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 = 1565117

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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
8696345 GT-AG 0 1.000000099473604e-05 109 rna-XM_020246770.1 1565117 5 15258839 15258947 Ananas comosus 4615 AAG|GTGAGAAATT...AAAATTTTATTA/CAAAATTTTATT...GCTAG|GTA 2 1 75.537
8696346 GT-AG 0 1.000000099473604e-05 92 rna-XM_020246770.1 1565117 6 15259248 15259339 Ananas comosus 4615 TAG|GTGAATACCA...TTTTTTTTGGTA/TAGCTATTGACA...TATAG|AGA 2 1 82.854
8696347 GT-AG 0 2.290799685140497e-05 76 rna-XM_020246770.1 1565117 7 15259446 15259521 Ananas comosus 4615 CAG|GTAAACAATA...AATTACTTAACC/ATACATTTTACT...CATAG|GTA 0 1 85.439
8703406 GT-AG 0 8.267632342881447e-05 502 rna-XM_020246770.1 1565117 1 15253356 15253857 Ananas comosus 4615 CTG|GTACTTACTA...GTTTTTTTTTTT/ATTGTTTGCAAT...TTAAG|TAG   0 2.171
8703407 GT-AG 0 1.000000099473604e-05 108 rna-XM_020246770.1 1565117 2 15254040 15254147 Ananas comosus 4615 TGA|GTAAGGGTTT...GGGTTTTTGAAA/GGATTGTTCAAT...TACAG|GAC   0 6.61
8703408 GT-AG 0 1.4829340289918471e-05 1323 rna-XM_020246770.1 1565117 3 15254325 15255647 Ananas comosus 4615 TTG|GTACGTAGAT...ATAGTTTTAAAT/ATTTGATTCACA...TACAG|GAA   0 10.927
8703409 GT-AG 0 0.0016176087507405 531 rna-XM_020246770.1 1565117 4 15255781 15256311 Ananas comosus 4615 TTG|GTATGGTAAA...TTTTTTTTAACA/TTTTTTTTAACA...TACAG|ATT   0 14.171

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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]);