PRKN gene Introns in families from Order Primates show common Open Reading Frames

Supplementary material:

01 Supplementary material. Contains Table 1, named: “PRKN gene determined in Primates in Gene database NCBI. Supplementary material”. Data are shown for the primate species identified for this study. In addition, a Folder with title “PRKN database”, that contains the subfolders of the 34 primate species for which the PRKN gene was reported until April 2023. Species used for this study are indicated with the title “0 Selected-species”, and those not used only with the species name. In turn, all have four subfolders:

01 PRKN gene and mRNA variants-Fasta format: contains the sequences of the mRNA variants in FASTA format and of the PRKN gene.

02 Alignment PRKN gene and mRNA variants: contains the PRKN gene and mRNA sequences in FASTA format and the result of the alignment between the gene and the variants. Additionally, a Word document with the manual verification of the previous result. This document is not included in the primate species folders that were not used in this study.

03 PRKN aminoacid variants-Fasta format: contains the amino acid sequences of the PRKN gene variants in FASTA format.

04 PRKN Protein variants domains: contains documents with the graphical representation of the PRKN isoform domains, in Scalable Vector Graphic (SVG) format.

02 Supplementary material. Table 2 in Excel document containing the positions of the introns and exons of PRKN gene the 16 primate species used in this study. The first sheet contains the size of the introns/exons and their location by species. In the following sheets, the species name, intron/exon position and size are indicated.

03 Supplementary material. Contains two files:

Figure 1. Document with the alignments of the Primate PRKN proteins encoded by each mRNA variant. Also, are indicated the amino acids whose codons contain the intron with their respective phase.

Table 3, named “Intron Phase for PRKN gene”, in Excel document containing the phases, codons, their respective amino acids and the location of the introns of the primate PRKN gene. The first sheet contains the consensus data for each species, grouped according to families. In the following sheets, the species name, the Phases, the codon and the respective amino acid for each intron are indicated. Phases 0, 1, and 2 are indicated in purple, red, and green letters, respectively. To Phases 1 and 2, the position of the intron in the codon is indicated with a vertical bar, whereas, for Phase 0, each codon is in separate boxes. The mRNA variants that showed loss or fusion of introns are indicated as “Non determine”. Variants with alternatively spliced mRNA and phase change are indicated in yellow boxes.

04 Supplementary material. Contains two Excel documents and a subfolder with the putative PRKN introns Open Reading Frame (ORF):

Excel file: Table 4, named “Positive ORFs”. The first sheet contains the general data of 5’-3’ and 3’-5’ ORFs, characterized for each species by intron and organized by families. The second sheet corresponds to the total number of exons determined for each ORF, with the previously mentioned organization. The additional sheets are divided by intron and the species are organized by families along with the different characterized ORFs.

Excel file: Table 5 named “ORFs Introns”. In the first sheet, the number of ORFs of the introns is indicated, according to the grouping performed in this study. The other Sheets correspond to both unique and common ORFs determined for each species per intron, organized by family.

Subfolder named “ORFs alignments”: Contains the alignments between the ORFs of each intron by species. Exclusive and common ORFs are also indicated.

05 Supplementary material. Contains two Excel documents with putative functional sites of PRKN introns ORFs protein:

Excel file: Table 6 named “Family Common Functional Sites”. The first sheet contains the general information of the functional sites characterized in the ORFs, determined in the introns of each species ordered by family. Also, the total count of ORFs per family. The other sheets correspond to the categories of cellular processes. Within these are the functional site according to the species that presented it, ordered by family and the total count of each site.

Excel file: Table 7 named “Protein Domain ORFs”. Functional sites determined only for ORFs common to two or more species are found. The position of each functional site is indicated according to the amino acid sequence and in relation to each species.

06 Supplementary material. Contains two subfolders that comprise BLAST and Protein Data Bank search from mRNA and PRKN ORF intron proteins:

BLAST subfolder comprises  a Word document and 7 plain text documents. The Word document corresponds to the sequences reported in the Transcriptome Shotgun Assembly protein (tsa_nr) and Expressed sequence tags (est) databases, for ORFs that are common between Homo sapiens and the other species, according to the intron. The plaintext-like documents correspond to BLAST analyses that yielded more than six sequences similar to the reference ORF. The documents are named according to the sequences analyzed: the ORF name and database (Protein or Nucleotide).

Protein Data Bank subfolder. Contains 6 files in .PDF format, that correspond to protein structures that showed similarities with human ORFs 32 and 11, from Introns 6 and 9, respectively. Each document contains the protein structure information indicated in the Protein Data Bank (PDB) and the amino acid alignment between the Intron ORF sequence and the PDB protein sequence. The documents are named according to the protein ID obtained in the PDB and the respective ORF.