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 = 38778483

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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
214504634 GT-AG 0 1.3528224450034462e-05 260 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 1 1243126 1243385 Zostera marina 29655 CAG|GTTCAATTTC...AATGTTTTAACT/AATGTTTTAACT...TGCAG|ATC 2 1 13.389
214504635 GT-AG 0 1.000000099473604e-05 69 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 2 1242887 1242955 Zostera marina 29655 CTG|GTACGTAGTA...ACATCATTGGTT/TCAACATTCAAT...TTTAG|GAG 1 1 25.121
214504636 GT-AG 0 2.694009213170145e-05 80 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 3 1242671 1242750 Zostera marina 29655 TAG|GTATGTGAAT...TAGTTCTTCACT/TAGTTCTTCACT...CACAG|GGC 2 1 34.507
214504637 GT-AG 0 5.341420883171136e-05 84 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 4 1242411 1242494 Zostera marina 29655 CAG|GTATTGCCAT...TTTATTTTAATC/TTTATTTTAATC...CTCAG|GTA 1 1 46.653
214504638 GT-AG 0 1.000000099473604e-05 45 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 5 1241855 1241899 Zostera marina 29655 AAG|GTGATGACCA...TTATTTATGATC/TATGAATTTATT...AACAG|ATT 2 1 81.919
214504639 GT-AG 0 0.0005194954093972 181 rna-gnl|WGS:LFYR|ZOSMA_1G01730_mrna 38778483 6 1241603 1241783 Zostera marina 29655 CTG|GTACAGTTTA...ACATCCTTACAT/TACTTACTTACT...TGCAG|GCA 1 1 86.818

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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]);