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)

130,224 rows where taxonomy_id = 4555

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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]);