were designed based on the sequence of goat and sheep. Two transcript splices were obtained with PCR and cloning and bioinformatics analysis of the sequence was made. The results showed that the length of coding sequence of soluble and transmembrane SCF gene in goat is 825 bp and 741 bp, respectively. The length difference was due to the deletion / insertion of 6th exon. The identity of SCF gene between goat and sheep or cattle was 98% and 97%, respectively. The phylogenetic clusters based on SCF gene sequence of thirteen species were the same as the zootaxy.
Cloning (programming)
Coding region
Sequence (biology)
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Sequence (biology)
Complete sequence
Alignment-free sequence analysis
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Single-strand conformation polymorphism
Coding region
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WE present the genomic structure of the human glutamate transporter GLT-1 coding region, the intronic sequences adjacent to the exons, and oligonucleotide primer sequences for single strand conformational analysis. The exon–intron boundaries were determined using long-distance PCR and direct sequencing. The human GLT-1 coding region is composed of 10 exons spanning > 50 kb of genomic DNA. The exons range from 127 to 251 bp in length. The intron lengths vary considerably from 2.2 kb to > 15 kb. These data provide the basis for implementing a comprehensive screen for genetic alterations in the human GLT-1 gene using genomic DNA as a template.
genomic DNA
Coding region
Primer (cosmetics)
Genomic Organization
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Overlapping genomic clones have been isolated that contain the alpha chain and COOH-terminal propeptide coding regions of the chicken type II procollagen gene. All type II procollagen exon sequences present in these clones have been identified and mapped by DNA sequencing. These include 43 exons coding for the alpha-chain triple helix, 1 exon coding for the junction between the COOH-terminal propeptide and the alpha-chain region, and 3 exons coding for the COOH-terminal propeptide and 3' noncoding sequences. With the exception of one additional intron between 2 exons coding for amino acids 568-585 and 586-603, exon-intron boundaries have been conserved when compared with genes for all other characterized genes for fibrillar collagens. The chicken type II procollagen gene differs from most other collagen genes in having introns of considerably smaller average size. The size distribution of the introns suggests that approximately equal to 80 base pairs may be a minimal functional size for introns in this gene. This size of intron may be necessary in a gene with a very large number of small exons to prevent aberrant splicing from removing exon sequence together with intron sequence.
Coding region
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With reference to the human interleukin 18 gene in GeneBank database, a pair of DNA primers was designed and synthesized. A 481bp fragment containing hIL-18 gene was successfully amplified by using RT-PCR and then cloned into PGEM-T plasmid, enzyme digested by EcoR I and Sal I indicated that there is one nucleotide different from the published hIL-18 cDNA sequence. The sequence analysis indicated that in the sequence of IL-18- PGEM-T contains all the coding sequence for mature protein of hIL-18. The result would promote the further research in molecular biology of hIL-18, such as the expression and the biological function research.
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Sequence (biology)
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We have isolated and characterized a segment of the chick alpha 2 collagen gene by screening a library of chick genomic fragments using as hybridization probe an alpha 2 collagen cDNA clone. Several clones were isolated and one of them, lambda gCOL 204, was used for further studies. The DNA of lambda gCOL 204 hybridizes to a unique species of mRNA the size of alpha 2 collagen mRNA. This mRNA can be translated into a unique polypeptide which comigrates in SDS-gel electrophoresis with pro-alpha 2 collagen. Electron microscopic analysis by R-loop technique indicates that lambda gCOL 204 contains 7Kb of the alpha 2 collagen gene. This 7 Kb piece constitutes the 3' end of the gene. The same clone also contains 9 Kb of DNA that is immediately adjacent to the 3' end of the alpha 2 collagen gene. The cloned segment of the alpha 2 collagen gene is interrupted by 8 intervening sequences of various lengths. The coding sequences for collagen in this clone add up to approximately 1,800 bp, which correspond to about 1/3 of alpha 2 collagen mRNA. DNA sequence analysis of a small coding segment of lambda g COL 204 reveals a characteristic collagen type sequence which encodes for an amino acid sequence identical to a sequence found in calf alpha 2 collagen. The sequence of this region of the protein has not yet been determined for the chick alpha 2 collagen.
genomic DNA
Coding region
Type I collagen
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genomic DNA
Coding region
Homology
Genomic Organization
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Analysis of the structure of the 3′‐end of the human α 2 (IV) gene demonstrated that the α 1 (IV) and α 2 (IV) genes have diverged extensively in spite of the apparent homology of the respective gene products. The NC‐1 domain and the 3′‐untranslated region are encoded by three exons in the α 2 (IV) gene but five exons in the α 1 (IV) gene. The two introns present in the NC‐ 1 domain coding part of the α 2 (IV) gene had the same location as two of the introns of the α 1 (IV) gene. The junction exon in the α 2 (IV) gene contains 53 bp coding for Gly‐X‐Y sequences whereas there are 71 bp in the α 1 (IV) gene. Three other Gly‐X‐Y coding exons studied from the human ⇌ 2 (IV) gene have sizes that differ from corresponding exons in the α 1 (IV) gene and only one intron location matches here between the two genes. None of the exons studied has 54 bp or multiples thereof.
Coding region
Homology
Exon trapping
Gene prediction
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Coding region
Exon shuffling
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