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 = 38778435

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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
214504278 GT-AG 0 0.0002409980473306 94 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 1 491535 491628 Zostera marina 29655 TAG|GTATGTACGT...TATTCATTATTT/TTTTATCTCAAT...AATAG|AGA 1 1 39.787
214504279 GT-AG 0 1.485125193559173e-05 86 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 2 491299 491384 Zostera marina 29655 TTG|GTACTGATTA...TAAGATTTGATT/TGGTTACTGATT...ATTAG|GAG 1 1 47.065
214504280 GT-AG 0 1.000000099473604e-05 116 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 3 491031 491146 Zostera marina 29655 AAG|GTACGTACGT...TAAACCTAAATA/GTTGTATTAAAC...TCAAG|GGT 0 1 54.44
214504281 GT-AG 0 0.0024319534412336 96 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 4 490718 490813 Zostera marina 29655 TCG|GTATATAACT...ATATTTTTATAT/AATATTTTTATA...ATCAG|GAG 1 1 64.968
214504282 GT-AG 0 0.0033483611408981 71 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 5 490409 490479 Zostera marina 29655 ACA|GTAAGTTTTA...ATTATTTTAACT/ATTATTTTAACT...TGCAG|TGG 2 1 76.516
214504283 GT-AG 0 0.0006858104993857 79 rna-gnl|WGS:LFYR|ZOSMA_1G00440_mrna 38778435 6 490179 490257 Zostera marina 29655 CTT|GTATGTATAA...TAGAACTTCATA/TAGAACTTCATA...TGCAG|GTT 0 1 83.843

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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]);