introns

Data license: ODbL · Data source: Larue & Roy, 2023 · About: Minor Intron Database (WtMTA)

id
INTEGER (primary key), globally unique identifier for each intron
dinucleotide_pair
TEXT, terminal dinucleotide sequences of the intron
is_minor
INTEGER, indicates if the intron is a minor intron (1) or not (0)
score
REAL, score representing the probability (0-100%) of the intron being minor
length
INTEGER, length of the intron in base pairs
transcript_id
INTEGER (foreign key referencing transcripts(id)), parent transcript
ordinal_index
INTEGER, ordinal position of the intron within the transcript (e.g., 3 for the third intron)
start
INTEGER, start position of the intron in the genome
end
INTEGER, end position of the intron in the genome
taxonomy_id
INTEGER (foreign key referencing genomes(taxonomy_id)), NCBI taxonomy identifier for species
scored_motifs
TEXT, motifs scored for the intron
phase
INTEGER, phase of the intron in coding sequence (0, 1, or 2 or null for introns outside of coding sequence)
in_cds
INTEGER, indicates if the intron is within the coding sequence (1) or not (0; e.g., UTR introns)
relative_position
REAL, relative position of the intron within the transcript (as a percentage of coding length)

9 rows where transcript_id = 8855886

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id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
47813009 GT-AG 0 0.0080698296546339 1093 rna-XM_027248848.1 8855886 1 39329924 39331016 Coffea arabica 13443 AAG|GTCTGCTTCT...ATTCTTTTAATG/ATTCTTTTAATG...CACAG|GTG 1 1 4.155
47813010 GT-AG 0 0.1652195655461292 406 rna-XM_027248848.1 8855886 2 39332709 39333114 Coffea arabica 13443 CAG|GTATACTTTT...TCTTTCTTCACA/TCTTTCTTCACA...CACAG|GAG 1 1 45.024
47813011 GT-AG 0 1.000000099473604e-05 111 rna-XM_027248848.1 8855886 3 39333375 39333485 Coffea arabica 13443 GTG|GTTAGTCCAT...TGCCCGTTAATA/ACGAGTCTCATC...TATAG|GTA 0 1 51.304
47813012 GT-AG 0 8.510227356526232e-05 124 rna-XM_027248848.1 8855886 4 39333696 39333819 Coffea arabica 13443 GAG|GTATTGTCAA...GCTGTTGTAATT/ACCAAATTCATC...TCCAG|ATC 0 1 56.377
47813013 GT-AG 0 1.000000099473604e-05 390 rna-XM_027248848.1 8855886 5 39334039 39334428 Coffea arabica 13443 CCT|GTGAGTATTA...GTTTCCATAGCC/CAAGAACTAACA...GTTAG|GTT 0 1 61.667
47813014 GT-AG 0 0.7862437083271296 602 rna-XM_027248848.1 8855886 6 39335395 39335996 Coffea arabica 13443 CAG|GTATCTTTCA...CCTCTTTTCACA/ACATATTTCATT...TGTAG|GCA 0 1 85.0
47813015 GT-AG 0 2.043677427505433e-05 207 rna-XM_027248848.1 8855886 7 39336093 39336299 Coffea arabica 13443 GAG|GTAAATTTGT...TGTTTTTTGTTT/TTTGGTCTCAGA...TGCAG|GTA 0 1 87.319
47813016 GT-AG 0 1.000000099473604e-05 185 rna-XM_027248848.1 8855886 8 39336399 39336583 Coffea arabica 13443 CAG|GTTAGTGAGC...GAGTTCATAGCC/ACTGAGTTCATA...TACAG|ATC 0 1 89.71
47813017 GT-AG 0 0.1615535049560145 657 rna-XM_027248848.1 8855886 9 39336774 39337430 Coffea arabica 13443 AAG|GTATCTCTGC...GATTTTTAAGCT/GGATTTTTAAGC...TGTAG|CCT 1 1 94.3

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CREATE TABLE "introns" (
"id" INTEGER,
  "dinucleotide_pair" TEXT,
  "is_minor" INTEGER,
  "score" REAL,
  "length" INTEGER,
  "transcript_id" INTEGER,
  "ordinal_index" INTEGER,
  "start" INTEGER,
  "end" INTEGER,
  "taxonomy_id" INTEGER,
  "scored_motifs" TEXT,
  "phase" INTEGER,
  "in_cds" INTEGER,
  "relative_position" REAL
  ,PRIMARY KEY ([id]),
   FOREIGN KEY([transcript_id]) REFERENCES [transcripts]([id]),
   FOREIGN KEY([taxonomy_id]) REFERENCES [genomes]([taxonomy_id])
);
CREATE INDEX [idx_introns_transcript_id]
    ON [introns] ([transcript_id]);
CREATE INDEX [idx_introns_taxonomy_id]
    ON [introns] ([taxonomy_id]);
CREATE INDEX [idx_introns_phase]
    ON [introns] ([phase]);
CREATE INDEX [idx_introns_is_minor]
    ON [introns] ([is_minor]);
CREATE INDEX [idx_introns_dinucleotide_pair]
    ON [introns] ([dinucleotide_pair]);
CREATE INDEX [idx_introns_score]
    ON [introns] ([score]);
CREATE INDEX [idx_introns_in_cds]
    ON [introns] ([in_cds]);