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)

6 rows where transcript_id = 2158729

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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
11719740 GT-AG 0 1.000000099473604e-05 78 rna-XM_008863744.1 2158729 1 2712613 2712690 Aphanomyces invadans 157072 ATG|GTGCGTAGGT...AAAGACTTAAAT/ACTTAAATGATC...CATAG|CCA 2 1 3.811
11719741 GT-AG 0 1.000000099473604e-05 52 rna-XM_008863744.1 2158729 2 2711118 2711169 Aphanomyces invadans 157072 TCG|GTGCGTCGTC...TTTTTTTCAGAG/ATTTTTTTCAGA...CGTAG|GTG 2 1 38.616
11719742 GT-AG 0 0.0018654376322673 52 rna-XM_008863744.1 2158729 3 2710637 2710688 Aphanomyces invadans 157072 TGG|GTATGCCAAT...GTGTCTTTGGTT/TGGTTGCTAACA...CGTAG|CCT 2 1 48.963
11719743 GT-AG 0 0.0033711315956621 59 rna-XM_008863744.1 2158729 4 2709832 2709890 Aphanomyces invadans 157072 GCG|GTACGTTTTG...CATGCCTCGACG/GACGTGCTGACG...GCCAG|GTG 1 1 66.956
11719744 GT-AG 0 0.0021569611252915 64 rna-XM_008863744.1 2158729 5 2709547 2709610 Aphanomyces invadans 157072 TTT|GTACGTTTTT...GCATGCGTGATG/GGAGAGCTGACG...GCTAG|GGC 0 1 72.287
11719745 GT-AG 0 1.3940751176220803e-05 52 rna-XM_008863744.1 2158729 6 2709294 2709345 Aphanomyces invadans 157072 CAT|GTAGATGCAT...GCGTCCTGGACG/ACGATTCTTACA...CGTAG|ACG 0 1 77.135

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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]);