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)

7 rows where transcript_id = 17888380

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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
95730660 GT-AG 0 4.81690848752496e-05 190 rna-XM_047275916.1 17888380 2 40042824 40043013 Hydra vulgaris 6087 GCA|GTAAGTAAAA...TTATTTTTAATA/TTATTTTTAATA...CACAG|ACC 0 1 5.334
95730661 GT-AG 0 1.000000099473604e-05 689 rna-XM_047275916.1 17888380 3 40042024 40042712 Hydra vulgaris 6087 AAG|GTGAGGTAGT...TTTCTTTTAAAT/ATTTTACTAAAT...TTTAG|CTG 0 1 8.641
95730662 GT-AG 0 4.665584296295641e-05 240 rna-XM_047275916.1 17888380 4 40041637 40041876 Hydra vulgaris 6087 GAT|GTAAATTTTG...ATATATATATAT/TATATATATATA...TATAG|GCA 0 1 13.021
95730663 GT-AG 0 1.000000099473604e-05 132 rna-XM_047275916.1 17888380 5 40040847 40040978 Hydra vulgaris 6087 CTG|GTAAGATTTT...AGTTTTTTAAAA/AAATGATTCATT...ACTAG|GAT 1 1 32.628
95730664 GT-AG 0 1.000000099473604e-05 171 rna-XM_047275916.1 17888380 6 40040434 40040604 Hydra vulgaris 6087 AAG|GTTAGTACGA...TTTTTTTTTTCT/TAATCGCTGAGA...TTTAG|AGA 0 1 39.839
95730665 GT-AG 0 1.000000099473604e-05 745 rna-XM_047275916.1 17888380 7 40039519 40040263 Hydra vulgaris 6087 CAG|GTTAGTTTAC...ATGTTTTTAAAT/ATTATATTGATA...TTTAG|CTA 2 1 44.905
95730666 GT-AG 0 1.000000099473604e-05 110 rna-XM_047275916.1 17888380 8 40037687 40037796 Hydra vulgaris 6087 CAG|GTAAAATATA...ATAACATTAGAC/ACAAAATTTATT...TTAAG|ACA 2 1 96.216

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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]);