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 = 8855918

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
47813345 AT-TA 0 0.0144857922418875 96 rna-XM_027257248.1 8855918 1 340018 340113 Coffea arabica 13443 ACC|ATGTACAAAG...TGTAGTTTGATC/TGTAGTTTGATC...CGCTA|GTG 1 1 34.712
47813346 GC-AG 0 1.000000099473604e-05 105 rna-XM_027257248.1 8855918 2 339483 339587 Coffea arabica 13443 TGA|GCCGGCCAAA...TGAGTGTTAATA/TGAGTGTTAATA...TTGAG|CAA 2 1 47.33
47813347 GT-AG 0 1.860146478695812e-05 303 rna-XM_027257248.1 8855918 3 339171 339473 Coffea arabica 13443 GGT|GTTGGTTGTT...GGTGCCTAAAAA/TGGTGCCTAAAA...GGAAG|TTG 2 1 47.594
47813348 GT-AG 0 2.4833524530939453e-05 90 rna-XM_027257248.1 8855918 4 338540 338629 Coffea arabica 13443 GAG|GTACGTAGCT...AAGATTTTAGTA/GCACCTCTAACT...TTAAG|AAA 0 1 63.468
47813349 AC-GT 0 0.0003291761832263 587 rna-XM_027257248.1 8855918 5 337267 337853 Coffea arabica 13443 GGG|ACACTTTGGC...GAGTGTTTACCC/AGAGTGTTTACC...ACGGT|GCA 2 1 83.597
47813350 GT-AG 0 1.000000099473604e-05 56 rna-XM_027257248.1 8855918 6 336846 336901 Coffea arabica 13443 CCG|GTGAGTACAA...ATCTCCTTTTCT/ATGTCTCTGATC...TGCAG|ACG 1 1 94.308
47813351 GT-AG 0 1.000000099473604e-05 1191 rna-XM_027257248.1 8855918 7 335473 336663 Coffea arabica 13443 AAG|GTCATGGAGG...TAGGCTATAATT/ATAATTTTCATG...TTCAG|ACC 0 1 99.648

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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]);